MOD 2

Disinfecting Agents

1. Alkylating agents: alkylate terminal hydroxyl, amino, carboxyl, sulfhydryl groups on proteins. Ethylene oxide gas used to sterilize heat sensitive objects, formaldehyde is a gas dissolved in water 2. Oxidizing agents: H2O2: topical 3-6% kills bacteria, not spores, 10-25% for instruments kills spores Iodine oxidizes essential enzymes, used to disinfect skin, kills spores, activity reduced by organic compounds so must clear skin first (best at low pH) Chlorine compounds oxidize sulfhydryl groups: HOCl 5-10% sterilizes infectious lab materials before discarding 3. Membrane disruption agents: quaternary ammonium, alcohols (ethanol/isopropanol, used to clean skin before iodine, disinfection of anal thermometers, 70% more effective than 95%), soaps/detergents

C. perfringens: Pathogenesis/Immunity

1. Alpha toxin: lecithinase produced by all 5 types. Phospholipase C which lyses WBCs, RBCs, platelets, endothelial cells. Massive hemolysis, inc vascular permeability/bleeding worsened by destruction of platelets. Further tissue destruction, hepatotoxicity, myocardial dysfunction 2. Beta: intestinal stasis, loss of mucosa (necrotic lesions), progression to necrotizing enteritis 3. Epsilon: trypsin activated protoxin, inc vascular permeability of GI wall 4. Iota: necrotic activity, inc vascular permeability 5. Enterotoxin: produced as bacteria transition from cell to spore, released in alkaline environment (SI). As cells finish sporulation, enterotoxin is released, binds to receptors on brush border. Insertion into cell membrane leads to altered permeability. Also superantigen leading to nonspecific strong T cell stim

C. perfringens: Disease

1. Anaerobic cellulitis: enters from surgery or trauma. In days skin becomes discolored (necrosis). Rapid spread, fever, tachycardia 2. Clostridia myonecrosis (gas gangrene): with (1). Gas produced under skin, crepitus on palpation. Intense pain within 1w of injury, followed by muscle necrosis, shock, renal failure, death in 2d. Gas from metabolism of dividing bacteria. Can see 'bubbles' on skin. 3. Food poisoning: usually self limiting and short. From beef, chicken, turkey, gravy. Short incubation period as they produce enterotoxin. Cramps with watery diarrhea, no fever or N/V/D. Lasts less than 24h

Bacterial Metabolism

1. Bacteria profoundly affected by environemnt (no specialized homeostasis cells, need immediate response) 2. Physical factors- temp usually 37C, pH 7.2-7.6 3. Nutritional factors: water, preformed organic compounds, need for AAs purines pyrimidines vitamins variable, inorganic ions (K,Mg,Fe,Na,PO4)- iron needed by aerobes for the cytochrome system. Siderophores solubilize iron and transport across PM, can serve as a virulence factor by competing with human transferrin, lactoferrin 4. Lab media: minimal medium is water and glucose, nutrient broth is a rich meat extract with complex proteins allowing bacteria to switch to using nutrients given to them instead of making them. Can be altered to encourage growth of specific pathogen and inhibit others.

Selective Toxicity of Antibiotics

1. Bactericidal: kills bacteria- PCN/cephalosporins inhibit CW formation, nalidixic acid and quinolones bind DNA gyrase to prevent DNA replication, aminoglycosides bind to 30S subunit to inhibit elongation 2. Bacteriostatic: stops growth and allows immune system to take control. Rifampin binds RNA polymerase to prevent transcription. Chloramphenicol, erythromycin, lincomycin bind bacterial ribosomes and inhibit peptide bond formation

S. pneumoniae: Treatment, Prevention, Control

1. CA Pneumonia- azithromycin, or for inpatients, combo of ceftriaxone with azithromycin or vancomycin 2. Sinusitis/OM: amoxicillin/clavulanate 3. Meningitis: ceftiaxone with vancomycin 4. Vaccines- two types: 23 valent pneumococcal polysac vaccine: anyone >2y. Polysaccharides are T independent, so doesnt work if <2. Not as effective in pts with asplenia, blood cancer, HIV, elderly, renal transplants 13 valent conjugated pneumococcal: for <2y. Polysacs conjugated to proteins to stim TH response. 4 doses at 2,4,6,12-15

Staphylococcus: Cell Wall Virulence Factors

1. Capsular polysac (slime)- not all strains. Help colonize host, help evade complement attack 2. Teichoic acid- aureus has polysac of ribitol teichoic acid, epidermidis has glycerol 3. Peptidoglycan- induce antibodies, elicit humoral and cellular immune response, attract leukocytes 4. Protein A- aureus only. Binds Fc part of IgG, may be secreted in small amounts during growth 5. Clumping factor- aureus, bound coagulase binds human fibrinogen. Completely different from free coagulase 6. Other binding sites for mammalian proteins like fibronectin and laminin 7. Altered PBPs like PBP2A have reduced ability to bind penicillins, related to mecA presence

Genetic Information in Bacterium: Chromosome, Plasmids

1. Chromosome: haploid genome. single, circular. each strand is a template for enzymatic synthesis of the opposite strand. When bacterium divides, one chromosome to each daughter cell. 2. Plasmid- autonomous, extrachromosomal, self replicating Not essential, much smaller, vary in size and copy number Conjugative plasmids code for functions that promote DNA transfer from one cell to another (sex pili). Some plasmids code for resistance, toxins, virulence factors

S. pneumoniae: Structure/Pathogenesis

1. Encapsulated- pathogenic strains. Purified capsular polysacs used in vaccine. Highly anti-phagocytic, still immunogenic 2. C-antigen: different from Lancefield. Polysac precipitates CRP in presence of Ca. CRP present in normal people, elevated in acute inflammation 3. Teichoic acid: activate complement, produce C5a mediated inflammation 4. Secretory IgA Protease: Usually IgA traps bacteria in mucus by binding bacteria to mucin so it can be cleared. This prevents this by breaking down secretory IgA (also in h flu, n meningitidis, n ghonorrhea) 5. Pneumolysin O: toxin, causes damage to epithelium, inhibits WBC respiratory burst, activates classical complement leading to anaphylatoxins (C3a/C5a). Leads to secretion of IL1/TNFa and migration/activation of inflammatory cells, feverl, tissue damage

Clinical Syndromes: Other Staph Species

1. Epidermidis: prosthetic/native valve endocarditis, infection of prosthetics/catheters/cardiac devices. Via biofilms. 2. Saprophyticus: UTIs. Resistant to novobiocin (diagnostic) 3. Lugdunesis: native valve endocarditis

Chromatin Function Inhibitors

1. Epipodophyllotoxin: Etoposide MOA- stabilizes and inhibits topo2 and DNA complex leading to strand breaks Use- solid tumors, lymphomas, leukemias Toxicities: myelosuppression (DLT), anaphylaxis, secondary leukemias, hypotension 2. Camptothecin: Irinotecan MOA- metabolized to active SN38 (1000x more potent), inhibits topo1 leading to single strand breaks Use- GI cancer (colonic, pancreatic) Toxicity- diarrhea (DLT), myelosuppression

Bacterial Surface Appendages

1. Flagella: move bacteria toward attractants/away from repellents (chemotaxis): thrust provided by rotation of basal body of propeller. Can be sheared off and will regenerate Motility used to classify bacteria Flagellar H antigens are species specific, used for ID 2. Pili: thin, hairlike appendages Common pili- protein at tip adheres to unique epithelial surface sugar, important in colonization (virulence factor). Changeable in order to outflank immune system (gonorrhea) Sex pili- cell-cell adhesion for conjugation (DNA transfer)

2 Important Bacterial Stains

1. Gram stain- differences in wall v envelope organizations Both + and - take up crystal violet and iodine, complex is trapped inside + cells by alcohol dehydration and reduced porosity of wall: turns violet Not trapped by the thin peptidoglycan of - cells, alcohol extracts complex and safranin counterstains them pink 2. Acid-fast stain: mycobacterium walls contain lots of waxes, making them impervious to lots of harsh chemicals and WBCs. The cost to bacteria is very slow growth

Infectious Disease Case Strategy

1. Is this an infection? Is it ongoing? If yes, what kinds of organism? 2. What is the source? 3. Do symptoms match your hypothesis? 4. What facts can you gather from history? 5. What laboratory data do you need? 6. What kind of intervention/treatment? Are you concerned about further spread?

Bacterial Growth Phases

1. Lag phase: bacteria adapt to culture medium, prep for rapid growth (generate proper redox potential, siderophore (Fe chelator) production, synthesize enzymes 2. Logarithmic phase: rapid division, maximum % viable. Cell divide by binary fission, exponential increase in numbers, lasts as long as nutrients are available or before buildup of toxic products, responsible for rapid onset of disease 3. Stationary phase: rate of division=rate of death. Viable cell number is constant, adaptive changes (synth of inclusion bodies, sporulation), still induces a host response, exotoxin production accelerates 4. Decline phase: cells die. Rate depends on nutrients, temperature, pH, O, moisture, etc. Bacteria survive for a long time.

Streptococci/Enterococci: Classification Schemes

1. Lancefield groupings: serologic properties based on antibody response to organism (IgM to CW carbs) 2. Hemolysis: ability to lyse erythrocytes in media completely (beta), incompletely (alpha) or not at all (gamma). Enterococci almost all gamma 3. Biochemical Properties: susceptibility to bacitracin, optochin, CAMP test, esculin agar, bile solubility

Gram Positive Cell Wall

1. Lipoteichoic acids in all gram+ bacteria- polymers of ribitol or glycerol, linked to lipid and peptidoglycan. Negative charge sequesters cations. Antigenic determinant- specific to each species 2. Peptidoglycan- 20-24 layers, backbone of glycan, forms majority of wall, autolysin cleaves peptidoglycan to allow new things in Tetrapeptides are crosslinked by transpeptidation where L-lys on one peptide is linked to D-ala on the next, which releases the next D-ala for another transpeptidation Penicillin binds the transpeptidase (PBP) because it has D-ala-D-ala as well, kills cell only if it is actively making CW. Autolysin opens wall, PCN blocks insertion of peptidoglycan, wall weakens and cell explodes from osmotic pressure 3. Lysozyme- common enzyme in human tissues, natural antibacterial defense- cleaves bond and kills bacteria

Clinical Syndromes: S. aureus

1. Localized cutaneous infections- impetigo, furuncle, carbuncle, folliculitis, cellulitis, abscesses 2. Scalded skin syndrome SSS- mostly young children 3. Toxic shock syndrome- multiple organs 4. Food poisoning- rapid onset 5. Wound infections 6. Bacteremia (endocarditis, pneumonia, septic arthritis)

MOD Overall Concepts

1. Microbes have physical and growth characteristics that distinguish them 2. Virulence factors are components of microbes that help them cause disease via pathogenic mechanisms 3. Transmission- microbe affects multiple hosts. Epidemiology describes hosts and patterns 4. Microbe is potential pathogen after isolated and identified via differential and diagnostic lab tests 5. Once identified as pathogen, intervention and infection control strategies initiated

S. viridans: Diseases

1. Mutans and mitis: use biofilms, common cause of cavities 2. Sanguinis: endocarditis. Makes dextrans which bind to fibrin-platelet aggregates on pts with damaged heart valves only, esp mitral. Most common: previous mitral valve damage (like RF), has dental work, leads to transient s. viridans in blood, leads to endocarditis. Splinter hemorrhages of fingernails classic symptom 3. Bovis: normal flora of GI tract, can cause bacteremia/subacute endocarditis following surgery, associated with colon cancer

Molecular Basis of Mutations

1. Nucleotide substitution mutations- silent if doesn't change AA, missense- substitutes AA, bad protein, nonsense- premature termination, short protein. 2. Deletion/insertion: if not in multiple of 3, causes frameshift and garbled AA sequence. If in multiples of 3, addition/loss of AA can ruin protein 3. Reversion- change in mutant back to wild type phenotype, sometimes to exact genotype

S. Pyogenes Diseases

1. Pharyngitis (strep throat)- most important (not most common) cause of sore throat. Fever, bright red throat with exudates on pharynx and tonsils. Often cervical lymphadenopathy. Diagnosed with throat culture or rapid group A antigen test (75% accurate) 1a. Scarlet fever- sequelae of pharyngeal infections in strains that produce Spe's. 1-2d after initial throat symptoms, rash on upper chest spreading to extremities. Area around mouth, palms, feet spared. White coating on tongue peels off, leads to strawberry tongue. Rash disappears in 5-7d. MNM, can be deadly

Bacteriophage Lytic Cycle

1. Replication: DNA/RNA genome copied 2. Transcription: DNA/RNA to mRNA to phage proteins 3. Assembly: DNA/RNA to structural proteins 4. Release: Cell Lysis

Bacterial Metabolism: Energy Production

1. Respiration- final electron acceptor is O. Obligate anaerobes require O2 to live (mycobacterium thrives in lung). Facultative anaerobes (most pathogens) convert glucose to pyruvate (glycolysis), send pyruvate to TCA to generate ATP when O available 2. Fermentation: when no O2 available Obligate anaerobes (clostridia) and facultative anaerobes (use fermentation when no ATP_ Note organic compounds are electron donors and acceptors, substrate level phosphorylation is source of ATP- no electron transport

Disease Patterns/Epidemiology

1. Sporadic infection- individual gets disease 2. Endemic infection- disease always present in population- equilibrium between host and agent, baseline infection level 3. Epidemic- incidence in population higher than normal 4. Barrier to epidemic- herd immunity

Bacterial Death

1. Sterilization- death of all organisms Heat- 100C 2-3min will kill cells, spores remain. 121C steam for 15min will kill spores. Dry heat (oven): 160C for 1 hour Filtration: 0.22u will remove all bacteria, used if solution can't tolerate heat (protein containing) 2. Pasteurization: 62C for 30min, destroys pathogen without affecting flavor 3. Disinfection: chemical substances able to kill microorganisms on surfaces, too toxic for internal application

S. pyogenes: Extracellular Products

1. Streptolysin O: lyses RBCs/WBCs. Highly immunogenic, ABs called ABO and used for typing 2. Streptolysin S: lyses RBCs/WBCs, non-immunogenic 3. Streptokinase: degrades fibrin, allows tissue invasion. Bacteria eats its way into tissue 4. Streptodornase: Degrades DNA, liquefies pus along with streptokinase. Immunogenic, basis for ADB titer 5. Hyaluronidase: degrades HA, augments tissue invasion 6. C5a Peptidase: inactivates most important chemotactic complement (C5a) 7. Protease: augments invasion and rapid spread

S. pyogenes: Treatment, Prevention, Control

1. Very sensitive to penicillins, cephalosporins 2. PCN allergic pts given oral cephalosporin or macrolide 3. Severe systemic infections- combined IV PCN with protein-synthesis inhibiting antibiotic like clindamycin 4. Necrotizing fasciitis- piperacillin/tazobactam, then add vancomycin. Drainage/aggressive debridement fast. 5. History of RF: long term antibiotic prophylaxis to prevent recurrence and before procedures that could induce transient bacteremia, like the dentist 6. Antibiotic therapy has no effect on acute glomerulonephritis

Gram Negative Cell Wall

2 lipid bilayers with thin peptidoglycan monolayer between In peptidoglycan, DAP replaces L-lys (in some gram+ too) 1. Outer lipid bilayer is a barrier excluding hydrophilic compounds (inc some abx). Lipoproteins are linked covalently to peptidoglycan Proteins: porins are most abundant Endotoxin- LPS in bacterial outer cell membrane. heat stable, causes IL1 release, fever, endotoxic shock. Lipid A is most toxic part, required for insertion into outer leaflet. O antigens are linked to KDO/heptose core, vital for ID of salmonella species 2. Periplasmic space- has hydrolytic enzymes (nucleases, alkaline phosphatase), binding proteins (for sugars, AAs, ions), and b-lactamase (destroys PCN) 3. Inner membrane is the plasma membrane

S. Pyogenes Diseases: Serious Complications

5. Necrotizing Fasciitis: deep in subcutaneous tissue. Spreads along fascial planes, extensive destruction of muscle/fat. Introduced into tissue through break in skin (trauma, burn, surgery, etc). Initial cellulitis, then bullae, gangrene, systemic symptoms. Toxicity, multiorgan failure, and death. Need surgery and antibiotics. 6. Toxic Shock/Sepsis: soft tissue inflammation at infection site, pain, fever, chills, malaise, N/V/D. Pain intensifies with progression to shock and failure of kidney/lung/liver/heart, similar to staph. Most pts are bacteremic, many have (5).

S. agalactiae: Disease

About 60% newborns born to group B + mothers colonized at birth. #1 cause of meningitis and septicemia in newborns Can cause UTIs, amnionitis, endometritis, wound infections in pregnant women Early onset disease: infants <7d. Bacteremia, pneumonia, or meningitis. Mortality <5% with rapid diagnosis but 15-30% who survive severe meningitis have lifelong neuro sequelae (blindness, deafness, cognitive disability) Late onset: 1w-3m of age, bacteremia with meningitis. Mortality 3%, neuro complications 25-50%

Causes of Disease: Encounter

Agent makes contact with potential host First normal encounter: birth (skin, vaginal canal) First normal barrier: placenta (rubella, syphilis, toxoplasmosis can cross placenta) Protection against agents (maternal antibody) Most disappear, some colonize, few cause disease Encounters can be exogenous or endogenous (encountered from in or outside body) Not every encounter leads to disease

Causes of Disease: Spread

Agent may broaden range of infection, or may disseminate to sites other than entry site Can happen before or after multiplication Barriers to spread are usually immunological Spread of microbe influenced by host anatomy and by its own physical characteristics Ability of agent to spread is dynamic process dependent on host-microbe interaction Increase in numbers from multiplication may allow it to spread to another host Successful adaptation of microbe to host characteristics can influence its ability to multiply, cause disease

Koch's Postulates

Allow strategies for disease control 1. Agent must always be found in diseased animal, not in healthy ones 2. Agent must be isolated from diseased animals and grown in culture 3. Agent isolated in culture must initiate and reproduce disease when re-inoculated 4. Agent should be re-isolated from experimentally infected animals

Cisplatin Toxicity Highlight: Nephrotoxicity

Amifostine is a free radical scavenger that binds/detoxifies reactive nucleophiles Can be given with Cisplatin to prevent nephrotoxicity or to prevent xerostomia from radiation to head/neck Toxicity: hypertension, N/V, sneezing, hypocalcemia

Cytarabine

Another pyrimidine analog MOA- prodrug, undergoes conversion to triphosphate nucleotide ara-CTP and is incorporated into DNA where it inhibits DNA polymerase, halts chain synthesis, and induces RNA miscoding Use: leukemia, lymphoma Toxicity: myelosuppression (DLT), high dose >1000mg/m2 can lead to high myelosuppression, N/V, cerebellar toxicity (neuro checks must be performed before high dose), and conjunctivitis (give with dexamethasone drops)

S. pyogenes Post-Infectious Sequelae: Acute Glomerulonephritis

Associated with pharyngeal and pyodermal infections Type 2 hypersensitivity, cannot be prevented by penicillin treatment of s. pyogenes Certain strains of group A strep have affinity for renal glomeruli Acute inflammation of renal glomeruli with edema, HTN, proteinuria, hematuria

Exchange of Genetic Information: Transduction

Bacteriophage mediated 1. Generalized: during replication, phage packages a piece of host DNA and injects into recipient. Homologous recombination occurs (replaces homologous gene). Can also be done in test tube by mixing virus capsid with any DNA, including cloned DNA (good for genetic engineering) 2. Specialized: during excision from host chromosome, phage takes adjacent gene with it

Enterococci: Structure/Pathogenesis

Biofilms- can adhere to tissue, form biofilms Antibiotic resistance- either inherently resistant or have acquired resistance genes to many antibiotics, probably because exposed to contant low doses in GI tract. Very resistant to PCN, vancomycin resistant (VRE) exist too

C. botulinum: Pathogenesis/Immunity

Botulinum toxin is heat labile, resistant to enzymes and low pH of GI tract, important because normally contracted via ingestion Released from bacteria as it dies. Travels to PNS, cleaves SNARE proteins involved in vesicle transport in motor neurons, inhibiting ACh release and leading to flaccid paralysis

Peptostreptococcus: Disease, Treatment

Can be isolated from all body sites, predisposed to subcutaneous soft tissue abscesses and DM foot ulcers Occur in association with pre-disposing conditions (prev surgery, immunodeficiency, trauma, DM, alcoholism) 1.CNS infections: isolated from brain abscesses that develop as sequelae of chronic ear/mastoid/sinus/tooth infection 2. URI, dental infection 3. Intra-abdominal infection: part of normal GI flora but often part of polymicrobial infections that follow abdominal trauma. Leads to liver abscess in alcoholics Treatment: Penicillin G and other cephalosporins Surgical debridement if necessary

Staphylococcus: Extracellular Products: Toxins

Can be virulence factors, can act at distant sites 1. Alpha toxin (a hemolysin)- hemolytic/necrotic. Coded by plasma and bacteria. May bind to target cell membranes, make permeable 2. Beta toxin (sphingomyelinase C)- mediates tissue destruction, degrades sphingomyelin. A+B together allow aureus to multiply during inflammatory response 3. Delta toxin- detergent, affects cell membranes 4. Gamma toxin- activity unknown 5. Leukocidin- in most aureus, attacks PMN/macrophages, permeabilizes cell membranes 6. Exfoliative toxin: causes SSS, ETA (chromosomal) or ETB (plasmid) forms. Cleaves desmoglein 1 in intracellular attachments in cells of granular epidermis layer. 7. Enterotoxins- types A-E, food poisoning. Heat stable, resist gastric/jejunal enzymes. Sx associated with ingesting preformed toxin A>D/B. Superantigen, stim peristalsis, may affect CNS 8. TSST1: not in all aureus, can be lethal. Superantigen

Peptostreptococcus

Can occur anywhere, even CNS Only anaerobic gram+ cocci Obligate anaerobe (O is poisonous) Catalase negative, not highly O sensitive Normal in mouth, upper respiratory, GI, female GU

Bacterial Surface Layers

Capsules or slime outside cell wall Viscous gel, high MW polysacs in some, loose amorphous slime in others Not essential, can remove physically or by mutation without killing Aids in adherence to tissues- virulence factor Resists phagocytosis- virulence factor The capsular antigen of s pneumo used in vaccines and in differentiating types

Cancer Chemotherapy:Alkylating Agents: Platinum Analogs

Cisplatin, Carboplatin MOA- covalently bind to purine DNA bases, form intrastrand adducts (not crosslinks). Repair complex notices adducts and turns them into strand breaks. If these are not repaired, cell death. Inhibits DNA replication Class adverse effects: irreversible nephrotoxicity, acute/delayed N/V, myelosuppression, neurotoxicity, ototoxicity, electrolyte imbalance Cisplatin has all of the above effects, severe N/V and is a severe radiation sensitizer, dosed using body surface area Carboplatin has myelosuppression (severe), N/V, and is a radiation sensitizer, dosed using AUC

Paclitaxel Toxicity Highlight: Hypersensitivity Reaction

Common with all taxanes, esp Paclitaxel Incidence decreases with each cycle, cycle 1 is 48% Signs and symptoms- diffuse intense erythroderma, pruritis, chest tightness, back pain, dyspnea, tachycardia, extreme anxiety, hypo/hypertension Initial manifestation occur within 5m Premedications must be given 30m prior: dexamethasone, histamine 1/2 blockers If hypersensitivity occurs: stop immediately, give diphenhydramine and hydrocortisone. If symptoms resolve, can resume after 30m but do not if symptoms were severe

Cancer Chemotherapy: Alkylating Agents: Nitrogen Mustard Derivatives

Cyclophosphamide MOA: cytotoxic effects from binding to reactive DNA molecules: aklylate N7 in guanine, causes crosslinking of the two strands and inhibits DNA replication Class adverse effects: myelosuppression, N/V, secondary leukemias, infertility, alopecia Use: solid tumors and hematopoietic malignancies Specific Toxicity: myelosuppression (DLT), delayed and acute N/V, SIADH, alopecia, hemorrhagic cystitis

S. agalactiae: Laboratory Diagnosis, Treatment

Diagnosis: CAMP test for CAMP factor in group B CAMP enlarges area of hemolysis formed by staph aureus. Plate s. aureus with s. agalactiae, zone of b-hemolysis gets larger, will not happen when you plate s. aureus with s. pyogenes Treatment: Susceptible to penicillin (DOC). In allergies, cephalosporin or vancomycin

Enterococci: Lab Diagnosis, Treatment

Diagnosis: looks very similar to s. pneumo. Esculin agar is used: esculin in bile rich media hydrolyzed by esculetin/dextrose from enterococci, turns media black brown. S. pneumo will remain yellow-gold. Treatment: largely resistant to PCN and vancomycin, so DOC are linezolid and daptomycin. Very difficult to eradicate VRE strain once colonized

S. viridans: Laboratory Diagnosis, Treatment

Diagnosis: need a-hemolytic strep that is not s. pneumo. Differentiated because optochin resistant. Place optochin disc (coated in Cu-salt-derived quinine) in blood agar, s. pneumo cannot grow around it, viridans can Treatment: people with history of RF or damaged heart valve should get PCN before dentist High dose, long durations necessary to treat subacute bacterial endocarditis

Combination Chemotherapy

Different tumor subtypes are really different diseases Personal medicine is allowing us to look at genetic fingerprint of rumor and devise drug cocktail to be most effective

Exchange of Genetic Information: Conjugation

Direct bacterium-bacterium plasmid transfer via sex pilus in gram - bacteria (gram + undergoes clumping) F plasmid codes for sex pili, replicates itself as it sends single strand through pilus. Second strand generated, so DNA is added (plasmid) Nonconjugative plasmids do not promote own transfer buy can be mobilized by conjugative plasmid in same cell In high frequency recombination Hfr, the plasmid inserts into donor bacterium genome. Homologous recombination: plasmid cut at oriT, genes closest transferred first, fertility genes transferred last. Need 100m to transfer whole bacterial chromosome and it is fragile, so those closes to oriT most likely to go through. Was used to map gene order on chromosome

Anti-Tumor Antibiotics: Anthracyclines

Doxorubicin hydrochloride Structure: 4 planar rings, from a fungus MOA- DNA intercalation between base pairs leads to unwinding of helix, topo2 inhibition prevents relegation of DNA during replication causing double strand breaks (can't relieve torsional strain), oxygen free radical generation leads to single strand breaks (via a hydroxyquinone) Use: solid tumors, leukemias, lymphomas Toxicity: myelosuppression (DLT), cardiotoxicity, vesicant, acute/delated N/V, mucositis, alopecia, discoloration of body fluids (doxorubicin: red/orange, mitoxantrone: blue/green)

Conjugation: Details

F+ to F-: in male (F+), fertility factor present away from chromosome and unidirectional transfer occurs to female (oriT first, then the rest of plasmid genes). Only single strand transferred and is reduplicated in donor. This transfer is fast so you can assume it is 100% complete. The F- cell is now F+ and they can no longer mate. No bacterial gene transfer. Hfr to F-: oriT and first half of fertility factor get transferred but transfer is slow so is interrupted. No tra, so F- does not become Hfr. Donor genotype remains same as DNA is restored. Homologous recombination occurs here

S. pyogenes Post-Infectious Sequelae: Rheumatic Fever

Follows pharyngitis, not cutaneous infections Inflammatory changes in heart, joints, blood vessels, subcutaneous tissues Heart shows pancarditis (endo-, peri-, myocarditis) with possible chronic progressive damage to valves Joint manifestations range from arthralgia to frank arthritis, multiple joints in migratory pattern Always vigorous AB response, ABs crossreact with myosin ASO or ADB can diagnose. Treating with penicillin prevents! JONES: Joints (polyarthritis), Heart problems (valves/myocarditis), Nodules (subcutaneous), Erythema marginatum, Syndenham's chorea (rapid involuntary hand/face movement)

Enterococci

Formerly group D strep, colonize GI tract 54 species, few cause disease, faecalis and faecium Not the same as enterobacteriacae (gram -) Gram+ cocci in pairs and short chains Microscopically cannot differentiate from s. pneumo Grow aerobically and anaerobically Bile resistant (different from s. pneumo) Normally gamma hemolytic

S. Pyogenes Diseases: Skin

From minor scratches/abrasions, insect bites 2. Impetigo/Pyoderma: weepy, red lesions with honey crusted discharge. Differentiate from staph by appearance 3. Erysipelas: acute skin infection. Localized pain, inflammation, LN enlargement, chills, fever, leukocytosis. Skin is raised and distinctly differentiated. Usually face, can be on legs. Preceded by respiratory tract infections 4. Cellulitis: Different from (3), involves skin and deeper subcutaneous tissue. Border between infected/uninfected not as clear, local and systemic signs still noted

Genetics: Basics

Genotype- changed only by DNA mutation Phenotype- can be changed by response to conditions Mutations: spontaneous are rare. Bacteria are haploid, so mutation changes only copy of gene (adaptability). Mutations are random, occur before selection Cistron- genetic units encoding proteins in same pathway. Single path may have several but 1 mutation can disrupt whole thing Selective media- allows well-suited mutants, not wild type to grow. Differential media allows both Ames test for mutagenic chemicals Mistakes during repair are mutations Chromosomal mutations can cause resistance to single abx Conditional mutants allow study of mutations in essential genes (can grow at 30C, not 40)

Streptococci/Enterococci: General Characteristics

Gram +, cocci seen in pairs or chains, small colorless colonies Facultative anaerobes, lactic acid producers Catalase negative (unlike staph) Growth medium: complex requirements, use blood agar or serum enriched medium Diverse collection of over 100 species covering a huge variety of diseases

Bacteria: Other Structures, Classification

Granules- food reserved, used in ID in various species Endospores- survival factor (bacillus/clostridium only)- tough to eliminate, very heat/chemical/desiccation resistant, can be used to ID Classification: based on cell structure (size, shape, motility, gram, growth), where found, DNA sequence (PCR), comparison to reference strain

S. pyogenes

Group A strep. Important pathogen- common, can cause rapid disease. Infections of skin/mucosal membranes, lifelong sequelae. Grows in pairs/chains, b-hemolytic, catalase negative, bacitracin sensitive Say aaaaah: A=strep throat

S. agalactiae

Group B Strep (only species). Old cause (with grp A) of child bed fever (puerpal sepsis), eliminating by handwashing and antibiotics Important cause of septicemia, pneumonia, meningitis in newborns Pregnant women checked for presence in vaginal canal at 35 wks (normal in 20-25%). If +, PCN 4h before delivery Gram + cocci in short chains in clinic, longer in culture b-hemolytic, catalase negative Bacitracin resistant (different from group A)

Homologous v Site Specific Recombination

Homologous incorporates short linear DNA in bacterial chromosome Must be some sequence homology RecA is required One to one exchange of DNA Site specific combines circular DNA (plasmids, temperate phages, transposons, chromosome) Requires homology only at restriction site No DNA lost Requires restriction endonuclease

Staphylococcus: Epidemiology

Humans major reservoir for aureus, epidermidis, saprophyticus, lugdunensis, haemolyticus. Aureus in up to 30%, nose most common, transiently skin/mouth/perineum. Others on skin, saprophyticus also on periurethra/urethra Aureus that has mecA gene is MRSA Relatively resistant to drying/heat, survive for long time on inanimate objects. Transmitted by fomites/human contact Aureus has subgroups based on susceptibility to panel of lytic bacteriophages, PFGE is done now instead Basically inactive in normal state in healthy host. When they gain entry they become more aggressive

Irinotecan Toxicity Highlight: Diarrhea

If neutropenic, can be life threatening Risk factors- short bowel syndrome, poor performance, prior history, loperamide noncompliance, UGT1A1 polymorphsm, liver dysfunction, Cyp450 inhibitors, combination therapy Monitor pts for complications Early onset via direct inhibition of ACh and cholinergic surge occurs within 24h, results in salivation, lacrimation, cramps, visual disturbances, diaphoresis, bradycardia, rhinitis, and flushing. not DLT, treated with atropine, will resolve without tx in 30m Late onset occurs in 2nd week via unknown mechanism, maybe intestinal damage from accumulation of SN38. Results in prolonged diarrhea leading to dehydration, electrolyte imbalance, sepsis. Complications: colitis, ulceration, bleeding, infection. DLT, can be life threatening, treated with Loperamide

Resistance Mechanisms By Cancer Cells

Increased DNA repair Altered metabolic or biochemical mechanisms Multiple drug resistance pumps like PGP- pump chemotherapy back out of cells

Causes of Disease: Entry

Infectious agent goes deeper into body Can result in colonization without crossing epithelial barriers but can still meet other barriers (GI tract: cilia, enzymes) Can result in colonization after crossing epithelial barrier- cut, transplant, intracellular Inoculum size can influence agent ability to overcome barriers

Causes of Disease: Multiplication

Infectious agent reproduces in host Some agents more independent of host than others Time needed: incubation period (may be no symptoms) Inability to multiply usually allows host defense to win Increase in numbers may give microbe the edge Microbiota can multiply in own niche, not considered pathogenic

Staphylococcus: General Morphology, Metabolism, Genetics

Isolated on blood agar plates: large, opaque, flat colonies S. aureus produces beta hemolysis and yellow/gold colony, while epidermidis/saprophyticus non-pigmented (white) and no hemolysis- diagnostic Aureus can grow in medium with high (7.5%) salt Gram stain: positive cocci, grape-like clusters Facultative anaerobes Produce catalase aerobically (diagnostic)

Exchange of Genetic Information: Transposable Genetic Elements

Jumping genes, can move from place to place. Add new DNA. 1. Insertion sequences: short, inverted terminal repeats. DNA between repeats encodes proteins needed for transposition of DNA like transposase (makes staggered cuts in host DNA and fills in ends). Insertion disrupts a gene, inactivating it and causing mutations 2. Transposons- longer, have extra genes (not just needed for transposition). IS-like stuff at the ends. After completion, is at original site and new location. Multiple abx resistant plasmids have collected transposons.

Bacterial Plasma Membrane

Lipid bilayer just like eukaryotes Functions: osmotic barrier, active trasport Respiratory chain components much like mitochondria (energy transducing systems, H+ ATPase of proton pump) Biosynthesis of phospholipids, peptidoglycan, LPS, capsular polysaccharides Excretion of hydrolytic enzymes

S. pyogenes: Structure/Pathogenesis

Lipoteichoic acid: adhesion molecule in all gram +, complexes with fibronectin on cell surface Encapsulated: 1. Hyaluronic acid: antiphagocytic, makes bacteria slimy. Opsonins (IgG, C3b) needed for phagocytosis. HA is same as in human tissue, so is not immunogenic. 2. M-Protein: major part of fibrils extruding from cell membrane, over 63 types. Inhibits opsonization by binding complement factor H which inhibits complement. Very immunogenic, antibodies made to different types. Serotype s pyogenes based on ABs made to M-protein. ABs can also cross-react with myosin in heart leading to rheumatic fever

Antimicrotubules: General MOA

MTs are protein polymers responsible for cell shape, movement- principle part of mitotic spindle that separates duplicate sets of chromosomes into daughter cells Anti-MTs interfere with assembly and disassembly by affecting equilibrium between free tubulin dimers and assembled polymer Cell cycle specific, act only on M (mitosis)

Clostridium Perfringens

Main cause of gas gangrene Spore-forming Large, gram+ rectangular rod, anaerobic Spores rarely observed (different from other clostridia) Rapid, spreading growth on sheep blood agar Beta hemolytic Found in soil and GI tracts of animals 5 lethal toxins: alpha, beta, epsilon, iota, enterotoxin- divide isolates into 5 groups

Bacterial Ribosomes

Many 70S with 30S and 50S subunits mRNAs have many ORFs, translated to multiple proteins Translation starts at AUG, first AA formylated methionine mRNA is unstable with no polyA, allows quick shut off of protein synthesis at end of transcription Gene expression thus controlled mainly at transcription Main target of abx: chloramphenicol, lincomycin, erythromycin bind to ribosome and inhibit peptide bond formation while aminoglycosides (streptomycin, kanamycin, neomycin) bind to 30S subunit to inhibit elongation Note mitochondrial eukaryotic ribosomes also 70S (ancestral bacteria probably invaded eukaryotic cell)

Goldie-Coldman Hypothesis

Mathematical model predicting innate resistance to drug by tumor cell Justification for giving several chemo drugs to patient If you give multiple drugs, must have: different MOA, non-overlapping toxicities Basis for overcoming cancer resistance mechanisms

Doxorubicin Toxicity Highlight: Cardiotoxicity

Mechanism: oxidative stress from superoxide/free radicals, low levels of antioxidant enzymes in heart cause apoptosis Presentation: acute within 1 week after anthracycline as EKG changes or pericarditis, arrhythmias reverse within hours, ST-T wave abnormalities reverse in 1-2w Chronic: dose dependent dilated cardiomyopathy and CHF, can be early (<1yr) or late, EF decreases by 20% to value >50% or >1% to value <50% Risk factors: inc cumulative dose, bolus infusion, old age, previous heart disease, previous mediastinal radiation Prevention:everyone gets MUGA/ECHO pre treatment, Dexrazoxane as treatment: chelator of divalent ions and ferric acid to prevent free radiacl formation. 10x doxorubacin dose given to prevent cardiotoxicity, 100mg for 2 days and 500mg for 1 to treat anthracycline extravasation Mitoxantrone and liposomal anthracyclines less risk

Cancer Chemotherapy: Antimetabolites: Folic Acid Analog

Methotrexate MOA- Antifolate, inhibits DHFR (responsible for reducing folic acid to tetrahydrofolate, an essential step in DNA synthesis). Decreasing FH4 decreases thymidylate and decreases de novo purine synthesis. Folic acid compounds only active in FH4 form so this inhibits DNA synthesis. Use: solid tumors, lymphomas. High doses allow diffusion into cells, CNS penetration Toxicity- myelosuppression (DLT), mucositis, hepatotoxicity, neurotoxicity, nephrotoxicity

Bacterial Growth

Necessary for disease (except some exotoxins) Measurement in broth culture: turbidity (light scattering)- measured in spectrophotometer, measures dead and alive Direct particle count: measures alive and dead in microscope Viable cell count: CFU on agar, one colony from one live bacterium Generation Time: average time needed to double population. Semi-log plot, pick two points on y that represent doubling of viable cell count, read time on x

Methotrexate Toxicity Highlight: Nephrotoxicity, High Dose Issues

Nephrotoxicity: prevented by: vigorous hydration and alkalinization of urine (pH>7 or methotrexate will precipitate in renal tubules), avoidance of nephrotoxic drugs (weak acids precipitate methotraxate (NSAID, penicillin), competition for tubular reabsorption (trimethoprim/sulfamethoxazole), inhibit clearance (PPI) High doses (>1000mg/m2) must be followed by leucovorin (folinic acid)- decreases myelosuppression and GI toxicity Counteracts depletion of folate in healthy cells Starts 12-24h after end of methotrexate infusion, continued until level is clear. Methotrexate levels monitored bc can accumulate in third space fluid (glucarpidase can bring down levels quickly if necessary- recombinant enzyme that hydrolyzes methotrexate)

S. pneumoniae

Non-groupable: no antibodies 30-35% carry as normal flora, 90 different types (only encapsulated types are pathogenic, 23 types- nearly all infections in kids, 88% bacteremia/meningitis in adults) Colonizes oropharynx, sometimes lungs, paranasal sinuses, middle ear. Can be transported in blood to brain, etc. Most important cause of pneumonia Lancet shaped gram+ diplococci, a-hemolytic Encapsulated in polysacs, major virulence factor Optochin sensitive, bile soluble Quellung reaction: indicates swelling of capsule, used to show antibodies are interacting with that serotype: shown by halo around bacterium Mobilizes inflammatory cells to focus of infection, creating inflammation and pathogenesis at site

S. viridans

Non-groupable: we do not make antibodies Many species, importantly mutans and sanguinis Most common cause of subacute bacterial endocarditis and dental cavities Alpha-hemolytic Not encapsulated, normal flora of oropharynx and GI Optochin resistant, Bile resistant (not lysed by low pH of bile)- both different from s. pneumo Can form biofilm- only pathogenic factor

Damage and Disease

Not uniform- varies with agent, site, extent of response Symptoms can come from direct cell damage by agent or from host immune/inflammatory response Outcome influenced by host factors like physical or immunologic state of host, race, nutritional status, etc. Pathogenesis of infection describes overall interaction between host and agents

Enterococci: Disease

One of most common causes of nosocomial infections Faecalis is more common, faecium worse (resistance) 1. UTIs- when displaced from GI or anus to urethra. Associated with catheterization 2. Peritoneal infections- surgical risk, tend to be polymicrobic, associated with leakage of intestinal bacteria. Could also be from trauma, diseases compromising intestinal lining 3. Endocarditis: like s viridans, in pts with damaged valves, can be dangerous. Janeway lesions- non-painful, macular lesions on palms/soles from septic emboli. Osler nodes: painful palpable red lesions on fingers/toes

Bacteriophage Lysogenic Cycle

Persistent infection with temperate phage (lambda/mu) 1. Lambda prophage integrates into specific site on chromosome or remains as plasmid 2. Mu prophage integrates at many sites like transposon 3. Replicate as part of chromosome 4. Prevented from lytic cycle by production of repressor protein 5. Can be induced by UV light into lytic growth

Exchange of Genetic Information: Transformation

Pieces of free DNA taken up Competence- ability of bacteria to take up free DNA, due to small protein released by bacterium that acts to expose DNA binding protein on the surface of neighbors One strand is degraded while the other enters This is homologous recombination: entering strand hybridizes to homologous gene on chromosome and replaces host DNA strand- no net DNA added Occurs in vivo (capsular polysacs in s pneumo) Recombination frequency: closer 2 genes are on chromosome, more likely to be cotransmitted in random DNA fragment (linked) Plasmids can be transformed to bacteria in lab after bacteria made competent via high salt/temperature

S. pneumoniae: Clinical Disease

Predisposing conditions: necessary to lead to disease. Either inhibit clearing bacteria from oropharynx (like cilia motility) or inhibit AB-mediated protection. Antecedent influenza (very common), COPD, CHF, alcoholism (s and k pneumo), asplenia (birth/removal or sickle), age >65 1. Pneumonia: #1 cause of typical bacterial pneumonia, when bacteria multiplies in alveoli. Rusty (bloody) sputum, lobar pneumonia consolidation, pain, high fever, difficulty breathing 2. Meningitis: #1 cause of adult bacterial meningitis, MNM. Bacterial meningitis can be treated and no tx is deadly. Viral is more common and harder to treat but usually recover 3. OM/Sinusitis: #1 cause of ear/sinus infections in children

Streptococcal Pyogenic Exotoxins

Produced by s. pyogenes, lead to disease Spe A,B,C act as superantigens, stimulate T cells, suppress antibody responses, stim release of inflammatory cytokines (IL1,TNFa) from monocytes/macrophages Associated with severe streptococcal diseases (necrotizing fasciitis, toxic shock, rash from scarlet fever)

Clostridium botulinum

Produces spores and toxin, toxin main disease mediator Causes paralysis, used in Botox, most potent toxin in world Different infections in adults and infants Gram+ rods Fastidious spore formers and anaerobes Botulinum toxin is a neurotoxin leading to flaccid paralysis Found in soil, improper food canning

Cyclophosphamide Toxicity Highlight: Hemorrhagic Cystitis

Secondary to acrolein, a metabolite which attaches to bladder mucosa causing damage and irritation Usually within days, but can be 3w post treatment Prevention: vigorous hydration to keep urine output >100-200mL/hr MESNA (mercapto ethane sulfonates sodium): sulfhydryl that binds acrolein and forms stable, nontoxic product Dose at 60-100% cyclophosphamide/ifosfamide (latter is more bladder toxic and must always be given with MESNA, usually only necessary for cyclo at doses >1500mg/m2)

Bacterial Nucleoid

Simple- no nuclear membrane or mitotic apparatus Chromosome is one double stranded DNA supercoiled circle- polyamines and Mg neutralize DNA charge (instead of histones) Chromosome replication: single origin of replication, bidirectional, semiconservative, needs topo1 to relax the supercoil and gyrase to reintroduce them Nalidixic acid and quinolones bind to bacterial DNA gyrase to prevent DNA replication Chromosome does not condense before cell division, is not segregated to daughter cells by mitotic apparatus Transcribed by RNA polymerase (coupled w translation- 5' end translated while 3' end transcribed)- prevented by Rifampin Chromosome copy number depends on stage of cell cycle, quiescent cell has one

Staphylococcus: Extracellular Products: Enzymes

Some can be considered virulence factors, help establish infection 1. Coagulase- aureus, binds human fibrinogen, acts with CRF to convert to fibrin clot. Differentiates aureus from others 2. Catalase- in all, converts H2O2 to water and oxygen 3. Hyaluronidase- hydrolyzes hyaluronic acid in acellular matrix of CT, facilitates spread. in 90% of aureus strains 4. Staphylokinase (fibrinolysin): digests fibrin clots, presence depends on phages encoding this protein 5. Lipase- hydrolyzes lipids. In aureus and 30% of others. Essential to invade cutaneous/subcutaneous tissues 6. Nuclease- aureus. Cleaves DNA/RNA 7. Penicillinase- b-lactamase, encoded by plasmid, can be transferred. Confers penicillin resistance.

Paclitaxel

Taxane antiMT MOA- promotes MT assembly, interferes with disassembly Use- solid tumors Toxicity: myelosuppression (DLT): give before Pt analog, peripheral neuropathy (DLT- can be severe and lead to myopathies): sensory/motor neuropathy, myopathic effects, inc neurotoxicity with weekly compared to q3wk dosing, hypersensitivity reaction

C. perfringens: Diagnosis, Treatment

Therapy must be initiated immediately so laboratory is just confirmatory Microscopic detection of gram+ rods in clinical specimen in the absence of WBCs good indicator. Cultures well on agar and blood culture broths Treatment: surgical debridement necessary for soft tissue infection like myonecrosis High dose PCN, hyperbaric oxygen

Exchange of Genetic Information: Summary

Transformation: no cell-cell contact requirement, no antecedent phage infection, yes competency required, yes naked DNA involved, yes homologous recombination Conjugation: yes cell-cell contact, no antecendent phage infection, no competency, no naked DNA, no homologous recombination for F+/F-, yes for Hfr/F- Transduction: no cell-cell contact, yes antecedent infection, no competency, no naked DNA, yes homologous recombination

Vincristine

Vinca alkaloid antiMT MOA- interacts with tubulin, disrupts microtubule function, inhibiting formation of mitotic spindle Use- leukemia, lymphoma, solid tumors Admin- absorption unpredictable so usually an IV infusion. Never given intrathecally, all vinca alkaloids fatal this way Toxicity- Peripheral neuropathy (DLT) and other neuro toxicities: parethesis in extremities, autonomic neuropathy (abdominal pain, constipation, urinary retention, orthostatic hypotension) Unlike most chemo drugs, does not cause myelosuppression and so can give it with myelosuppressives

Genetic Information in Bacterium: Bacteriophage

Viruses (obligate intracellular parasites Capsid (protein coat)- polyhedral, filamentous, or complex forms, have DNA or RNA but not both Phage infection of bacterium: 1. Adsorption- random collisions, specific phage protein binds specific bacterial receptor 2. Uncoating/penetration- DNA/RNA injected across CW, into cytoplasm 3. Restriction enzymes in bacteria degrade DNA with different methylation pattern (bacterial immune system) Phages carry genes for: O antigen control (salmonella) Botulinum toxin (c botulinum) Erythrogenic toxin (s pyogenes) Diphtheria toxin (c diphtheria)

Flaviviruses: Dengue Fever: Immunopathology

4 distinct closely related serotypes (DEN1-4) Recovery from infection provides ABs and lifelong protection from that serotype, but ABs will be unable to neutralize a different strain (though some cross-reaction may occur). If pt contracts a second serotype of dengue, immune complexes may form, and this leads to dengue hemorrhagic fever Dengue normally affects monocytes and macrophages, so when AB binds virus it helps virus bind to target cells using Fc receptor as a secondary receptor Antibody Induced Enhancement of Infection

Bacterial Cell Wall

Thick, continuous barrier around all bacteria except mycoplasma Protects cell membrane from physical and osmotic damage Maintains shape: spheres (cocci), rods (bacilli), spirals Forms septum separating daughter cells in division Interacts with host defense Used in serological identification Enzymes to make wall targets for antibiotics

2 Main Types of Fungi

1. Yeasts: reproduce by budding or mitosis (asexual). Normally acellular, produce round, pasty, mucoid colonies 2. Molds: multicellular with threadlike hyphae that elongate via apical extensions. Hyphae come together to form matlike mycelia, forming filamentous, hairy, wooly colonies. Hyphae are multicellular and can be septate or aseptate. Either way, cytoplasm flows freely throughout hyphae. Pseudohyphae lack the free-flowing cytoplasm

Specific Candida Species

1. albicans- most common, fluconazole resistance rare 2. glabrata- inc incidence, maybe fluconazole resistant 3. tropicalis- GI tract is source, infection in neutropenic pts or post abdominal surgery 4. parapsilosis: can be carried on hands, under nails. Cause of NICU outbreaks, catheter infections 5. krusei- fluconazole resistant, infects neutropenics 6. lusitaniae- resistant to amphoB, treat with fluconazole

Adenovirus: Diseases, Serotypes

1. endemic respiratory disease: serotypes 1,3,5,7,14,21,etc 2. acute respiratory tract disease: 7,14,21 3. Pneumonia: 3,4,7b,14,21 4. Epidermic keratoconjunctivitis: 8,9,11,19,35,37 5. Pharyngoconjunctival fever: 1,2,3,4,5,7 6. Gastroenteritis: Group F serotypes 40,41,42 7. Pertussis-like syndrome: 5 8. Hepatitis: 1-5,7,21 9. Menigoencephalitis: 2,7 Changes in pathogenicity of serotypes: increased prevalence of 14 in civilian and military populations. More frequent occurrence of severe/fatal disease. Fatal disease occurs in immunocompromised as well as healthy young adults. This suggests novel strains have evolved

Picornavirus: Multiplication Cycle 2

5. Newly synthesized polymerase uses genomic RNA to make cRNA (minus sense), used as template to make more positive sense RNA 6. New +RNA can be used for translation and as template, eventually packaged into capsids to become new virions 7. Final cleavage event cleaves VPo to VP4 and VP2 to make new virions infectious 8. 500+ infectious particles released by cell by vacuoles or lysis. Poliovirus replication in single cell can be fast and aggressive. Log phase begins 2h after uncoating, peaks by 8h. A nonstructural protein causes host cell cap binding protein to be inactive, so host mRNA cannot be translated, only viral mRNA 9. Special characteristics: rhinovirus: max replication at 33C, acid labile

Foodborne Trematodiases

56m people globally, 7000 deaths Infected through raw fish, crustaceans, vegetables that harbor metacerariae Most common species are clonorchis, opisthorchis, fasciola, paragonimus Most prevalent in E Asia and S America, result in severe liver and lung disease In clonorchiasis and opisthorchiasis, adult worms lodge in smaller bile ducts of liver, causing inflammation/fibrosis of adjacent tissues, eventially cholangiosacrcoma- severe, fatal bile duct cancer Safe and effective medicines for prevention and treatment

Cancer Chemotherapy: Antimetabolites: Purine Analog

6-Mercaptopurine MOA- inhibits purine synth by incorporating into DNA and causing miscoding in replication. Competes with hypoxanthine and guanine to become activated in cell by HGPRT to form TIMP. TIMP is metabolized to 6-thioguanosine which is incorporated into DNA Use: acute lymphoid leukemia ALL Toxicity: myelosuppression, mucositis, N/V, hepatotoxicity Drug-Drug Interactions: Allopurinol, a xanthine oxidase inhibitor- 6MP is metabolized by XO, so taking both increases dose and toxicity of 6MP. Should reduce dose by 75% Azanthoprine- metabolized to 6MP, so both will increase concentration and toxicity

Cidofovir: Interactions, Resistance, Complications

6. Interactions: Probenecid can affect metabolism/excretion of other drugs. Reduce zidovudine by 50% or hold day of dosing. Rifampin, ketoprofen, chlorpropamide, dapsone, methotrexate, tri-sulfa, ddC, NSAIDs held day of dosing. Inc nephrotoxicity with other nephrotoxics 7. Resistance: mutations in DNA polymerase documented for CMV, cross-resistance with GCV 8. Complications: nephrotoxicity, neutropenia, uveitis, alopecia, ocular hypotony. Probenecid toxicity includes rash, fever, nausea 9. Contraindications: known hypersensitivity to cidofovir or probenecid, Creatinine >1.5, CrCl<55

Flaviviruses: West Nile: Signs & Symptoms, Treatment

90% asymptomatic or undifferentiated fever, unremarkable recovery Incubation 1-6d, usually mild fever, HA, myalgia, anorexia, rash in about 50% at end of fever. Resolves in 3-6d West Nile Neuro-Invasive Disease: encephalitis, meningitis, or poliomyelitis in about 1/150. Serious illness can occur at any age but people over 50 (esp >70) at higher risk. HA, high fever, neck stiffness, stupor, disorientation, coma, tremors, convulsions, muscle weakness, paralysis Treatment: supportive only. No vaccine.

Opportunistic Fungal Infections: Aspergillus: Disease, Diagnosis, Treatment

4. Disease: most common opportunistic mold infection in world. Allergic bronchopulmonary aspergillosis (ABPA), aspergilloma (fungus ball colonizing old lung cavity), and invasive aspergillosis (usually in lungs/sinuses of immunocompromised hosts) 5. Diagnosis: histopathology- sepate, acute angle branching hyphae invading sterile tissue ABPA- asthma-like with elevated IgE against aspergillus, eosinophilia, fleeting pulmonary infiltrate Culture- may be hard to know if real or a contaminant 6. Treatment: corticosteroids for ABPA, no treatment necessary for aspergilloma, voriconazole or amphoB for invasive disease

Cancer Chemotherapy: Antimetabolites: Pyrimidine Analog

5-Fluorouracil, Cytarabine 5FU MOA- acts as false pyrimidine, inhibiting formation of thymidine by inhibiting thymidylate synthase which is RLS, inhibits DNA syntehsis Use: GI Cancers (colon, pancreas), head/neck cancer, breast cancer Toxicity: bolus infusion-myelosuppression, continuous infusion-mucositis, diarrhea, hand/foot syndrome, other- cardiotoxicity, photosensitivity, skin reactions, alopecia, N/V, ocular toxicity Leucovorin given but not as rescue: increases stability of 5FU binding to thymidylate synthase, increases efficacy

Picornavirus: Diagnosis, Epidemiology

Definitive diagnosis 1. Culture from parynx or stool- polio, coxsackie B typing accomplished via activity of specific ABs or by isolation of culture from involved site 2. Serologic assays: IgM detection or rise in IgG 3. Reverse transcriptase PCR: is sample can be obtained while virus still present Epidemiology: 1. Polio associated with poor sewage/sanitary conditions 2. Infections found worldwide 3. Higher prevalence during late spring through early fall in US 4. Polio and Coxsackie A more severe in adults, Coxsackie B more severe in children

Host Range/Susceptibility

Depends on: accessibility (physical barriers) availability of receptors on host cells (tropism) proper intracellular environment host defenses virulence characteristics of virus

Germline Mosaicism

Described in many conditions: germline has mutation but not the body Mutation must occur post-zygotically during early embryonic development Mutation may affect only cells destined to form eggs/sperm Responsible for recurrence of disease in second child when parent appears not to be carrier: new mutation propagated only in the germ cells Relatively common in Duchenne/Becker MD

H. pylori: Diagnosis, Treatment

Diagnosis by microscopy on stool samples not recommended: hard to see and cannot differentiate from nonpathogenic helicobacters Urease activity test: abundance of urease allows for detection in under 2h. Positive direct test 100% specific and sensitive. Noninvasive test of human breath after consumption of isotopically labeled urea used Treatment: very difficult, three pronged plan used: 1. Proton pump inhibitor 2. Amoxicillin 3. Clarithromycin

Rickettsia: Diagnosis, Treatment

Diagnosis by symptoms, but can be confirmed with PCR or immunofluorescence. Serology takes about 2 weeks (too slow- for R. rickettsia, death in 10d) Treatment: doxycycline, even for pregnant women and children

C. trachomatis: Diagnosis, Treatment

Diagnosis: 1. cytologic or serologic finding 2. Direct detection of antigen in clinical specimens using direct immunofluorescence or ELISA 3. PCR Treatment: 1. ocular/genital infections: azithromycin or doxycycline for 7d 2. Newborn conjunctivitis/pneumonia: erythromycin for 10-14d 3. Lymphogranuloma venerum: doxycycline for 21d or erythromycin if doxy is contraindicated (pregnant women, children, etc)

Borrelia: Diagnosis, Treatment

Diagnosis: Western Blot. False negatives can be given in primary and tertiary Lyme disease. ELISA also available. W Blot is part of tick panel given to detect B. burgorferi, anaplasmosis, ehrlichiosis, babesia. Treatment: Doxycycline, steroids For relapsing fever PCNs or tetracyclines more effective Prevention involves avoiding ticks and their habitats, wearing protective clothing, applying repellants A vaccine for B. burgdorferi was removed from market in 2012

Listeria: Pathogenesis/Immunity

Facultative intracellular pathogen 1. Ingested with contaminated food, survives digestion 2. Adheres to host cells via interaction of surface proteins with glycoprotein receptors on host cell. Internalized in phagolysosome in enterocytes/M cells in Peyer's patches 3. Low pH of phagolysosome activates listeriolysin O and 2 phospholipase C enzymes, allowing listeria to break out into cytoplasm of cell 4. Replicates in cytosol, using bacterial protein Act A, create actin rockets that propel bacteria to PM and create filopod, eventually pushing through PM to adjacent cell 5. Adjacent cell ingests bacteria and process repeats 6. Replication in macrophages after passage thru intestinal lining carries bacteria to liver and spleen, leads to disseminated disease which can reach brain (meningitis)

Drugs for Uncomplicated Malaria

Falciparum: artemisinin derivative with lumefantrine, atovaquone with proguanil, qunine with doxycycline/clindamycin, or mefloquine Vivax and ovale: chloroquine and primaquine Malariae and knowlesi: chloroquine

Fungi: Basic Info

Few are pathogenic, and those are opportunistic Degrade organic matter (some can eat through tissue) No photosynthesis. Exist in 1 of 4 forms: 1. Saprobes- live on dead/decaying matter 2. Symbionts: live together in mutally advantageous way 3. Commensals: live in close relationship: one benefits, other is not benefitted nor harmed 4. Parasites: live on host, they benefit, host is harmed Fungi are eukaryotes with a rigid cell wall of chitin with glucan or mannan. Cell membrane contains ergosterol.

Dracunuculus medinesis: Life Cycle

Fiery serpent of the Biblical Israelites- humans only host Life cycle: adult worms in body cavity and surrounding tissue of human host. Pregnant females migrate to subcutaneous tissues of infected humans, esp ankles/wrists, secrete products which cause formation of papule/blister On contact with water, blister erupts, uterus of F worm prolapses, releasing rhabditiform larvae into water Larve penetrate water flea, molt twice to infective L3, wait to be swallowed in unfiltered drinking water Larvae exsheath in duodenum and penetrate mucosa, endergo 2 molts and are now mature adults

Nocardia: Characteristics, Structure, Diagnosis

Filamentous gram+ rods, partially acid fast (mycolic acids in CW), non-spore forming, urease positive Catalase positive (pts with CGD have increased risk Obligate aerobes found in soil Primary virulence factor is ability to avoid phagocytic killing Phagocytes kill microbes via H2O2 and superoxides but Nocardia's catalase and superoxide dismutase protect them Replicate within macrophage by preventing fusion of phagosome-lysosome, preventing acidification of phagosome, and avoiding killing Diagnosis: Usually distributed throughout tissue and abscesses making it easy to detect and recover them Appear similar to a israelii, but weakly acid-fast.

Artemisinin Derivatives: Combination Therapy

Have short half life, 1-2h, so used in combination with other active agents (lumefantrine, amodiaquine, mefloquine, sulfadoxine-pyrimethamine, doxycycline, or atovaquone-proguanil) and not used for prophylaxis Can be given po, IV, IM, rectally Mild toxicity: N/V, inc liver enzymes, dec reticulocytes/neutrophils Resistance: clinical evidence in Cambodia, Thailand, Vietnam, Laos, Myanmar. Primarily from mutation in propeller protein resulting in prolonged ring stage which is less susceptible to artemisinin, and an enhanced stress response

Tissue Tapeworms: Structure

Head (scolex) with hooks and suckers No digestive tract Neck- immature segments Strobilia (proglottids) develop into independent hermaphroditic reproductive units

Trypanosoma brucei: Life Cycle, Disease

T. b. gambiense and rhodesiense cause W/E African sleeping sickness (Human African Trypanosomiasis) Life cycle: indirect, vectored by bite of Tsetse fly. Epimastigote form found in insect host, trypomastigote in vertebrate host. Parasites develop into infective form (metacycling trypomastigote) in salivary gland of fly and are transferred into host in a bite. Other animals can be reservoirs. Clinical disease: Acute phase: found in blood, formation of ulcer at bite site. Irregular fever, HA, lymphadenopathy Chronic: CNS involved, behavioral symptoms, inc sleepiness, anorexia/malnutrition, paralysis, coma, death

Congenital Syphilis

T. pallidum can cross placenta starting in 2nd trimester Latent infections, multiorgan malformations, or death of fetus Most infected infants born with asymptomatic symphilis, then get sniffles (rhinitis) where mucus is infectious, containing spirochetes Disease spreads, infant develops maculopapular rash Infants can also be born with what looks like secondary syphilis Hutchensonian (notched) teeth, bone deformities, blindness, deafness, CV syphilis common in untreated infants who survive initial disease

Leptospira

Thin coiled spirochetes with hook at one or both ends Obligate aerobes, growth at 28-30C Thin, highly motile, can penetrate intact mucous membranes and skin through small cuts/abrasions Transmitted in fresh water, about 200 cases/yr worldwide, over half in Hawaii Common reservoirs are small mammals where they cause asymptomatic infections and colonize renal tubules allowing them to be shed in large numbers in urine, thus contaminating fresh water

Human CMV: Congenital Infection

#1 cause of congenital disease (.5-2.5% of births) Immature immune system acts like immunocompromised Transplacental blood transmission, ascending infection from cervix. Prenatal diagnosis via amniocentesis or chronic villus sampling Transmission from maternal primary infection (30-40% transmission rate, 85-90% asymptomatic, 10% will have neuro sequelae). Careful counseling necessary Sequelae: fatal or severe, usually from primary maternal infection: microcephaly, intracerebral calcification, petechiae, jaundice, thrombocytopenia, hepatosplenomegaly, hearing loss, mental retardation Symptoms less severe with maternal recurrent infection

Fungal Reproduction

'Imperfect' fungi- where sexual reproduction not seen yet 1. Asexual- In yeast using spores, sporangiospores and conidia. Sporangiospores are asexual spores made in containing structure called sporangia. All spores can grow a new organism, are easily killed (unlike bacteria). Can come from nuclear fission (mitosis, thallic reproduction), budding (producing blastosphere), or germ tube becoming pseudohypha. Asexual state of fungus is anamorph 2. Sexual: meiotic via fusion of 2 nuclei. Mating usually between 2 mycelia (heterothallic reproduction), but can occur within one (homothallic). Sexual state is telomorph. Molds copulate at tips of hyphae- hyphae grow toward each other in response to sex hormones, tips blend together. Fusion leads to formation of zygote and sporangium. Sporangia allow for budding to release spores and create new organism

C. botulinum: Disease

1. Adult botulism- when adults ingest preformed toxin built up over time in anaerobic alkaline condition (canned beans, tuna, not acids like tomatoes). 25 cases/yr in US. Blurred vision, fixed dilated pupils, drooling, dry mouth. Paralysis is descending and moves to GI with constipation/pain. No fever. Death from respiratory paralysis, 10-20%. 2. Infant botulism- 75 cases/yr. 2-6m of age (crawling, floor time), when babies ingest vegetative bacteria/spores in soil/dirt/dust/honey/formula. Bacteria grows in GI without competition, produces toxin, leading to floppy baby- flaccid paralysis. Weakness, crying, constipation, FTT, then flaccid paralysis/respiratory arrest. Mortality 1-2% 3. Wound botulism: very rare, time course longer and GI symptoms less pronounced

Malaria Drugs: Atovaquone, Malarone

1. Atovaquone: lipophilic analog of ubiquinone, interferes with mitochondrial electron transport. Given orally, absorption inc 2-3x with fatty meal. 1/2 life is 1-3d, eliminated in bile and feces. Some GI upset, fever, rash, HA, insomnia. Used for malaria (below), babesiosis, p. jirovecii and toxoplasmosis 2. Malarone: atovaquone-proguanil, active in liver and blood stages. Causes some abdominal pain, N/V, HA Prophylaxis and therapy of chloroquine resistant falciparum For malaria prophylaxis, start taking 1-2d before entry and 1w after exit

Picornavirus: Multiplication Cycle 1

1. Attachment and penetration via receptor-mediated endocytosis. Receptors are immunoglobulins and integrins. Binding to receptor induces conformational change in capsid, internal VP4 protein is lost. Virion RNA delivered through vesicle membrane to cyytoplasm 2. Genome acts as mRNA (can be infectious) 3. Translation of genome into polyprotein- 5' noncoding region is substitute for cap 4. Polyprotein cleaved into small proteins by 2 virally coded proteases. Some products are structural proteins (VP1-4), some are nonstructural: RNA dependent RNA polymerase, 3 proteases (2A, 3C, 3D)

Virus Replication in Cells

1. Attachment: virus protein binds to specific PM receptor on host 2. Penetration: most viruses taken up in coated pits which form vesicles 3. Uncoating: virus envelope fuses with endosome membrane at low pH 4. Transcription: mRNA synthesized 5. Translation: of viral mRNA and transport of membrane associated proteins carried out by cell machinery 6. Replication: genome (not virus), varies in cells infected 7. Assembly: components of virion are self-assembling 8. Release: enveloped viruses bud through membrane, naked viruses released at cell lysis Note: when this takes place in multiple cells, cytopathogenic effect occurs and can be diagnostic (vacuolation, cell fusion, bodies, lysis)

Non-Venereal Treponemes

1. Bejel caused by pallidum endecium in Middle East. Primary lesion in oral cavity, secondary in oral mucosa, tertiary lesions are rare 2. Yaws caused by pallidum pertenue in Tropics, primary on skin, secondary systemic rash, tertiary rare 3. Pinta caused by T. carateum in CA/SA, primary on skin (erythematous papule), secondary on skin (altered pigmentation), tertiary is areas of altered pigmentation and hyperkeratoses

Identification of Fungi: Biochemical and Serology

1. Biochem: especially Candida. Can be identified to species level using biochem/physio assays like bacteria. Most common is carb assimilation (ability to use a specific carb as the only source of C). Nitrate assimilation, carb fermentation also used 4. Serology: assays detect fungal specific antigen or ABs Antigen detection: histoplasma/blastomyces in urine, cryptococcal in serum or CSF, aspergillus/galactomannan in serum, b-glucan of candida or aspergillus in serum AB detection: histoplasma or coccidoides in serum

Nocardia: Disease States and Treatment

1. Bronchopulmonary disease: from inhalation of pathogen, almost only in immunocompromised w reduced T cell fxn. Slow growth curve. Cough, dyspnea, fever, cavitation and spread to pleura. Should be part of differential especially in immunocompromised pt with pneumonia with cavitation and dissemination to CNS or subcutaneous. Particular affinity for neural tissue leads to brain abscesses. 2. Cutaneous/Lymphocutaneous lesions: from traumatic implantation, even with normal immune systems. Mycetoma- painless chronic subcutaneous infection with draining sinus tracts. Primarily on feet with localized subcutaneous swelling and involvement of underlying tissues, muscles, bone. Sinus tracts form. Note: affinity for neural tissue and painless lesions means sometimes initial presentation is meningitis due to multiple brain abscesses Treatment: trimethoprim-sulfamethoxazole

Identification of Fungi: Yeast Identification

1. Candida: non-encapsulated extracellular yeast with pseudohyphae 2. Cryptococcus: large, round yeast cells surrounded by thick capsule 3. Histoplasma: small, round, extra- and intracellular forms, often within macrophages 4. Blastomyces: Large, round with single bud from mother, broad based 5. Coccidoides: giant spherule containing endospores 6. Paracoccoides: multiple buds around mother cell: look like pilot wheel or mickey mouse ears 7. Sporothrix: small, cigar shaped cells 8. Penicillinum: small, oval shaped cells with transverse septum (divides by fission)

Opportunistic Fungal Infections: Candida

1. Candidemia: bloodstream infection. Risk factors: central venous catheter, parenteral nutrition, broad spectrum abx, chronic renal failure/hemodialysis. Up to 40% mortality. Treatment: remove infected catheter, echinocandin, amphoB, or fluconazole 2. Disseminated candidiasis: spread in blood to end organs Endophthalmitis: retinal infection, vision loss Endocarditis: IVDUs, post valve replacement Chronic disseminated candidiasis

N. meningitidis: Pathogenesis, Disease States

1. Carrier state- health people carry meningococci in nasopharynx with no disease (when carrier rate >20% of community, risk of epidemic increases). Transmission from carrier to carrier is respiratory (sneezing) 2. Clinical manifestations: bacteremia without sepsis, meningococcemia (septicemia) without meningitis, meningitis, and meningococcemia with meningitis 3. Humoral immunity develops to capsule. Does not change carrier state but helps protect against septicemia and meningitis. Complement proteins lyse organisms. 4. From nasopharynx, organisms reach blood stream (meningococcemia)- high fever, hemorrhagic rash. Maybe fulminant sepsis, DIC, circulatory collapse (Waterhouse-Fridrichsen). Can invade CNS, cause meningitis

VZV: Vaccines

1. Children 12m to 12y Efficacy 80-85% for any VZV diseae Large number of breakthrough cases of wild type virus (usually <50 lesions, shorter duration, lower fever incidence) Low incidence of latency followed by zoster in children (must identify reactivating strain as Oka). 2 dose regimen now: 12-15m and 4-6y, at least 3m apart Two formulations: alone or with MMR (MMRV) 2. Adults over 12 2 doses at least 28d apart, not to immunocompromised Zostovax approved for >60y, single dose 14x potency of kids vaccine to prevent singles and post-herpetic neuralgia Initial results indicate it is effective

Drugs for Malaria Prophylaxis

1. Chloroquine: in areas without resistant p. falciparum 2. Malarone (atovaquone+proquanil): in areas with multidrug resistant falciparum 3. Lariam (mefloqune): in areas with chloroquine resistant falciparum 4. Doxycycline: areas with multidrug resistant falciparum 5. Primaquine: terminal prophylaxis of vivax and ovale No drug is 100% effective, must take other preventative measures

Quinolones

1. Ciprofloxacin: a fluoroquinolone. Very broad spectrum, including gram- rods (inc pseudomonas), mycobacteria, many gram+, but poor for anaerobes. Inhibits DNA gyrase. My increase theophylline levels, interfere with clearance of caffeine PK: well absorbed from GI, half life 4h, 35% bound, excreted in urine/feces, penetrates into cells well Toxicity: N/V, rash, occasional CNS, C diff is rare 2. Levofloxacin: better against strep than cipro. Used for CA respiratory infections. Activity against Legionnaire's, mycoplasma, strep pneumo.

Newer Macrolides

1. Clarithromycin: 2-4x more active against susceptible strep and staph. Active against moraxella catarrhalis, legionella, m pneumo, borrelia. Possible dec in GI toxicity, well absorbed, BID dose 2. Azithromycin: 2-4x less active than erythro against staph and strep, otherwise similar spectrum with increased activity against H flu, salmonella, campylobacter. Decreased absorption with food. Long half life, elimination half life of 3d which allow for shorter courses of treatment QD dose, active against chlamydia

Cidofovir: MOA, Indications, Dosage

1. Classification: nucleotide monophosphate cytidine analogue, diphosphorylated by cellular kinases for activity 2. MOA: incorporated into DNA by DNA poly, stops synth 3. Indications: AIDS-related CMV retinitis (only FDA approved), ACV and foscarnet-resistant HSV, VZV, CMV, emergency poxvirus treatment 4. Dosage: IV only, 60h half life allows Qweek dosing for induction, Q2wk for suppression, must be given with probenecid to decrease renal tubular toxicity 5. Modification: If creatinine rises >.3-.4, reduce dose to 3mg/kg. If rises >0.5 or proteinuria 3+, stop drug

Filoviridae: Marburg/Ebola: Treatment, Prevention, Control

1. Convalescent Serum: used to treat Dr. Brantly. Passive immunity, serum from surviving pt transferred to ill pt, allows AB mediated clearance of virus 2. Zmapp: artificially produced AB therapy (Rush Grad). Tobacco plants genetically modified to transiently produce Zmapp antibodies (composed of 3 monoclonal ABs specific for Ebola variants) 3. Supportive care and rehydration improve survival chances

Identification of Fungi: Microbiological

1. Culture: similar to bacteria (blood, chocolate agar). Some grow slowly, need weeks of incubation and would be overgrown by bacteria in these media. Fungal specific media used (Sabaroud's Agar- glucose, peptones, pH 5.6), held for 4 weeks, sometimes grown at both 25C and 37C. ID relies on examination of hyphae, spores, how spores formed. Other FSM: potato-glucose agar, V8 juice 2. Fungal blood culture: Fungal isolator system inc isolation of fungi in blood. Venous blood then lysed, centrifuged. Sediment with cell debris and fungal cells plated on FSM for 4 wks 3. Germ tube test: commonly used for candida albicans. Yeast colonies mixed with serum, held at 37C for 3h. Micro exam shows tube structures (germinating hyphae) emerging from cells. C. tropicalis can give false positive.

Clinical Presentations of Anthrax

1. Cutaneous anthrax: most common. Painless papule at site of inoculation progresses to ulcer and enlarging black eschar indicative of necrosis from LT. Surrounding edema and lymphadenopathy from ET. Systemic symptoms and 20% mortality without treatment, recovery with treatment 2. GI Anthrax: very rare in US. Ulcer at invasion site, regional lymphadenopathy, edema, sepsis. Almost 100% mortality. IF organism invades upper respirator, ulcers in mouth/esophagus. If in cecum/ileum, N/V, malaise, systemic disease 3. Inhalation anthrax

Incomplete Penetrance Examples

1. DYT1- a type of hereditary dystonia Idiopathic torsion dystonia gene, auto dominant with IP Always same mutation, GAG insertion, gain of function Only 30-40% carriers get disease, unclear why but not environmental 2. Familial Seizures Channel genes: K,Na,Ca,Cl,AChR Auto recessive or dominant with IP Many individuals with mutation never have a seizure Same mutation, same family can give different seizures

Flaviviruses: Dengue Fever: Signs and Symptoms

1. Dengue fever (breakbone fever): incubation 4-10d. Abrupt onset of high fever, HA, extreme joint/bone pain (feels as if bones are breaking). Occasional rash. Fever can be biphasic and WBC/platelet counts may be reduced. Severe, flu-like illness that affects infants, young children, adults, but rarely causes death 2. Dengue hemorrhagic fever: potentially deadly complication of (1). Plasma leakage, fluid accumulation, respiratory distress, severe bleeding, organ impairment. 3-7d after first symptoms in conjunction with decrease in fever temperature, include severe abdominal pain, persistent vomiting, rapid breathing, bleeding gums, fatigue, restlessness, blood in vomit. Occurs after second exposure to dengue virus

Ganciclovir/Valganciclovir:

1. Dosage: GCV IV or oral (bad BA), VGCV oral Modifications similar to ACV 2. Interactions: other bone marrow suppressors, inc seizure risk with Imipenem, inc effect or toxicity with HIV/HBV antivirals and mycophenolate 3. Complications: bone marrow suppression, neutropenia, thrombocytopenia. Less commonly fever, rash, anemia, inc liver function tests, vomiting, eosinophilia, inc BUN/creatinine, CNS toxicity Potential teratogen, contraindicated in pregnancy 4. Resistance: mutations in CMV UL97 gene HSV isolates show cross resistance with ACV 5. Contraindications: documented hypersensitivity Concomitant marrow suppressors (GCSF and GMCSF used to support WBC)

Opportunistic Fungal Infections: Mucormycosis

1. Ecology- wide distribution 2. Mycology: 5 major genera: rhizopus (bread mold, most common cause of disease), mucor, rhizomucor, absidia, cunninghamella 3. Lab features: can be contaminant and sometimes hard to grow. Hyphae are large, nonseptate, branch at right angles Exact species ID is hard, depends on appearance of spores 4. Disease: usually in immunocompromised. Rhinocerebral or sinoorbital disease (in diabetics with ketoacidosis)- infection of nares, palate, sinuses, orbit, brain Pulmonary disease- necrotizing pneumonia GI disease- malnourished patients ingest spores in food Cutaneous- infection post trauma, burn patients 5. Diagnosis: demonstration of large, non-septate hyphae in tissue, blood cultures usually negative. Tissue culture can confirm. 6. Treatment: high dose amphoB

Opportunistic Fungal Infections: Aspergillus: Ecology, Mycology, Lab Features

1. Ecology: one of most common molds in environment: soil, decaying organic matter, dried herbs/spices 2. Mycology: over 900 species, 4 important: fumigatus, niger (black pigment), flavus (yellow pigment), terreus 3. Lab features: spores are airborne, can cause lab contamination Culture- rapid growth on most media, best at 37C but is thermotolerant and can still grow at 45C Mycelia appear rapidly, brown-yellow and wrinkled Hyphae are septate, branch at 45 degree angles

Opportunistic Fungal Infections: Cryptococcosis

1. Ecology: yeast associated w soil, pigeon guano worldwide 2. Mycology: C neoformans divided into serotypes A-D. Grows at 37C, usually in 2-4d. Characterized by round yeast forms surrounded by large polysac capsule with narrow based budding 3. Disease: lungs portal of entry via inhalation Acute infection usually asymptomatic, pneumonia possible Meningitis: cryptococci have predilection for CNS, dec mentation and elevated CSF pressure are bad signs Osteomyelitis, skin infection, prostatitis. Common infection in advanced HIV. 4. Diagnosis: India ink stain of CSF positive in 50%. Cryptococcal antigen can measure capsular antigen: + in over 90% in blood, CSF. False positives with trichosporon Culture: gold standard 5. Treatment: amphotericin and 5-FC, fluconazole

Enterobacteriaceae: Specific Pathogens

1. Escherichia coli: most common cause of UTI and travelers diarrhea. Causes diarrhea through multiple plasmid-mediated mechanisms. Important cause of neonatal meningitis 2. Klebsiella: large colonies, mucoid appearance (from large capsule). Cause of lobar pneumonia in compromised hosts 3. Enterobacter, citrobacter, serratia: causes of nosocomial infections in compromised hosts 4. Yersinia pestis: plague 5. Proteus: major cause of UTIs (along with E coli/Klebsiella) swarming growth on plate, urease positive

Difference Between Plasmodium Species

1. Falciiparum: No hypnozoite, double signet ring only in RBC, malignant tertian fever (48h) 2. Ovale: yes hypnozoite, trophozoite and schizont in RBC, benign tertian fever with relapse 3. Vivax: yes hypnozoite, Schuffner's dots in RBC, benign tertian fever with relapse 4. Malaria: no hypnozoite, circular merozoite array in RBC, quartan/malarian fever (72h) 5. Knowlesi: No hypnozoite, trophozoite and schizont on RBC, malignant tertian fever Note: hypnozoite is dormant hepatic form

C. jejuni: Disease

1. GI infections: acute enteritis with bloody diarrhea, fever, and severe pain. Generally self-limiting but can last longer than 1 week 2. Guillain-Barre: autoimmune disorder of PNS (symmetric weakness over several days, recovery requiring months). Association due to cross-reactivity between LOS of some strains of campylobacter and PNS 3. Reiter's: one of several seronegative spondyloarthropathies associated with campylobacter

C. tetani: Diseases, Treatment

1. Generalized tetanus: most common is rigid paralysis of masseter leading to trismus/lockjaw. Risus sardonicus is characteristic smile from sustained contraction. Opisthonos also common. 30% mortality from exhaustion of chest muscles, respiratory failure 2. Neonatal tetanus: associated w initial nfection of umbilical stump, progressing to general tetanus. Mortality 90%. More common but almost only developing world Treatment: vaccination using tetanus toxoid, chemically inactivated tetanospasmin. Creates a pool of antibodies to clear toxin which must happen before it enters nerve. Series of three doses, booster every 10 years Passive immunization- can give human Ig to neutralize unbound toxin

VZV: Laboratory Diagnosis, Treatment

1. Growth in cell culture: human fetal diploid lung cells (shell vials, tube cultures): CPE similar, slower than HSV 2. Scrapings from base of lesion- Tzanck smear: syncytia, Cowdry type A inclusions (acidophilic, intranuclear), fluorescent antibody for viral proteins 3. Serology: can screen for immunity, needs ELISA or EIA, presence of IgM and rise in titer with zoster Treatment: 1. Children: none needed, vaccine now available 2. Adults and immunocompromised patients: acyclovir, valacyclovir, famicyclovir, Varicella-Zoster Immunoglobulin, Vaccine within 3-5d of exposure

Situations to Choose Serology Testing

1. HC worker exposed to a virus, wanting to know if titer is present. (If not, should not be in contact with patients for a few weeks) 2. Exposed to a virus and finds out she is pregnant, wants to see if she has ABs 3. Child is immunocompromised, plays with child who comes down with virus 4. Person develops suspicious symptoms for virus, want to check for IgM antibodies (example: WNV)

Antiviral Agents for DNA Viruses: by Disease

1. Herpes simplex/Varicella zoster: acyclovir, valacyclovir, famciclovir Acyclovir resistant: cidofovir, foscarnet 2. Cytomegalovirus: ganciclovir, valganciclovir Ganciclovir resistant: foscarnet, cidofovir 3. HPV: imiquimod, interferon

Ehrlichia/Anaplasma: Disease

1. Human monocytic ehrlichosis: caused by E. chaffeensis after infection of monocytes/macrophages. 1-2w after bite: flu-like, high fever, HA, malaise, myalgia. Late onset rash in 30-40%. Leukopenia, thrombocytopenia, elevated serum transaminases develop. Mortality low, >50% hospitalized 2. Human anaplasmosis: by A. phagocytophilum. Granulocytes primarily infected. 5-10d after exposure, similar symptoms as above. Over half need hospitalization, severe complications include demyelinating polyneuropathy, facial palsy

Imiquimod and Trichloroacetic Acid

1. Imiquimod: HPV genital warts, topical agent Immune response activation causes secretion of cytokines like interferon Causes nonspecific inflammation and dermatitis, HA, flu like symptoms, diarrhea, fungal infections 2. Trichloroacetic acid: HPV genital warts, topical agent Chemical coagulation of proteins

B. fragilis: Disease

1. Intra-abdominal infections: most common organism in abdominal infections, can lead to abscesses. Enterotoxin-producing strains can cause self-limiting watery diarrhea. Usually gastroenteritis infections seen in children under 5 2. Gynecologic Infections: mixtures of anaerobes are responsible for female genital tract infections, and B fragilis is commonly associated with abscess formation

Flaviviruses: Others

1. Japanese encephalitis: endemic to Japan, Korea, China, SE Asia. Vaccine for children, travelers, and pigs. Killed Vaccine. 2. Tick-borne encephalitis: endemic to former USSR.

Mycoplasma and Ureaplasma: Disease

1. M pneumo: usually asymptomatic, most common symptom is tracheobronchitis. Low fever, malaise, HA, dry nonproductive cough 2-3w after exposure, acute pharyngitis possible. Symptoms generally worsen and can persist 2w or more. Pneumonia also possible: atypical/walking pneumonia. Diagnosis is by symptoms, patchy infiltrate on CXR, and cold agglutinins (ABs specific for RBCs that agglutinate as blood is cooled, positive in about 60% of M pneumo pts). 2. U. urealyticum: GU tract colonized with myco- and ureaplasma so tough to know how they work in disease. Accepted that urealyticum, M genetalium, and M hominis cause nongonococcal urethritis NGU, PID, and spontaneous abortion/premature birth. Women often asymptomatic carriers.

Poxvirus: Diseases

1. Molluscum contagiosum: only strictly human poxvirus disease, usually benign. Umbilicated skin papules with caseous plug, resolves spontaneously but takes a while. Spread by close contact (sexual, camps, daycare, sports). More widespread papules in immunocompromised (HIV) 2. Orf- zoonotic. Single nodular lesion at point of contact with infected animal, usually hand or forearm. Lesions resolve after 3-4w. Diagnosed from symptoms, history 3. Monkeypox- smallpox but milder. Mainly in Africa, 2003 outbreak in IL. Prairie dog pets infected by contact with exotic African rodents. Can use smallpox vaccine or cidofovir for therapy. Others: vaccinia, cowpox

Classification of Fungi

1. Mucormycetes: Rhizopus, Mucor, Lichtheimia, Basidobolus. Sexual: zygospores, asexual: sporangiospores 2. Basidomycetes: cryptococcus, malassezia, trichosporon. Sexual: basidiospores, Asexual: conidia 3. Pneumocystidomycetes: Pneumocystis jirovecii. Sexual: yes, Asexual: binary fission 4. Sacccharomycetes: candida, saccharomyces. Sexual: not seen, asexual: conidia 5. Eurotiomycetes: dermatophytes, blastomyces, histoplasma, aspergillus, fusarium, scedosporium. Sexual: ascospores, asexual: conidia by budding

L. monocytogenes: Disease

1. Neonatal Disease: two forms: early onset (in utero), late onset (at/soon after birth). Early- abortion, stillbirth, premature birth. Granulomatosis infantiseptica is severe early form, causes abscesses/granulomas. Late- meningitis or meningoencephalitis with septicemia. Signs not unique, other meningitis causes like groupB strep must be excluded 2. Infections in pregnant women: 20x more susceptible, most infections during 3rd trimester when cell immunity most impaired. Nonspecific flu-like symptoms, may resolve on own but can transmit to fetus 3. Listeriosis in healthy pts: usually asymptomatic or mild flu-like, acute self-limiting gastroenteritis for 2d. More severe in elderly. 4. Meningitis: most common form of disseminated listeria in adults. Not specific signs so should always be suspected in pts with organ transplants, cancer, pregnant women. 20-50% mortality with significant sequelae.

Aminoglycosides: Toxicity

1. Neuromuscular blockade: reduces amount of ACh released from motor nerve endings, leads to paralysis. Susceptible pts are those receiving certain anesthetics, those with MG and Parkinson's. Reversed with Ca gluconate or neostigmine 2. Ototoxicity: toxic to hearing and balance. Streptomycin esp toxic to vestibular, amikacin to hearing, gentamicin and tobramycin to both. Risk factors are pre-existing renal failure, treatment >10d. t1/2 in perilymph of ear is 10-12h (5-6x that of serum) 3. Nephrotoxicity: can cause acute tubular necrosis manifested by loss of concentrating ability and non-oliguric renal failure

Flaviviruses: Dengue Fever: Treatment, Prevention, Control

1. No specific treatment. For hemorrhagic form supportive care and maintaining fluids is vital. No NSAIDs as they can worsen hemorrhage 2. Vaccine: no approved vaccine. First vaccine was registered in early 2016, tetravalent, Theiler 17D backbone. WHO recommends considering introduction in high endemicity areas 3. Vector control: avoid mosquitoes, pesticide and insecticide, genetically sterilized mosquitoes

Antiviral Agents for DNA Viruses: by Mechanism

1. Nucleoside analogues: acyclovir/valacyclovir, famciclovir, ganciclovir/valganciclovir, trifluridine 2. Nucleotide analogue: cidofovir 3. Pyrophosphate analogue: foscarnet 4. Immune activation: Imiquimod, recombinant IFN alpha-2a/2b

Human CMV: Primary Infection

1. Perinatal: transmission via cervical secretions at birth, breastmilk, saliva, transfusion. Usually mild or asymptomatic, premature infants can have more severe disease Can have neuro sequelae (mental retardation, hearing loss) Shed virus for long time, source of infection 2. Normal Adults: rate of infection low (10-15%) until adolescence. Inc in day care (saliva, urine). Sexually transmitted. High level of virus in cervical secretions, semen Socioeconomic status related to prevalence Infectious mono-like syndrome (like EBV but heterophile-negative)

Ectoparasite Treatment

1. Permethrin toxic to scabies, head/body/pubic louse 1% cream rinse used for affected areas. For scabies, 5% from neck down for 8-14 hours, repeated in one week Adverse reactions: transient burning, stinging, itching, pruritis 2. Malathion: 0.5% lotion applied to dry hair, combed 4-6h later to remove nits/lie 3. Crotamiton: cream or lotion. Scabies: 2 applications from chin down at 24h intervals, with cleansing bath afterwards

VZV: Types of Disease

1. Primary: chickenpox. Highly communicable, transmitted by aerosol. Fever, rash on trunk/scalp. Asynchronous lesions- successive crops every 3-5d Most severe disease is in adults (pneumonias). Can be fatal in immunocompromised, neonates Cell-mediated immunity controls but allows reactivation 2. Congenital and Neonatal Congenital varicella syndrome: low birth wt, cutaneous scarring, microcephaly, chorioretinitis, cataracts Congenital disease in under 1.5%, if exposure in first 28w Congenital disease in 2nd half of gestation not seen but may develop zoster early in life Transmission 5 days before to 2 days after birth can produce severe disease in 17-30% of newborn infants- high mortality if untreated

HSV 1 and 2: HSV1 Infection

1. Primary:classic transmission via saliva, oral contact w break in skin. Clear vesicles to pustular lesions to ulcers to crusted lesions. Gingiovostomatitis/herpes labialis/cold sores, herpetic whitlow (infection of finger), herpes gladiatorum (infection of body). Herpes keratitis: infection of cornea to recurrent infection with possible immune component, can lead to blindness. Eczema herpeticum in kids with active asthma. Encephalitis 2. Latent: asymptomatic, viral DNA in sensory cells of trigeminal nerve ganglia 3. Recurrent: virus replicates, travels down sensory nerve fiber to infect epithelial cells in area of original infection. Symptoms usually milder. Recurrent keratitis leads to corneal damage, blindness

Malaria Drugs: Dihydrofolate Reductase Inhibitors

1. Proguanil: a metabolite (cycloguanil) inhibits plasmodial DHFR. Kills erythrocytic forms but also has some intrahepatic activity. Well tolerated with rare hematologic toxicity, used in combo with atovaquone 2. Pyrimethamine: structurally similar to above, 1000x more active against parasitic v mammalian enzyme. Used with sulfonamide in treatment of chloroquine resistant falciparum and used for toxoplasmosis 3. Sulfonamides and sulfones: PABA analogues, competitively inhibit falciparum dihydropterate synthase. Combined with DHFR (above) to enhance action. Resistance appears quickly if used as monotherapy. Toxicity: bone marrow suppression if QD, prevented by use of folinic acid

C. diphtheriae: Disease

1. Respiratory diphtheria: 2-4d incubation, transmission by aerosols. Initially colonizes epithelial cells in oropharynx and causes localized damage from toxin. Onset sudden with malaise, ST, quickly spreading thick, hard, firm exudate that can cause local obstruction and asphyxiation in young kids as it grows across larynx. Exudate is a pseudomembrane (like in c diff) firmly adhered to tissue. Difficult to dislodge, can cause bleeding on removal 2. Myocarditis: exotoxin (not bacteria) can travel to heart, cause inflammation in majority of patients 1-2w after illness, as pharyngeal symptoms begin to improve 3. Neurotoxicity: exotoxin leads to demyelination of nerves near post pharynx causing local paralysis, can spread to oculomotor/ciliary paralysis, peripheral neuritis 4. Cutaneous diphtheria: uncommon, acquired via skin contact with infected people. Papule, then chronic nonhealing ulcer, sometimes with pseudomembrane

Aminoglycosides: Mechanisms of Resistance

1. Ribosomal resistance (mutation leads to inability of drug to bind/interact with ribosomal units- rare) 2. Dec uptake of drug (changes in membrane transport may inhibit drug uptake, decreasing conc in ribosomes. Uncommon, plays a role in resistance in pseudomonas in some growth conditions (anaerobic, low pH) 3. Aminoglycoside modifying enzymes (transferase enzymes- most common) can change aminoglycoside structure and activity via acetyltransferases, adenyltransferases, and phosphotransferases. Many resistance genes coding for these are on transposons 4. Aminoglycoside resistant enterococci: have intrinsic low level resistance, maybe because they have anaerobic metabolism and oxidative metabolism enhances uptake. Still active synergistically with CW agents against them. High level resistance increasingly common, might be from chromosomally induced changes in target site or permeability/plasmid induced drug inactivation. When this occurs, not useful even synergistically

Famciclovir

1. Structure: Prodrug of penciclovir, extensively absorbed in gut and deacetylated in blood, intestine, liver Oxidized in liver to PCV with 65-75% BA Anabolism much like ACV- needs TK for phosphorylation 2. Indications: Treatment/suppression of HSV, tx of VZV 3. Dosage: oral only. Modifications for CrCl under 60. 40-50% pts over 50 with zoster will need dose modification 4. Interactions: None 5. Complications: HA, nausea, fatigue most common. Cross resistance with ACV 6. Contraindication: documented hypersensitivity

Foscarnet

1. Structure: inorganic pyrophosphate analogue 2. MOA: inhibits viral DNA polymerases and reverse transcriptases at PP binding sites during DNA chain elongation. Does not need phosphorylation for activity. 3. Indications: CMV, HSV, VZV, including ACV/GCV resistant mutants 4. Dose: IV only, lower dose effective for HSV/VZV 5. Modification: excreted by kidneys so modify with RI. Modification must be made frequently because of changing renal function with nephrotoxicity 6. Interactions: other nephrotoxics like amphotericin B 7. Complications: nephrotoxicity. Others: altered serum electrolytes, N/V, seizures, anemia, mucosal ulcerations from direct drug toxicity 8. Contraindications: significant RI, other nephrotoxics (amphotericin B, aminoglycosides, pentamidine) 9. Resistance: clinically resistant CMV and HSV seen in HIV/AIDS pts and transplant recipients (mutations in DNA polymerase)

Specific Sulfa Agents and Uses

1. Sulfasoxazole- very soluble, mostly for UTIs 2. Sulfamethoxazome- combined with trimethoprim 3. Sulfadizine- less soluble, highly active, good CSF levels 4. Sulfadoxine- long t1/2, used with pyrimethamine for prophylaxis/treatment of malaria 5. Salicylazosulfapyridine- used for UC 6. Topical used in burn treatment Uses: UTIs, nocardia, pneumocystis carinii (w trimethoprim), toxoplasmosis, malaria, listeria (w trimethoprim), aerobic bacteria if susceptible

Cestode Treatment

1. Taeniasis: caused by t. saginata, t. solium and treated by praziquantel, caused by neurocysticercosis and treated by albendazole 2. Echinococcosis: caused by e. granulosus and e. multilocularis, treated by albendazole Note: conflicting studies on whether antiparasitic therapy leads to better seizure control or improved resolution of cysts

C. trachomatis: Disease

1. Trachoma: leading cause of infectious blindness, transmitted by eye seeking flies, fingers, fomites. Blindness from scarring (follicular lesions, eyelashes). Chronic disease with diffuse inflammation causes eyelids to turn inward and now eyelashes abrade cornea. 2. Non-gonococcal Urethritis: most infections in women asymptomatic but can develop symptoms (can lead to salpingis, endometritis, PID, sterility). In men urethral discharge, dysuria, pyuria. Can lead to neonatal conjunctivitis and pneumonia during birth 3. Neonatal inclusion conjunctivitis: as infants pass through infected canal. 5-12d after, eyelids swell, hyperemia, copious purulent discharge. If treated topically can lead to pneumonia so oral therapy recommended 4. Lymphogranuloma venereum: chronic STI prevalent in Asia, Africa, SA. Initial small painless lesion (often overlooked), then significant swelling of draining LN

Arthropod-borne, Rodent-borne, and Filoviruses: 3 Clinical Syndromes

1. Undifferentiated fever: fever of unknown origin. High fevers, HA, myalgia, arthralgia, malaise. Usually 3-10d, resolve with no sequelae. Nonspecific so cannot know cause 2. Undifferentiated fever + hemorrhagic fever: all of above plus profuse bleeding into skin, severe GI pain/cramping mostly from thrombocytopenia. Leads to shock, can be highly fatal. Do NOT treat with NSAIDs 3. Undifferentiated fever + encephalitis: all of (1) plus severe headache, stiff neck, altered consciousness or mental state. Can be complicated by seizures, strokes, coma, may result in permanent neuro sequelae. Maybe significant mortality

Flaviviruses: Yellow Fever: Signs and Symptoms

2 Stages 1. incubation 1-6d after bite. Many asymptomatic but when symptoms occur look like undifferentiated fever (N/V, muscle pain (backache), HA, LOA). Resolve in 3-4d 2. Not in all pts. Within 24h of recovering from (1), high fever with venous stasis and tendency to hemorrhage. Bleeding from nose, eyes, mouth, or stomach. Leads to prostration, kidney involvement, degenerative changes in liver (jaundice), heart dysfunction. Councilman bodies in liver- virus formed inclusions in hepatocytes made of extra protein and nucleic acids in the infected cells. Black vomit is common. 50% die in 7-10d

Gene Conversion

2 similar genes, one is converted to other via unclear mechanism (maybe from mispairing in DNA replication) Often involves genes which have been duplicated in evolution and one copy is more functional than other Example: SMA: failure of anterior horn cells to develop (hypotonia, weakness, areflexia) Chromosome 5 has big, ancient duplicated region with many genes. SMN has telomeric and centromeric copies SMNt is important copy. This is common region for deletion and SMNt could get deleted and cause disease Often it is not deleted but whole/part converted to SMNc, and it behaves like it is missing bc SMNc does not fully compensate the function. Disease will be milder (partial compensation)

Ivermectin

2015 Nobel prize Mechanism: opens glutamate-gated Cl channels in nematodes and arthropods, leading to influx of Cl and paralysis. Well tolerated. Used for: luminal and tissue helminths (does not kill adults) Onchocerca volvulus, strongyloides stercoralis, arthropods including scabies

Rickettsia

Abnormal bacteria Two groups: typhus causing and spotted fever causing Rods, obligate intracellular parasites Have LPS and a minimal peptidoglycan layer Cannot be grown on artificial medium Energy vampires: steal ATP from host cells Ricketsii: reservoir ticks, vector ticks Prowazekii: reservoir humans/flying squirrels, vector lice

Dihydrofolate Reductase Inhibitors

Act synergistically with sulfa via sequentially inhibiting steps in folate synthesis pathway Resistance may develop quickly if used alone Interfere with transfer from FH2 to FH4, the active metabolite

A. israelii: Disease

Actinomycosis- chronic granulomatous lesions become suppurative, form abscesses connected by sinus tracts 1. Cervicofacial: most common, lumpy jaw. In pts who have had recent dental work, jaw trauma, poor oral hygiene. Actinomyces in mouth invade diseased tissue, nontender lump on jaw eventually becomes abscess. Draining sinus tracts form along jaw and neck. Macroscopic colonies of organisms look like grains of sand, seen in abscesses and tracts, called sulfur granules (yellow/orange) 2. Pelvic: associated with IUD placement. From benign vaginitis to extensive tissue damage, tubal-ovarian abscesses, ureteral obstruction 3. CNS: uncommon. Solitary brain abscess. Rarely meningitis, subdural empyema, epidural abscess

Complex Multifactorial Trait Inheritance

Actually most common type of inheritance Defines normal and abnormal traits Sum of activity of many interacting genes produces phenotype Probably involved in learning disability, autism, mild MR, behavior, psych diseases, normal personality traits, learning profiles Long way from understanding this

B. fragilis: Pathogenesis, Immunity

Adheres to epithelial cells and extracellular molecules like fibrinogen via fimbriae Adheres to peritoneal surfaces more effectively than other anaerobes due to its polysaccharide capsule (which is antiphagocytic and major virulence factor) Produces SCFA succinic acid during anaerobic metabolism which inhibits phagocytosis and intracellular killing Toxin: a heat-labile Zn metalloprotease toxin causing morphologic changes in epithelium which leads to Cl secretion and fluid loss. Also induces IL8 secretion by intestinal epithelial cells which contributes to inflammatory damage

Spirochetes

All gram- and helical Treponema (syphilis), borrelia (Lyme), leptospira (leptospirosis) Cannot be seen on gram stain: too thin Must use Darkfield microscopy- place sample on light microscope, shine light from side showing white spiral against black backdrop All motile, have internal flagella between inner and outer membranes, allowing it to twist on its axis

Haemophilus Influenza

All haemophilus species are small gram- rods found in mucus membranes of humans Growth required supplementation with hemin (X factor) and nicotinamide adenine dinucleotide (NAD, V factor). Both found in blood agar, but sheep's blood must be heated to destroy V factor inhibitors, giving chocolate agar CW has LPS and endotoxin components of other gram- rods, and most have polysac capsule with six antigenic serotypes a-f, b was most infections historically Type b vaccine introduced and disease is now rare, most infections by non-typable strains (though b still a problem worldwide) Disease is nearly all pediatric: 1. Epiglottitis- inflammation/swelling can block airway 2. Meningitis 3. Cellulitis/otitis/respiratory infections

Viral Genetics, Mutants

All progeny synthesized during normal replication of single virus are genetically identical (clones), virus is haploid Mutants are genetically altered, usually from point mutations during transcription, usually through misincorporation of nucleotides by viral replicase (polymerase) proteins Can alter receptor usage (tropism), replication efficiency, targets for enzymes Mutants can be candidates for live attenuated vaccines Examples: SARS getting new hosts, some viruses only able to grow at reduced temperatures

Aminopenicillins and Carboxypenicillins

Aminopenicillins have similar activity and broader spectrum than natural PCNs. Destroyed by b-lactamases. Bactericidal for gram-/+ bacteria. Used for URI, UTI, meningitis Ampicillin, amoxicillin, pivampicillin, metampicillin, talampicillin, epicillin Carboxypenicillins are excellent for pseudomonas. Carbenicillin, Ticarcillin

B. anthracis: Reservoirs and Colonization

Anthrax is zoonotic disease acquired from animals or animal product- spores on hides, tusk, intestines of herd animals and in ground where they have grazed. Humans infected by contact with animals or soil with spores. Animal transmission rare in US because of vaccination in animals 1. Spores engulfed by macrophages, carried to regional LN 2. Germinate in macrophage, become bacteria 3. Bacteria escape and proliferate in lymph, enter blood 4. Proliferation leads to mass septicemia with 10^7-8 bacteria/mL of blood. If strain has LT or ET virulence factor, systemic toxemia and death

Quantitation

Antibody neutralization Higher dilution of AB, less AB in test well Higher dilution of AB inhibition, more AB in pt sample Dilution of AB that inhibits virus function or activity is the titer of the sample Neutralization assays can also be performed to measure inhibition of CPE, though this is a less quantitative assay

Unstable Trinucleotide Repeats

Any sequence (CTG, CGG, CAG, GAA described) Small expansions at threshold of instability do not show symptoms. Protomutation: alleles likely to become unstable Premutation: allele is unstable on transmission but does not cause disease in carrier Can expand or contract (more likely to expand) Sex preference for expansion Expansion over generations results in worse disease or more people with disease (anticipation)

Arenaviridae: Lassa Virus

Arenaviridae overall named because virion has pebbly appearance. Zoonoses- cause disease in rodents, can be transmitted to humans. Natural reservoir is bats and rodents, humans are dead end. Lassa: endemic to W Africa, best known of the hemorrhagic fevers. Fever, coagulopathy, petechiae, occasional visceral hemorrhage with liver/spleen necrosis and no vasculitis. Hemorrhage and shock possible, as well as cardiac and liver damage. No lesions in CNS unlike LCMV. Pharyngitis, diarrhea, vomiting possible. Death in 50%. Spread by contact so medical personnel at risk. Can be treated with Ribavirin.

EBV: Mechanisms of Malignant Disease

Associations with malignancies in specific regions: 1. African Burkitt's Lymphoma: children in malarial Africa. Monoclonal B cell lymphoma of jaw. EBV DNA in tumors, but only express EBNA1 antigen. Chromosomal translation of c-myc, geographic distribution suggests cofactor (malaria, diet, environment, etc) 2. Nasopharyngeal carcinoma: S china, epithelial cell tumor, EBV DNA in tumor cells Associations with other malignancies: 3. Leukemia/lymphoma in T cell deficient patients: polyclonal leukemia linked to B cell proliferative disease- X linked lymphoproliferative disease 4. Post-transplant lymphoproliferative disease/lymphomas: AIDS, immunosuppressed transplant recipients 5. Hodgkin's disease

Ehrlichia and Anaplasma

Atypical bacteria Force phagocytosis like Rickettsia but remain in the phagosome Two forms: elementary and reticulate bodies Intracellular location protects them from AB responses, but bacterial stim of proinflammatory cytokines activates macrophages that can opsonize bacteria when extracellular 2500 cases/yr in US. Ehrlichia mostly MW and coastal Atlantic, Anaplasma mostly upper MW and NE Over 90% disease in mid-April to late October Reservoir: deer, mice, chipmunks, voles, canine Vector: tick bite

Coxiella

Atypical bacteria: C. burnetti causes Q fever Reservoir: mammals, birds, ticks, Vector: aerosols Slow replicating intracellular pathogen and can regulate cell signaling pathways in host so death is delayed. Infects macrophages and monocytes. Extremely stable, survives in soil/milk for years. Human infections after inhalation of airborne particles from contaminated course (like unpasteurized milk in dairy workers)- ticks do not transmit to humans <150 cases/yr in US, most exposed are asymptomatic or have mild flu-like sx. Some develop hepatitis, pneumonia, subacute endocarditis. Diagnosis by serology or PCR Treatment with doxycycline

Bartonella

Atypical bacteria: bacilliformis, henselae, quintana Henselae: reservoir: fleas, vector: cat scratch, fleas Causes bacillary angiomatosis and cat scratch fever. Cats are asymptomatic carriers, disease transmitted with scratch, bite, or contact with contaminated feces of cat's fleas. Leads to chronic regional lymphadenopathy of draining LN. Dissemination to liver, spleen, eye, or CNS possible Quintana: reservoir: lice, vector: lice/contaminanted human feces Causes trench fever, prevalent in WW1. Severe HA, fever, weakness, pain in long bones (tibia). Louse feces spread from person-person. Can lead to recurrent fevers, bacillary angiomatosis if immunocompromised Treatment: effectiveness of antibiotics against cat scratch fever has not been shown, azithromycin used if anything

Chlamydia and Chlamydophila

Atypical bacteria: trachomatis, pneumoniae, psittaci Trachomatis causes chlamydia, most common bacterial STI, also #1 cause of infectious blindness. If caught early and treated is curable. Obligate intracellular parasites Like Rickettsia, cannot be grown in artificial medium and are ATP-vampires Has elementary bodies (resistant to harsh environmental barriers, allow to survive outside host cells) and reticular bodies (allow to replicate in host cell cytoplasm) C. trachomatis: reservoir: humans, vector: eye seeking flies and STI C. pneumoniae: reservoir: humans, vector: aerosols

Sulbactam

B-lactamase inhibitor similar in structure to clavulanic acid Oral or parenteral with a b-lactam. IV or IM with ampicillin (Unasyn). Dosage adjusted for RI Good activity against gram+ cocci, including b-lactamase producing S aureus, gram- aerobes (but not resistant E coli or pseudomonas), and anaerobes Good for mixed intra-abdominal and pelvic infections

Parvovirus: MOD of B19

B19: spread by respiratory and oral secretions, infects mitotically active erythroid precursors (bone marrow) Receptor is P blood group antigen Erythema infectiosum or Fifth Disease Viremic stage can cross placenta, maternal primary infection (hydrops fetalis) Late stage immune response: rash, arthralgia, arthritis Antibody is important for recovery, immunity Aplastic crisis in pts with underlying anemia, reticulocytopenia

Polyomaviruses: BK, JC

BK: immunocompetent: likely respiratory route of infection early in life. Asymptomatic, 100% seropositivity by age 10. Latent infection in kidney. Immunocompromised: hemorrhagic/nonhemorrhagic cystitis, ureteral stenosis, polyomavirus associated nephropathy (probably reactivation in transplanted organ leads to loss of alograft) JC: Respiratory route, 70% seropositivity. Latent infection in kidney, monocytes, lymphocytes. Crosses BBB by replicating in capillary endothelial cells. Increased incidence in AIDS patients, some association with transplantation, lymphoma, leukemia Progressive Multifocal Leukoencephalopathy PML: subacute demyelinating disease, immunocompromised pts, motor dysfunction, visual deficits, progressive dementia

Babesiosis: Life Cycle

Babesia microti: complicated 2-host life cycle During meal, Ixodes tick introduces sporozoites to white-footed mouse. They enter RBCs and start budding. In blood, some parasites differentiate into M and F gametes (cannot be distinguished with microscope), ingested by tick, the definitive host. In tick, gametes unite and create sporozoites. No transovarial, vertical, hereditary transmission in small babesia. Humans enter cycle when bitten by infected tick. Sporozoites introduced, enter RBCs, undergo budding. Multiplication of RBC-stage responsible for clinical manifestations. Humans are usually dead-end hosts but transmission possible via blood transfusion

Vancomycin

Bactericidal, interferes with CW synthesis Mostly for PCN resistant staph (including MRSA) and enterococcal. Adverse reaction after IV admin: chills, fever, phlebitis. Red man syndrome can happen with rapid admin. Increase in resistance recently, especially in staph and enterococci Prevents CW synth by binding to D-Ala-D-Ala on peptidoglycan, slower killing kinetics than beta-lactams Used in gram+, including sepsis, endocarditis, meningitis, C diff colitis Both oral and IV, renal t1/2 6h.

Aminoglycosides: Basics

Bactericidal, mainly against aerobic gram- rods. Poorly absorbed from GI tract so usually give IV or IM Most commonly used for nosocomial infection with highly resistant organisms. Have some use against staph, used in combo with PCN or vancomycin for enterococci. Sometimes used for mycobacterial infections. Dose/duration dependent renal/ototoxicity are important limiting factors. -mycin from streptomyces, -micin from micromonospora Examples: streptomycin, gentamicin, tobramycin, amikacin, neomycin, kanamycin, sisomicin, netilmicin Note spectinomycin is different but very related. Does not have glycosidic bonds or amino sugars, used for gonorrhea

Aminoglycosides

Bactericidal, mostly gram- bacilli Passively diffuse through outer CW, AT through PM into cytoplasm. Needs O, so not effective against anaerobes. Bind irreversibly to 30S ribosome, cause irreversible inhibition of protein synthesis. Poorly absorbed from GI, so large doses given po before intestinal surgery to sterilize bowel. Usual route IM or IV. Usually reserved for serious gram- infections in hospitalized patients Orally can cause N/V/D. Parenterally can cause nephro- and ototoxicity. In long period administration, irreversible damage and permanent hearing loss has occurred

Cephalosporins

Bactericidals, similar structure and MOA to penicillins Usually more resistant to b-lactamases than PCN. Some bacteria, usually gram-, can make cephalosporinase Grouped into 4 generations Oral- GI disturbances (diarrhea, rash). Gen 1 can cause nephrotoxicity, esp in pts with RI or dehydration. Can cause disulfiram reaction when combined with alcohol, so patients cannot consume any alcohol while on these drugs. Some allergies, but lower than PCN. Some are allergic to both, so don't give cephalosporins to those who have had life-threatening PCN reactions

Chloramphenicol: MOA, Resistance

Bacteriostatic, binds 50S subunit and blocks binding of aminoacyl tRNA. Bactericidal for H flu, S pneumo, N meningitides. Selectivity: Mammalian cells have 80S ribosomes but mitochondria may be affected Activity: Broad spectrum. Gram+ (not good for staph), gram- (not good for pseudomonas), anaerobes, Rickettsia Resistance: Bacteria/cell impermeable to drug Acetyl transferase acetylates drug to inactive form

Clindamycin

Bacteriostatic, binds 50S subunit. Very active against most anaerobic bacteria and gram+ cocci. Pharmacology: 90% GI absorption, not decreased by food. Penetrates most tissues (poor CSF, but does penetrate brain). Metabolized by liver. Toxicity: 20% diarrhea, pseudomembranous colitis Uses: anaerobic infections, gram+ cocci in PCN allergy, toxoplasmosis (with pyramethamine)

Tetracyclines: MOA, Uses

Bacteriostatic, reversibly binds to 30S subunit of ribosome and blocks aminoacyl tRNA and subsequent addition of new AAs. May minimally inhibit mammalian protein synthesis, but does not achieve high levels in mammalian cells Broad spectrum, all are nearly equivalent but lipophilic agents (minocycline, doxycycline) have slightly higher gram+ activity. Uses: acne, Rickettsial infections, Chlamydial infections, mycoplasma, cholera, brucella, helicobacter, Lyme, Mycobacterium marinum, Meningococcal carrier state

Linezolid: MOA, Pharmacology

Binds to 50S subunit and prevents formation of complex that initiates protein synthesis. Activity: gram+, especially staph, strep, enterococci, gram+ anaerobic cocci, and gram+ rods (corynebacterium, listeria). No cross resistance with other classes. Static for staph, enterococci, Cidal for strep. Pharmacology: well absorbed from GI regardless of meal. PO and IV dosing the same (bioavailability ~100%). 80% of agent appears in urine, 30% as active. 10% metabolized drug in feces. Parent drug conc not changed by renal failure but metabolites can accumulate (cleared by dialysis)

Flaviviruses: Yellow Fever: Transmission/Epidemiology

Bites of Aedes aegypti mosquito. Jungle (monkey to man via mosquito) and urban (man-man via mosquito) cycles Urban cycle leads to large epidemics. 47 countries in Africa, CA, SA endemic for virus. In 2013, 84-170k severe cases, 26-60k deaths in Africa alone 30% mortality. Travelers can bring it back so vaccination is vital. In 17-19C has been brought to NA/Europe Current outbreak: Angola, DRC

Schistosomiasis: Life Cycle

Blood flukes: hematobium, mansoni, japonicum. One of most common parasites worldwide, >260m infections Found in tombs of mummies Life cycle: adults (dioecious) in blood vessels: hematobium in vessels of bladder wall, mansoni/japonicum in intestine Eggs with spine erode through wall, shed in urine/feces Miracidia emerge, penetrate freshwater snail host, undergo development through spirocyst stages to yield infective cercariae Infection when cercariae directly penetrates bare skin, starts migratory phase: transform to schistosomula (larval migratory form) in skin, travels to lungs, travels to liver (worms pair off, mate) Paired worms migrate against hepatic portal circulation to vessels of intestine and bladder Prepatent period of 5-12w, depending on species

Tetracyclines

Broad spectrum bacteriostatics actively taken up by bacteria. Bind to aminoacyl tRNA site on 30S ribosome reversibly to inhibit synthesis. Work in gram- and gram+. Foods, especially those with Ca (milk) or antacids/mineral supplements interfere with absorption. They bind Ca molecules and form insoluble compounds so should be given 1 hour before or several hrs after meals Used in combo in treatment of H pyori ulcers. Tigecycline is structurally related, spectrum includes MRSA, enterococci. Most common SE are N/V/D. Overgrowth and superinfection of non-susceptible organisms, esp fungi (candida albicans) can occur. Can produce photosensitivity Because of Ca binding, no to children under 8 or pregnant/nursing women because deposited in growing bones/teeth

Chloramphenicol

Broad spectrum, reserved for serious, life-threatening (typhoid fever, some meningitis) MOA: inhibits protein synthesis (bacteriostatic) SE: N/V/D. Potentially very toxic. Bone marrow depression, producing anemia and other blood disorders. Usually reversible Should not be given to infants under 2 weeks, as infant livers cannot metabolize it and accumulation leads to toxic blood levels and gray baby syndrome

Bunyaviridae: Arthropod-Borne

California Encephalitis Group Widely distributed, at least 10 viruses. Vector is Aedes aegypti mosquito, reservoir likely rabbits, squirrels, or field mice. Most importantL California encephalitis (prototype), LaCrosse Virus, Jamestown Canyon Virus. California and Jamestown are rare, LaCrosse endemic to this area and most common: seizures in 60%, death in 1%. Symptoms of all 3: fever, HA, mild-severe CNS involvement most often seen in children. No treatment, supportive care only. No vaccine.

Plaque Assay

Can determine number infectious particles in sample Dilute virus suspension is used to infect cell monolayer under a layer of agar containing nutrients. The virus can only spread to one layer at a time. After several rounds of replication, plaque (hole in monolayer) forms Each plaque is initiated by one single infectious particle called a plaque forming unit (pfu). Correlations can be made between number of pfu needed to cause disease and virulence of virus Neutralization assay measures ability of polyclonal AB to inhibit infectivity of a known amount of virus by blocking viral binding to the host cell In a plaque reduction neutralization assay, number of pfu is reduced in presence of AB if AB is specific for that virus. If there is little or no reduction, AB has no relevance or is not generated to a strain closely related to the virus.

Fungi: Thermal Dimorphism

Can grow as mold and as yeast depending on temperature. Molds grow at room temp (25C) and yeast at body temp (37C) by undergoing gene switch Histoplasma, Blastomyces, Coccidoides, Paracoccidoides, Sporothrix can do this

Mucosal Infections: Candida

Candida is yeast, part of normal flora of GI and female GU Overgrowth can result in symptomatic infection of mucous membranes (mouth, esophagus, vagina) Chronic, recurrent infections can occur in immunocompromised (HIV, DM) Other predisposing factors include antibiotic or steroid use, neutropenia, chemotherapy Types of mucosal infection: oral candidiasis (thrush- creamy white plaques), vaginitis, esophagitis (associated with dysphagia, odynophagia), cystitis (bladder infection associated with foley catheter, DM, broad-spectrum abx)

T. pallidum: Diagnosis, Treatment

Cannot be cultured, so diagnosis is serological: 1. Nontreponemal tests measure IgG/IgM against lipids released from damaged cells in early phases. Antigen used is cardiolipin. VDRL and RPR most common tests, lack specificity especially in pregnant women and patients with AI disease 2. Fluorescent Treponemal Antibody-Absorption Test: indirect fluorescent AB test where t pallidum is immobilized on glass slides and used as antigen. Slide overlayed with pt serum mixed with nonpathogenic treponemes. Fluorescein labeled antihuman ABs addd to detect ABs in blood 3. T pallidum particle agglutination TP-PA: microtiter agglutination. Gelatin particles sensitized with t pallidum and mixed with dilutions of pt serum. If ABs present, particles agglutinate Treatment: PCN primary treatment

Other Beta-Lactams

Carbapenems and Monobactams, structurally similar to penicillins (replace sulfur with C) Broad antibiotic spectrum, similar to generation 4 PCN Carbapenems also have inc resistance to bacterial beta-lactamases Aztreonam classified as monobactam, highly resistant to penicillinase and is given IV for resistant gram- infections. Not effective against gram+ or anaerobics. Given IV q8h (t1/2 90m), cilastatin added to prevent hydrolysis by renal dehydropeptidases. Can cause seizures. No oral absorption

Carbapenems/Monobactams

Carbapenems: Imipenem, meropenem, doripenem, ertapenem. Used in serious bacterial infections (pneumonia, sepsis). Prevents CW synth by inhibiting transpeptidases and PBPs Not orally absorbed, IV every 6-8h. Cilastatin added to prevent hydrolysis in renal tubule so imipenem not degraded Causes seizures, esp at >2g/day Monobactams: aztreonam. Often confused as aminoglycoside because of similar activity against gram-, enterobacteriaceae, pseudomonas Prevents CW synthesis by inhibiting transpeptidases only No cross sensitivity with beta-lactam like compounds, used in pts with immediate hypersensitivity to PCN Same IV admin as above

R. rickettsii: Pathogenesis and Immunity

Cause Rocky Mountain Spotted Fever, most common disease causing rickettsiia in US, but is in SE US (NC, SC, TN, OK), not in Rocky Mountains Spread by dog and wood ticks Outer membrane protein A on surface adheres to endothelial cell, forcing it to phagocytose organism Once released from phagosome, multiplies in cytoplasm Can move from cell to adjacent cell, lysing as it goes Mass endothelial lysis leads to vasculitis causing hypovolemia/hypoproteinemia from loss of plasma into tissues

Plasmodium: Life Cycle, Disease

Cause malaria, most widespread parasitic disease (250m) Life cycle: 1. sporogony: sexual reproduction in mosquito gut gives infectious sporozoites that migrate to salivary glands of F mosquito, injected in meal Schizogony: 2. Exoerythrocytic cycle: hepatic: sporozoites invade liver, undergo asexual division 3. Erythrocytic form: merozoites released from liver, infect/reproduce in RBCs (cyclic reinfection possible) 4. Gametogony: after a few RBC division cycles, merozoites develop into M/F gametocytes, picked up by F mosquito. Sexual cycle takes place in mosquito again. Disease: paroxysmal fever: chills/fever/sweats. Anemia, splenomegaly, hemoglobinuria (blackwater fever, in falciparum only)

Trichinella Spiralis: Life Cycle, Disease

Cause trichinosis, found throughout world Life cycle: larvae encysted in striated muscle When eaten in raw meat, released in stomach, molt and become tiny adults. Then mate in intestinal lumen, M passed in feces and F burrows to submucosa and deposits live larva, which are carried via blood/lymph to other tissues Larvae reach striated muscle, coil in the cell and are now infective Disease: Intestinal phase: abdominal discomfort, diarrhea within 24h Muscle penetration: fever, HA, periorbital edema, muscle pain. Muscle damage, most severe in myocarditis, high level of eosinophilia

Babesiosis Treatment

Caused by Babesia microti DOC: quinine+clindamycin or atovaquone+azithromycin Some pts (those with severe illness) benefit from supportive care: antipyretics, vasopressors, blood transfusions, exchange transfusions, mechanical ventilation, dialysis

Filariasis

Caused by several genera/species of worms 1. Wuchereria bancrofti, Brugei malayi/timori cause elephantiasis. Vector: mosquito. Lymph swelling of legs/genitalia, asymptomatic, inflammatory, or obstructive. Diagnosis via microfilaria in blood, travel history. Tropical and substropical 2. onchocerca volvulus causes river blindness via black fly. Corneal/iris damage, skin nodules (allergic/inflammatory reaction to worms), hanging groin. Diagnosis via skin scrapings, microfilariae in blood, travel history. Africa, SA, CA, Mexico 3. Loa loa causes calabar swelling via deer fly. Toxic reaction to adults/larvae leads to large bumps on face and extremities. Painful, itchy, large microfilaria. Diagnosed by adult migrating across nose or conjunctiva, travel history. African equatorial rain forest.

Toxoplasmosis Treatment

Caused by toxoplasma gondii Ocular: pyrimethamine+sulfonamide+folinic acid or trimethoprim+sulfamethoxazole Maternal/fetal infection: spiramycin (first and early second trimesters), pyrimethamine/sulfadiazine and leucovorin (late second and third trimesters) Pyrimethamine-sulfonamide is first line for treatment and suppression. Sulfa can be replaced with clindamycin or atovaquone if toxicity develops Trimethoprim-sulfamethoxazole for primary prophylaxis Dapsone+pyrimethamine or atovaquone are alternative prophylactics

HHV6: Pathogenesis, Diagnosis

Causes exanthem subitum or roseola, long-recognized childhood disease (A causes, B rarely causes roseola and its disease associations are unknown) High level of seropositivity at early age, 90% of adults Spread by oral secretions Bone marrow and lung disease in BMT patients May accelerate HIV infection of CD4 cells in coinfection Roseola: infection, 4-7d infection, 4d high fever, fever gone rash appears, recovery and lifelong latency Diagnosis: Not routinely done Cocultivation of PBMCs with stimulated primary cord blood lymphocytes or inoculated with saliva (not performed in the clinical lab) Immunohistochemistry with monoclonal ABs, variant specific Qualitative and quantitative PCR from PBMCs, plasma, or serum

Cephalosporins: Second Generation

Cefaclor, Cefonicid, Cefprozil Activity against anaerobes, can be useful against beta-lactamase producing H flu and Morazella catarrhalis. Good for sinusitis, LRI, otitis. Less gram+ coverage than first generations, but greater gram - coverage: H flu, Enterobacter, Neisseria, Proteus, E coli, Klebsiella, Serratia (HEN PEcKS)

Cephalosporins: First Generation

Cefazolin, cefadroxil, cephalexin Very active against gram+ cocci like pneumo, staph, strep Oral prep useful for staph, strep, UTIs Cefazolin has good presence in most tissues (no CNS) so used for surgical prophylaxis for at-risk pts. No activity for MRSA or enterococci Some gram- coverage: Proteus, E coli, Klebsiella pneumoniae (PEcK)

Cephalosporins: Fourth Generation

Cefepine, cefozopran, cefpirome, cefquinome Resistant to beta lactamase hydrolysis but more potent hydrolyzers can deactivate Equal gram+ coverage as gen1, better gram- coverage including pseudomonas Can cross BBB, so useful for meningitis Empiric for nosocomial infections Cephalosporins overall: gram- 3>2>1, gram+ 1>2>3, pneumo 1/3>2, nothing against listeria, enterococci, myoplasma Given IV q8h (t1/2 90m)

Cephalosporins: Third Generation

Ceftriaxone, cefoperazone, cefotaxime, cefdinir Oral agents have activity against pseudomonas, reduced activity against gram+. Expanded, broad spectrum gram- coverage Expanded beta-lactamases have dramatically reduced use Can cross BBB

Polyomaviruses: Diagnosis, Treatment of JC/BK

Cell culture is possible but not used for diagnosis PCR analysis of patient urine, CSF In situ hybridization of tissue biopsies PML diagnosed histologically from biopsy- enlarged cells with basophilic intranuclear inclusions Treatment and prevention: no drug regimens but cidofovir appears to have some activity No prevention because exposure so early JC viral loads decreased with antiretroviral therapy for HIV (likely related to restored immune function)

Trypanasoma cruzi: Life Cycle, Disease

Chagas disease/American trypanosomiasis. Major problem in Mexico, CA, SA Life Cycle: amistogote and trypomastigote stages in humans. Amistogotes multiply in reticuloendothelial cells (macrophages) and myocardial cells. Some transform to trypomastigotes which circulate in blood but no blood replication takes place (unusual). Trypomastigotes ingested by reduviid bug in blood meal. Development occurs in blood. When it takes blood meal, it defecates, and trypomastigotes rubbed into wound Disease: inflammatory reaction at bite (chagoma). Acute: trypanosomes in circulation, fever, lymphadenopathy, myalgias. Chronic: trypanosomes in RE, forming amastigotes which divide, develop, and rupture cells- megacolon and megaesophagus

V. cholerae: Disease

Cholera Usually O1 gives asymptomatic infections or self-limited diarrhea, but sometimes causes severe, fatal diarrhea Symptoms usually 2-3d after consumption, can be 12h, abrupt onset watery diarrhea and vomiting, fever rare Severe infection can lose 1L fluid/hr. As more lost, feces streaked stool becomes color/odor free, speckled with mucus (rice water stool). Leads to electrolyte/fluid loss, dehydration, cramps, metabolic acidosis, hypokalemia, hypovolemic shock, cardiac arrhythmia, renal failure Mortality 70% if untreated, but prompt fluid/electrolyte replacement means survival

Mosaicism

Chromosomes and/or genes differ in different populations of cells in a single individual This means mutation occurs sometime after zygote formed, during mitosis Phenotype is usually less severe (Turner, Downs) Common in UTR disease, especially in germline Signs of disease can localize to specific body area with mutation (ex- segmental neurofibromatosis)

Quinolone Derivatives: Quinine

Cinchona alkaloid Used for severe malaria from chloroquine-resistant falciparum, given orally with doxycycline or clindamycin , or given IV as quinidine (dextroisomer) Toxicity: GI side effects common Cinchonism: tinnitus, HA, nausea, blurred vision Hypotension Causes hyperinsulinemia leading to hypoglycemia Myocardial depression, cardiac conduction abnormalities Blackwater fever: hemolysis, hemoglobinuria, renal failure Also used in combination with clindamycin for treatment of Babesiosis

Parvovirus: Characteristics

Classification: autonomous: human pathogens B19, human bocavirus Dependovirus: adeno-associated virus. Requires helper virus, high level infection in humans but no association with disease. Integrates chromosome 19, potential vector for gene therapy Characteristics: smallest DNA viruses No envelope, icosahedral capsid Single-stranded linear genome Require growing cells or helper virus for replication

C. botulinum: Diagnosis, Treatment

Clinical diagnosis by confirmation of toxin in food, pt serum, feces, or gastric fluid Treatment: 1. Ventilatory support for respiratory paralysis 2. Trivalent botulinum antitoxin- inactivates unbound toxin in blood 3. Antibiotics- controversial because death of organism leads to release of more toxin 4. Prevention- by destroying spores (almost impossible) in food and preventing spore fermentation by maintaining food in acid pH or storage at 4C, or destroying toxin by heating to 60C for 10m 5. Children under 1 should avoid honey until GI microenvironment has formed

HHV7

Close homology with HHV6, also causes roseola High level of seropositivity in adult population Controversial evidence for association of HHV6 and 7 with ptyriasis rosea Diagnosis: same as HHV6 Only Herpes beta/gamma that is not an opportunistic AIDS infection

Flaviviruses: St. Louis Encephalitis

Close to WNV. Maintained in bird-mosquito cycle, humans are dead-end. Relatively rare (7/year), from Canada to Argentina with concentration in eastern and central US. Signs/Symptoms: <1% clinically apparent, majority undiagnosed. Incubation 5-15d. Abrupt fever, HA, dizziness, nausea, malaise. Can intensify over several days, most will spontaneously recover. Neuro-invasive SLEV can occur: stiff neck, confusion, disorientation, dizziness, tremors, unsteady. Coma possible. Generally milder in children. 90% of elderly with SLEV get encephalitis. Treatment is supportive, no vaccine

H. pylori: Pathogenesis/Immunity

Colonization: 1. Blockage of acid production by bactericidal acid-inhibitor protein allows it to survive in low pH of stomach 2. High urease neutralizes gastric acid with ammonia 3. Motile, then pass through gastric mucus and adhere to gastric epithelium using surface adhesion proteins, helps them evade immune system (blankets in host proteins) 4. Localized tissue damage mediated by urease byproducts and VacA protein, that penetrates epithelial cells and damages them by making vacuoles 5. CagA gene acts as syringe, injects itself into host cell, interferes with normal cytoskeletal structure 6. PAI genes induce IL8 from neutrophils, leads to release of proteases and ROS, contributes to gastric ulcers 7. Has LPS on outer membrane with lipid A and O side chains. Lipid A has low endotoxin activity, O chain looks like human blood antigen, protects from immune clearance

Acyclovir/Valacyclovir: Complications, Resistance, Contraindications

Complications: phlebitis with IV admin Reversible nephrotoxicity from crystallization Neurotoxicity with serum oconcentration >25 Confusion, delirium, lethargy, tremors, seizures, coma Nausea, vomiting, lightheadedness, diaphoresis, rash are uncommonly reported HUS/TTP noted in AIDS and stem cell transplant patients given 8gm/day for long time Drug resistant mutants: thymine kinase deficient is 95%, TK altered 5%, DNA polymerase altered is rare Contraindications: none except hypersensitivity No documented teratogenicity, carcinogenicity, mutagenicity Not approved for use during pregnancy but no documented birth defects when used in early stages

Corynebacterium diphtheriae

Corunebacterium is ubiquitous in animals, normally colonize skin, upper respiratory, GI, GU in humans. Only known host of C. diphtheriae Gram+ club shaped rod in short chains/clumps Aerobic, facultatively anaerobic, nonmotile Catalase positive, grow well on Loeffler's and K Tellurite Produce diphtheria toxin Remember ABCs: ADP-ribosylation of EF2 B-prophage encoded toxin Corynebacterium diphtheriae Elek's test, erythromycin

Leishmania: Life Cycle, Disease

Cutaneous (major, tropica, mexicana), mucocutaneous (braziliensis), or visceral (donovani) disease Life cycle: amastigote found in humans, promastigote in insect vector Sandfly injects promatigote into human, engulfed by RE cells where it develops to amastigote, which is found in host cells/tissue. Parasitized host cells or free parasites from ruptured cells ingested by sandfly, cycle goes on Disease: L. donovani: visceral leishmaniasis, dum-dum fever, Kala Azar: hepatosplenomegaly, fever, anemia Tropica/Major: cutaneous leishmaniasis, oriental sore, Aleppo/Baghdad boil: ulcerating cutaneous sore, secondary infections Braziliensis: mucocutaneous leishmaniasis, espundia, uta, chiclero ulcer: mucocutaneous ulcerations, secondary infections

Cellular Response to Infection: Cytopathic Effects, Adaptive Response

Cytopathic Effects: virus replication can alter host protein synthesis, transcription, DNA replication, membrane stability Most viruses eventually kill infected cells Adaptive Response: IFN synthesis induced by virus infection and by double stranded RNA. Acts like a hormone binding to specific receptor on other cells, inducing an antiviral state in neighboring uninfected cells. Short lived Effects: inhibits translation (protein kinase phosphorylates eIF2), destruction of mRNA (2-5A synthetase), inhibition of DNA synthesis IFN also acts on NK cells (not antigen specific) and lymphocytes IFNa- leukocytes IFNb- fibroblasts IFNg- antigen or mitogen stimulated T cells

N. meningitidis: Diagnosis, Treatment

Diagnosis: blood and CSF culture, observations of gram- diplococci in white cells in CSF, use of counter-immune electrophoresis or other techniques Virulence is due to antiphagocytic capsule. Endotoxin stimulates release of lymphokines that trigger septic shock (TNF, PAF, etc) Original DOC was sulfa until resistance, now penicillin or third generation cephalosporins Prevention- immunity from ABs against capsular polysacs and complement cascade. Deficiencies in C5-C8 more likely to have disease and recurrence

C. jejuni: Diagnosis, Treatment

Diagnosis: commercial immunoassay for detection is available. When compared with culture sensitivity is 90% Treatment: Infections are normally self limiting, manage with fluids/electrolytes. Antibiotic therapy with erythromycin and azithromycin for severe infection or septicemia Prevention: proper food prep, no unpasteurized dairy, and implementation of safeguards to prevent contamination of water. No vaccine.

V. cholerae: Diagnosis, Treatment

Diagnosis: early in disease, direct microscopic exam of stool can be rapid, presumptive diagnosis during outbreaks Immunoassays for detection of toxin or O1/O139 LPS used for diagnosis in endemic areas Culture must be done on special selective agar thiosulfate citrus bile salts sucrose (TCBS agar) and enrichment broth Treatment: Poor sanitation associated with community outbreaks Prompt treatment with fluid/electrolyte replacement vital Azithromycin Bacteria shed in stool, so sanitation/sequestration important

L. monocytogenes: Diagnosis, Treatment

Diagnosis: gram-staining CSF usually shows no organisms. Grows well in blood agar, showing narrow beta-hemolysis. May need to do cold enrichment where specimen is stored in fridge for long time (can grow at near freezing) Treatment: most antibiotics only bacteriostatic. Ceftriaxone and Vancomycin are preferred for CA meningitis but must add ampicillin if listeria suspected. People at high risk should avoid raw/partially cooked foods of animal origin, soft cheese, unwashed raw vegetables No vaccine

Legionella: Diagnosis, Disease

Diagnosis: growth on buffered charcoal yeast extract BCYE Immunoassay to detect soluble legionella serogroup 1 specific LPS in urine (90% specificity for serogroup 1 only). Serogroup 1 responsible for 80-90% community onset disease but only 50% hospital acquired Direct/Indirect immunofluorescent assay DFA/IFA Epidemiology: both soil and water sources, especially showers, water towers, excavation dust Disease: pneumonia- lobar and slowly progressive. Pontiac fever (a flu like syndrome)

Babesiosis: Diagnosis, Epidemiology

Diagnosis: high index of suspicion Symptomology: hemolytic anemia and thrombocytopenia, proteinuria, hemoglobinuria, elevated liver enzymes BUN and creatinine In symptomatic pts, usually diagnosed by examining blood and seeing parasites in RBCs. To be certain, sent to CDC or state health department Epidemiology: 1700 US cases in the 27 states that report, 95% in 7 states (CT, MA, MN, NJ, NY, RI, WI). Tickborne transmission well established there. 85% of cases between June and August Median age 62, 65% male

Ehrlichia/Anaplasma: Diagnosis, Treatment

Diagnosis: microscopy not a valid tool and serology/PCR preferred. Both are part of tick test panel using serology. Treatment: doxycycline is recommended, should not be delayed to wait for diagnosis confirmation. Rifampin can be used in place of doxycycline

Parasitology: Diagnosis, Treatment

Diagnosis: must know what stage of life cycle is detected in infection. If you are looking for a worm when it is actually an egg, you won't find it. Treatment: Again, must know life cycle to devise preventative measures which are usually preferable to chemotherapeutic measures

Papillomaviruses: Diagnosis, Treatment

Diagnosis: no culture system Hybrid capture assay (Digene): high risk reported but low risk forms not detected Type by DNA hybridization using linear array Real time PCR detection of 14 high risk types by commercial assay Treatment/Prevention: avoidance of close contact Cryotherapy, chemical treatment, surgical wart removal Vaccine for 6,11,16,18 covers 70% cervical cancers, 90% genital warts, recommended for M and F 9-26 New Gardasil 9 valent: 6,11,16,18,31,33,45,52,58

B. fragilis: Diagnosis, Treatment

Diagnosis: specimens must be collected and quickly transported to lab using oxygen free transport system Sequence analysis of species-specific genes (like 16S ribosomal RNA gene) is reliable, time consuming, expensive Treatment: Metronidazole, carbapenems, and b-lactam/b-lactamase inhibitors are most effective Virtually all b. fragilis make b-lactamases so they are resistant to PCNs and many cephalosporins Antibiotic therapy with surgical debridement necessary for serious anaerobic infections

Arthropod-borne Infection: Diagnosis, Prevention, Control

Diagnosis: usually RT-PCR testing of viral mRNA in blood or urine. Serology can be helpful (rubella). Usually lab diagnosis just confirmatory: symptoms either self-limited (no intervention) or need care before lab diagnosis possible Prevention/Control 1. Vector control- eradicate vector- insecticides or genetically sterilized vectors 2. Avoid bites- repellant, long clothes, nets 3. Immunization Yellow fever- Theiler 17D vaccine is live attenuated, highly effective, booster every 10y Japanese B- formalin inactivated viral vaccine WEE/EEE: killed vaccine used for horses, lab workers with high exposure

A. israelii: Diagnosis, Treatment

Diagnosis: very difficult as they are slow growing, strictly anaerobic. Culture from sulfur granule could take 2w to show thin, gram+, branching rods Treatment: 1. Abscess drainage or surgical debridement 2. Prolonged antibiotic tx: PCN is DOC but carbapenems, macrolides, clindamycin also work. Can be months-long

Leptospira: Diagnosis, Treatment

Diagnosis: via culture or darkfield microscopy, or ELISA for IgM antibody as an alternate. Organism can be isolated from blood in first week of disease, later in urine Treatment: not usually fatal. Should be treated with IV PCN or doxycycline Vaccination of livestock and pets reduces incidence of disease in populations with which humans interact often

C. diphtheriae: Pathogenesis/Immunity

Diphtheria toxin: tox gene that encodes for exotoxin introduced to bacteria by a beta-phage. Follows same structure as anthrax: A and B subunits B subunit receptor is heparin binding epidermal growth factor on many cells, including cardiac and nerve. A subunit causes ADP ribosylation of EF2, inhibiting ribosome function, stopping protein synth, causing death Organism is not invasive but exotoxin can travel through blood to heart, brain, and kidneys

Schistosomiasis: Disease, Epidemiology, Morphology, Diagnosis

Disease: localized dermatitis, toxic reactions, pulmonary congestion and fever. Bloody stools and hematuria. Renal, hepatic, intestinal pathology from reaction of host to eggs clogging vessels. Can cause hepatosplenomegaly, bladder cancer Epidemiology: hematobium in Egypt, sub-Saharan Africa Mansoni in Africa and SA Japonicum in China, Philippines, Indonesia Morphology: adult worms in pairs (mate for life) Eggs: hematobium are oblong, terminal spine mansoni oblong, lateral spine japonicum short elliptical, lateral spine Diagnosis: travel history/residence in endemic area Eggs in stool/urine, can be hard to find so must check often and in high quantitiy. Colonic biopsy sometimes used.

E. granulosus: Disease, Epidemiology, Morphology, Diagnosis

Disease: majority of human cysts in liver/lung. Chronic liver dysfunction (pressure necrosis), palpable abdominal mass with discomfort, respiratory distress (cough w CP). Anaphylactic shock possible if cysts rupture. Epidemiology: endemic in sheep/cattle raising areas of many parts of world, including US (AZ, NM, UT) Morphology: Adults found only in dogs/carnivores are small, usually with 3 proglottids Eggs found only in dogs are taeneoid Cysts look like typical cysts Diagnosis: history of exposure to endemic area and contact with dogs, evidence of slow-growing cystic tumor. Serology for confirmation at surgery

D. medinesis: Disease, Epidemiology, Morphology, Diagnosis

Disease: nonspecific symptoms, eosinophilia, nausea, diarrhea, asthma Cutaneous ulcers secondarily infected with bacteria/fungi Inflammatory reaction to dying adults and larvae Epidemiology: Africa except S, SW Asia, India, NE South America, West Indies. Major control has reduced endemic areas to foci in S Sudan, Mali, Chad, Ethiopia In 1986, 3.5m cases/yr in 35 countries in Africa and Asia In 2015 22 cases, a 99.99% decline Morphology: adult F 50-120cm, M 12-29mm Diagnosis: ulcerated blisters with protruding worms

C. difficile: Diseases, Diagnosis, Treatment

Diseases: watery diarrhea, pseudomembranous colitis Diagnosis: visualization of pseudomembrane, presence of exotoxins via PCR/ELISA Treatment: Discontinuation of implicated antibiotic (normally clindamycin, fluoroquinolones, ampicillin) Treatment with oral vancomycin or metronidazole can help manage severe diarrhea, colitis, relapses (20-30%)

Poxvirus: Smallpox: Dissemination, Vaccination

Dissemination: infection by inhalation or contact with scabs. Replicates in URT, spread to lymphatics by macrophages. Spreads to spleen, liver, marrow, others through blood. Hemorrhage of small vessels in skin produces rash/pustular lesions Problems of Vaccination: who should be vaccinated? Risks associated can be severe (disseminated lesions, encephalitis). Currently risks outweigh likelihood of exposure for most. Military vaccination for protection from biowarfare.

Linezolid: Toxicity, Uses

Does not effect cyp450 system. Decreased platelets have been seen in 2-4% of cases. Weak MAOI, so patients on adrenergic/serotonergic agents or those taking >100mg tyramine per day may have enhanced effect. Uses: particularly useful for PCN resistant S pneumo, methicillin resistant and vancomycin intermediate strains of staph, and vancomycin resistant strains of enterococci

Incomplete Penetrance

Dominant or recessive diseases Not everyone with mutation expected to produce disease actually gets it, and no difference between affected and unaffected family members in mutation or protein level Unknown factors (interacting proteins from polymorphisms in other genes) probably cause this IP Variant: both dominant and recessive, but disease more likely/severe in recessive form, can occur as dominant Tourette's, PARK and Parkinson's GTPCH deficiency- one gene mutated you get DOPA responsive dystonia, two you get severe neonatal onset static encephalopathy with movement disorder, seizures

Poxvirus: Diagnosis, Treatment

Electron microscopy for characteristic morphology Cell culture and chicken embryos Species specific PCR ELISA for zoonoses and molluscum, usually self limited Cidofovir approved for treatment of all, vaccine for potential smallpox threat Expression vector for vaccines: large genome size allows insertion without affecting replication Vaccinia vector is attenuated. Produce recombinant vaccinia virus carrying foreign gene Foreign genes derived from more virulent organisms (MERS, influenza, HIV) Vaccines are under development

Plasmodium: Epidemiology, Morphology, Diagnosis

Epidemiology: Worldwide distribution in tropics/subtropics (CA, SA, Africa, Middle/Far East, SE Asia). SE Asia serious area for drug resistance. Blacks more resistant than whites: sickle cell trait (lower K in RBCs), Duffy negative RBCs (missing receptor for P. vivax invasion), G6PDH deficiency (depletion of pentoses needed by parasite for RNA/DNA synthesis) Morphology: 3 stages in RBCs: ring trophozoite (signet ring), schizont (multiple individual merozoites), gametocyte Diagnosis: detection and species determination of RBC stages in blood smear with Wright-Giemsa stain Thick/thin smear must be done just after fever peak in P. falciparum (bc infected cells rapidly adhere to capillary endothelium and are quickly removed from circulation). Can be done anytime in other species

T. cruzi: Epidemiology, Morphology, Diagnosis

Epidemiology: disease in CA/SA/Mexico, a few cases in Texas and California. Reservoir hosts (raccoons, rodents) as far north as MD, IL. Dogs, cats, bats, armadillos also reservoirs Morphology: trypomastigotes: short, stumpy, C or U shape, with flagellum and undulating membrane Amastigotes: small, comma shaped usually found in tissue aggregates: pseudocysts Diagnosis: history of reduviid bite, chagoma Patchy edema, often unilateral on face (Romanas) Microscopic detection of trypomastigotes in blood up to 1-3w post infection Xenodiagnosis: dissection of lab-raised reduviid, allowed to bite infected patient: test for parasites in hindgut

T. brucei: Epidemiology, Morphology, Diagnosis

Epidemiology: gambiense found in W Africa, carried by woodland fly, reservoir wild/domestic animals, humans, disease course 2-4y. rhodesiense in E Africa, vector is riverine fly, reservoir wild/domestic animals, course 2-6m In 2013, 6300 cases, 50% fatal, most of remaining with permanent brain damage. Area about the size of US cannot be used for livestock/agriculture because of parasite Morphology: long, slender forms with 1 flagellum and an undulating membrane Diagnosis: Clinical/travel history, with neuro deficit and enlarged posterior cervical lymph nodes (Winterbottoms). Micro exam of blood, CSF, bone marrow, trypomastigotes, or specific AB tests

Giardia lamblia/intestinalis Treatment

Epidemiology: more commonly in children or groups in close quarters: travelers, campers, municipal water supplies. Can exist in other mammals Clinical findings: >7d duration of illness with at least two of: diarrhea, flatulence, foul-smelling stools, nausea, abdominal cramps, excessive fatigue Treatment: tinidazole or metronidazole Nitazoxanide or paromomycin are alternatives

Leishmania: Epidemiology, Morphology, Diagnosis

Epidemiology: threatens 350m in 88 countries where disease is endemic. 12m cases worldwide, 1.5m annually. Donovani: Mediterranean basin, India, E Africa Tropica: Middle East, Mediterranean basin Brasiliensis: jungle areas, S America Mexicana: rural C and S America Vectors are sand flies Morphology: in amastigote (intracellular) form in macrophages, contains nucleus and kinetoplast- dot and dash Diagnosis: travel history. For cutaneous/mucocutaneous: demonstration of amastigotes in ulcer scraping Visceral: demonstration in bone marrow, liver/spleen biopsy

Brucella: Epidemiology, Immunology

Epidemiology: very important to ID risk factors Milk products (killed by pasteurization Slaughterhouse workers Over 500k cases worldwide Control of bovine disease Immunology IgM and IgG titers rise: pay attention for 4x increase or a single titer of 1:160 or more Cell mediated immunity plays a role

T. gondii: Epidemiology, Morphology, Diagnosis

Epidemiology: worldwide distribution, serological evidence indicates high exposure rate with rare infection. Several strains are known Morphology: Tachy and bradyzoites are similar: crescent shaped. Tachy in a paritophorus vacuole, brady in pseudocyst Diagnosis: Microscopic examination of biopsy specimens for merozoites or cysts. Isolation of organism in tissue culture or in lab animals Serodiagnosis complicated because of high level of ABs in normal population. Pre- and post sera may be useful, as is IgM in neonates only

T. spiralis: Epidemiology, Morphology, Diagnosis

Epidemiology: worldwide except Asia, mostly US/Canada Individuals who do not eat pork are not infected (Jews, Hindus, Muslims, SDA) Morphology: encysted larvae is coiled inside lemon shaped nurse cell, may be surrounded by inflammatory infiltrate Diagnosis: patient history of raw pork consumption Muscle biopsy, squash preparation Serology

Aminoglycosides: Spectrum of Activity

Excellent against aerobic, facultative gram- rods including enterobacteriaceae, pseudomonas, haemophilus. Active against MSSA but not used. Agents most used against gram- are amikacin, tobramycin, gentamicin Streptomycin has most activity against TB and is DOC for plague. Amikacin great agains mycobacterium as well, including M. avium-intracellulare Spectinomycin used for PCN resistant N gonorrhoeae Neomycin usually as part of bowel prep before GI surgery or to dec gut organisms for treatment of hepatic coma. Topically used on burns Gentamicin/Streptomycin especially are synergistic with PCN against enterococci and PCN-resistant strep. Addition to PCN in early staph endocarditis can result in more rapid clearing. Synergy also shown for pseudomonas, listeria, corynebacterium

Actinomyces israelii

FIlamentous gram+ rod, facultative/obligate anaerobes Not acid fast (diff from Nocardia), non-spore forming Grow slowly in culture, produce chronic, slow-developing infections. Colonize upper respiratory, GI, female GU Low virulence potential and cause disease only when normal mucosal barriers disrupted (trauma, surgery, infection) Infections are endogenous, no person-person spread

Trematode Treatment

Flukes 1. Schistosomiasis: caused by s. mansoni, s. japonicum, and s. haematobium, treated with praziquantel 2. Intestinal flukes: Fasciolopsis buski, treated by praziquantel 3. Foodborne trematodes: caused by clonorchis sinensis, opisthorchis viverrini, paragonimus, treated with praziquantel 4. Liver flukes: fasciola hepatica, treated with triclabendazole and bithionol

Trematodes

Flukes: adults are flat, leaf shaped, with simple digestive tract (bifurcated blind pouch) Most hermaphroditic though not blood flukes Complex life cycles requiring 1-2 intermediate hosts. Embryonated eggs shed in feces, need water to survive. Miricidium emerges from egg and penetrates first intermediate host (usually a snail), where different development stages occur leading up to cercariae, which is infective for second intermediate host (plant, fish, crustacean). There, metacercaria develop that is infective for definitive host Found mostly in intestine, liver, lung, and blood

Trifluorothymidine (Trifluoridine)

Fluorinated pyrimidine nucleoside Topical agent for herpes keratoconjunctivitis No reported drug interactions with topical use

Parvovirus: Laboratory Diagnosis

For both B19 and Bocavirus Based on clinical presentation ELISA for IgM and IgG PCR for the genomes No cell culture No antiviral drugs

Nitroimidazoles

For intestinal and urogenital protozoan infections Mechanism: prodrug enters cell (diffusion), then nitro group is reduced by electron transport proteins which promotes formation of free radicals. These interact with nucleic acids and proteins causing cell death Metronidazole and tinidazole: completely absorbed orally, penetrate all body fluids, metabolized in liver and excreted in urine Toxicity: HA, nausea, dry mouth, metallic taste Disulfiram effect Inhibits acetaldehyde dehydrogenase Facial flushing, tachycardia, hypotension, dyspnea, N/V, HA, blurred vision, vertigo, anxiety within 15-30m of alcohol ingestion that lasts for hours Peripheral neuropathy, neutropenia

Helicobacter pylori

Found in 1983 causing type B gastritis (at pyloric end) In US, 50% of adults are carriers Motile with flagella, helical/spiral shaped gram- Urease positive (necessary for stomach invasion) Oxidase positive, catalase positive LPS contained in outer membrane Requires media supplemented with blood, serum, or charcoal in 30-37C microaerophilic conditions Cause of 95% of duodenal ulcers, half of stomach adenocarcinomas

H. pylori: Disease

Found in 70-100% pts with gastritis, gastric ulcers, duodenal ulcers, gastric adenocarcinoma, gastric MALT lymphoma Humans primary reservoir, colonization persists for life unless specifically treated 1. Acute phase: fullness, N/V, hypochlorydria (dec acid production in stomach) 2. Chronic: gastritis in gastric antrum where acid suppressed and can spread to entire stomach. 10-15% of pts with chronic gastritis progress to peptic ulcers. Recognition of role in gastric/duodenal ulcers dramatically changed treatment of PUD. Chronic gastritis eventually leads to replacement of gastric mucosa with fibrosis, proliferation of intestinal-type epithelium

Imprinting

Gene(s) marked imprinted have different activity on maternal and paternal chromosomes Usually turned off specifically on one or the other Tend to be in clusters in specific areas of certain chromosomes, not all chromosomes have imprinted genes Thought to maintain sexual reproduction in species If person inherits two copies of imprinted chromosome from same parent, will have disease defined by the specific genes which are inactivated on both chromosomes Normally would have active chromosome from other parent This is uniparental disomy

HHV8: Characteristics, Infection

Genome discovered in Kaposi's sarcoma samples Closest homology with EBV Now have complete genome sequence No cell culture system Infection: B cell is primary target Limited infection of endothelial cells, monocytes, sensory nerve cells In Kaposi Sarcoma endothelial spindle has virus Original epidemiology of KS was elderly Mediterranean men, now opportunistic in AIDS pts Very low seroprevalence in normal population

N. gonorrhoeae: Disease

Gonorrhea: found in GU tract, likes columnar epithelium Carrier rate high, asymptomatic females Little to no immunity- repeat infections can be from lack of immunity or from large number of antigenic variants. Produce extracellular IgA protease: may help alter local immune response Virulence may be from pili, allowing organisms to attach to epithelial cells, resist phagocytosis. 4 types of colonies- 1-2 have pili, are virulent. 3-4 do not, less virulent Elicit inflammatory response- purulent urethral/vaginal discharge. Esp in women, infection can become chronic and asymptomatic (up to 70%). Ophthalmia neonatorum- infection of eyes of newborns by passage thru infected canal. Blindness prevented by treating eyes of all newborns with 1% AgNO3 or erythromycin/tetracycline Most common manifestations of sepsis are arthritis and dermatitis (3%, F>M). Repetitive in complement deficiency

Rhodococcus equi

Gram+ rod, acid fast, initially rodlike and ten revert to cocci Only human rhodococci pathogen, mostly in immunosuppressed Originally veterinary pathogen of herbivores, then opportunistic pathogen of farmers and vets. Usually immunocompromised pts show invasive pulmonary disease (nodules, consolidation, abscesses) and evidence in blood to distal sites (LN, meninges, skin). Infections very difficult to treat, extended spectrum macrolides (azithromycin, clarithromycin) or fluoroquinolones used

Arcanobacterium hemolyticum

Gram+ rod, slow growing, difficult to isolate bc of slow growth, not typically cause of significant/critical disease, often found on college campuses Most notable is a form of self-limiting pharyngitis. Disease is not severe and slow growth allows immune system to clear. Can cause scarlet rash with the pharyngitis More severe infections can cause wound infections, abscesses, septicemia, endocarditis, but very rarely

Bacillus anthracis

Gram+ rods arranged in chains (trains) Obligate aerobes, spore forming Produce toxins (virulence factors) Non-hemolytic, non-motile Protein (poly D glutamate) capsule (virulence factor) Spores have potential to be weaponized

Bacillus cereus: Characteristics, Structure, Pathogenesis

Gram+ rods in singles or pair (boxcars) Spores visible creating clear area in gram+ rods Obligate spore forming aerobe, produce toxins (VF), associated with reheated rice 1. Emetic toxin: heat stable, proteolysis resistant preformed in food (rice, pasta). N/V, cramps. Preformed so symptoms in 1-6h, resolved in 8-10h. No fever. Keeping rice/pasta warm allows for spore germination, toxin production 2. Diarrheal toxin: heat labile, stims adenylate cyclase-cyclic adenosine monophosphate system in intestinal epithelial cells. Profuse, watery diarrhea in 8-18h. Associated with meat and vegetables, not preformed, produced by bacteria after ingestion. Nausea, cramps, diarrhea.

Neisseria: General Info

Gram- cocci Aerobic, non-motile, non-spore forming Difficult to grow (autolyze easily) Oxidase positive: have cytochrome oxidase in their cell wall, use tetramethyl-p-phenylenediamine as substrate (turns purple) Differentiate species by fermentation: N. gonorrhoeae: produces acid from glucose N. meningitidis: glucose, maltose N. lactamica: glucose, maltose, lactose N. sicca: glucose, maltose, lactose, sucrose Gonorrhoeae and meningitidis are most important

Neisseria Meningitidis: Microbiology, Antigens

Gram- diplococcus, polysaccharide capsule (forms basis for subgrouping). Optimal growth at 35-37C in 5-10% CO2 on blood agar base, trypicase soy agar, or supplemented chocolate agar Polysaccharide capsule: major groups (A,B,C,X,Y,Z,W-135,29E)- major virulence factor Non-capsular CW antigens: Lipoologosaccharide (endotoxin-like) and outer membrane proteins Have been shown to have pili to help attach to human cells

Neisseria Gonorrhoeae: Microbiology and Antigens

Grows best at 35-37C in 5-10% CO2 on chocolate agar Thayer-Martin medium: vancomycin, colistin, and nistatin to inhibit growth of competing normal flora Differentiate from meningitidis by fermentation Does not have a capsule Pili: colonies can be P-, P+, P++. Helps attach to cells, contributes resistance by killing neutrophils Lipooligosaccharide Outer Membrane Proteins Protein I: associated with LOS, serves as porin, may facilitate endocytosis. Some serovars associated with serum resistance- cannot be killed by human serum Protein II: transparent or opaque Protein III

Filoviridae: Marburg/Ebola: Transmission/Epidemiology

Highly fatal hemorrhagic shock syndrome, natural reservoir is fruit bat. Spread through contact with blood, secretions, organs, bodily fluids. Can happen through hunting of infected animals and bushmeat. Easily spread through human-human transmission via direct contact (broken skin, mucous membranes) with blood, etc. and with surfaces and materials (latex gloves, gowns, etc) HC workers at high risk and after patient has died body is still infectious, so burial ceremonies can spread it (this has played big role in current epidemic) Ebola has sexual transmission (V,A,O) as well. Can survive in semen of men for years. Male Ebola survivors should be tested at 3m and, if positive, every month thereafter until get negative result twice in a row.

C. tetani: Pathogenesis/Immunity

Highly sensitive to oxygen, does not survive well in soil, but spores allow it to survive in adverse environments. Spores enter a wound where oxygen becomes limiting As oxygen becomes limited, anaerobic growth leads to spore germination, vegetative growth, production of neurotoxins tetanospasmin and tetanolysin. Tetanospasmin produced when cell is lysed, responsible for disease Tetanospasmin internalized in endosomal vesicles, transported to motor neuron soma in spinal cord. Cleaves SNARE, inhibiting release of glycine/GABA, leading to muscles remaining contracted- rigid paralysis Tetanospasmin is very potent. Amount necessary to cause death is so much lower than amount of bacteria needed for immune response that survivors don't develop memory

C. pneumoniae

Human pathogen, causes sinusitis, pharyngitis, bronchitis, pneumonia Infections transmitted person-person through aerosols and respiratory secretions Persistent cough/malaise, usually no hospitalization Cannot be differentiated from other atypical pneumonias (like M pneumo) by symptomology Treatment: Macrolides, doxycycline, levofloxacin

HSV 1 and 2: Epidemiology, Latent v Lytic Infection

Humans only host but can replicate in lots of animal cells Primary infection: HSV1 after decline of maternal antibodies, HSV2 at onset of sexual activity Prevalence higher in lower socioeconomic groups, HSV1 antibodies at 70% at 14, HSV2 20-80% starting at 14 Cell mediated immunity important in control AB response does not eliminate virus bc of latency Lytic Infection: Rapid effect on cell within hours. Shuts off host protein synthesis/DNA replication, produces high titer of infectious virus. Cell lysis or fusion, characteristic CPE Latent Infection: only immediate early functions expressed initially, latency associated transcripts in sensory ganglia that innervate sites of initial infection. No cellular damage

Echinococcus granulosus: Life Cycle

Hydatid cyst disease Life cycle: adult worm lives in intestine of dogs/wolves Eggs passed in feces, eaten by sheep, cattle, moose Eggs hatch in intestine, oncosphere penetrates intestinal wall and is carried via bloodstream to other organs, especially liver and lung Oncosphere develops into hydatid cyst (larval form) Dogs/wolves infected by ingestion of cyst with lots of protoscolices (immature adults) Humans are infected by accidental ingestion of eggs in feces of infected dogs

Drugs for Severe Malaria from P. Falciparum

IV artesunate followed by atovaquone-proguanil, clindamycin, or mefloquine OR IV quinidine followed by doxycycline, tetracycline, or clindamycin

Adenovirus: Structure, MOD

Icosahedral, no envelope, with fibers at vertices for attachment and serotype. Linear double stranded DNA genome with terminal protein at each 5' end. 6 subgroups, over 50 serotypes. Encodes proteins for mRNA and DNA synthesis like DNA polymerase. Lytic, persistent, and latent infection in humans No animal reservoir Original oncogenes E1A and E1B Oncogenic in animals but so far not in humans Multiple routes of infection: aerosol, close contact, fecal-oral Capsid resistant to GI inactivation/dessication Attacks mucoepithelial cells of respiratory tract, GI, conjunctiva, cornea through direct cell damage Serotype determines tissue tropism and disease Persists in lymphoid tissue (tonsils, adenoids). AB is important for recovery and immunity

B. anthracis: Diagnosis, Treatment

Identified by overwhelming numbers of organism in wound, LN, blood Can be seen when peripheral blood is gram stained (one of the few). PCR tests exist. Spores rarely seen. Vaccines: control of human disease requires control of animal disease through vaccination and burning/burial of animals that die of anthrax. Complete eradication unlikely because spores can live for 10000y in soil Treatment: ciprofloxacin or doxycycline

P. westermani: disease

Immature metacercariae attach and penetrate gut wall, migrate through diaphragm to enter pleural cavity. In 20d they reach lungs, become adult worms in cystic cavities in 5-6w Long migratory time allows for ectopic sites of development: liver, heart, intestine Lung involvement leads to cough with bloody sputum, pulmonary pain, pleurisy. Tough to differentiate from other lung disease like TB, pneumonia Low grade fever common. Fatalities in heavy pulmonary infection and in myocardial involvement

Toxoplasma gondii: Life cycle, Disease

Important infection of immunocompromised and neonates Life cycle: sexual stage in intestine of cat, infective oocysts shed in feces. Asexual stage in sheep, cattle, mice, humans that ingested infective oocysts. Sporozoites invade cells and become tachyzoites (acute) and/or bradyzoites (chronic), together called merozoites. Or, ingestion of raw meat with asexual stages in it can lead to infection. Maternal-fetal, transfusion, transplantation also noted Disease: only extraintestinal infection is known in humans. Usually asymptomatic/self-limiting, ABs in about 80% people worldwide. Immunocompromised pts get lymphadenopathy, fever, HA, anemia, muscle pain. Serious lesions in retina, CNS involvement possible. In 1st trimester of pregnancy, high risk of congenital defects (retinochoroiditis, hydrocephalus, microcephalus)

N. gonorrhoeae: Diagnosis, Treatment

In acute disease, smears of fresh exudate show intracellular gram- diplococci and are presumptive for disease in men, but cannot be used to diagnose women 99.9% of cases are sexually transmitted, epidemic proportions throughout world DOC is penicillin but resistance is spreading: Transfer of penicillinase plasmid by transformation/conjugation Alternate drugs: ceftriaxone, spectinomycin. DOC in Chicago is ceftriaxone

Picornavirus: Members, Structure

Includes Rhinoviridae, enteroviridae (poliovirus, coxsackie, echovirus, enterovirus), aphthoviridae, cardioviridae, hepatoviridae (Hep A), cosavirus Virion Structure: icosahedral capsid with canyons/pockets No envelope Capsomere subunits generated by proteolytic processing Interior genome- positive sense RNA 5' end has no cap structure, has VPg protein 3' end: polyA

Filoviridae: Marburg/Ebola: Clinical Disease

Incubation 2-21d. First is sudden onset of fever, fatigue, muscle pain, HA, sore throat. Followed by severe vomiting (black), diarrhea, rash, impaired kidney/liver function. Both internal and external organs will hemorrhage (eyes, gums, bloody diarrhea). Most severe hemorrhagic fevers. Current Outbreak: 7 Ebola outbreaks in Africa since 1976 Current began in 2014 in W Africa and is largest ever. 28k cases in Guinea, Liberia, Sierra Leone, 11k deaths (mortality rate almost 50%). Previous epidemics as high as 80%. Liberia and Guinea have discharged final pts.

Togaviridae: Rubivirus: Signs and Symptoms

Incubation 2-3w. In children, usually mild. Low grade fecer, HA, lymphadenopathy, cough, rhinitis, telltale maculopapular rash. In adults can be more severe and include arthralgia, arthritis. Thrombocytopenia, encephalopathy are rare. Congenital Rubella Syndrome: defects dependent on gestational age of infection. Neonatal purpura, cataracts, glaucoma in first two months. Heart disease associated with entire first trimester. Cognitive deficits/deafness in first 4 months, retinopathy first 5 months. Thrombocytic purpura from extramedullary hematopoiesis (blueberry muffin baby) Hepatitis and hepatomegaly often noted. Bones can be malformed, celery stalking seen (ends of bones do not fuse properly)

Flaviviruses: Zika: Signs and Symptoms

Incubation period unclear. Likely most remain asymptomatic or develop undifferentiated fever that is mild and self-limiting with recovery in 2-7d. Most commonly acute fever, maculopapular rash, joint pain, conjunctivitis, HA. Complications: 1. Pregnancy: can cause microcephaly and other severe neuro defects including blindness, deafness, impaired growth, absent/poorly developed brain structures, miscarriage/stillbirth. No reports of transmission via breastfeeding. 2. Guillain-Barre: bilateral weakness of arms and legs, sometimes Bell's Palsy and weakness in swallowing. Occasional difficulty breathing. Lasts weeks to months, most fully recover, some have permanent damage.

Interferon Alpha (Recombinant)

Inducer of innate immune response Previously used for HPV warts (now imiquimod and trichloroacetic acid used instead) Antiviral for hep B and C

Cellular Response to Infection: Chronic Infection

Interaction between virus and host shifts towards symbiosis, not death- can lead to viral latency or persistent infection Extent of replication may vary in host cell: low grade shedding of virus particles, partial restriction of viral replication, latency Effects of immune response to chronic viral infection may vary: no disease, chronic inflammatory response

EBV: Laboratory Diagnosis

Infectious mononucleosis: atypical lymphocytes (activated T cells) and lymphocytosis in blood Heterophile antibody by monospot and ELISA Antibodies to viral antigens No cell culture for the virus Other EBV infections: use serological profile Markers of infection 1. EBV Nuclear Ag: nonstructural, early in all infected/transformed cells 2. Early ag-restricted: cytoplasm, first sign of lytic infection 3. Early ag-diffuse: nucleus/cytoplasm, lytic infection 4. Viral capsid ag: late ag, lytic infection 5. Membrane ag: cell surface, envelope glycoproteins 6. Heterophile ab: reacts with Paul-Bunnell ag on animal RBCs, result of B cell proliferation

Unstable Trinucleotide Repeats: Myotonic Dystrophy

Inheritance is dominant with anticipation DM1 (95%)- CTG repeat in 3' untranslated region of myotonin kinase, DM2 (5%): CTG repeat in 3' UTR of different gene In DM1, 5-37 repeats is normal, 38-50 is premutation, 51-100 possible disease-causing, 101-200 maybe motor symptoms, 200-thousands typical disease Transcribed, not translated Earlier and more severe disease with bigger mutation Sex bias for expansion: paternal for small expansion, maternal for large (severe congenital form maternal inheritance only) Gain of function mechanism- mRNA disease- mRNA with repeat interacts with RNA and DNA binding proteins in nucleus, interferes with transcription or RNA processing of other genes

Unstable Trinucleotide Repeats: Fragile X

Inheritance: X-linked with anticipation, 2 different diseases based on mutation size. Behaves like dominant with less severe effects in women, correlating w/ X-inactivation CGG repeat in promoter (5' UTR) of FMR1 gene. 12-35 normal, 36-44 protomutation, 45-54 gray zone, 55-200 premutation (FXTAS), 200+ full mutation (FXS) Transcribed, not translated As repeats increase, frequency but not severity inc over generations. Sex bias is maternal, only woman can pass full mutation as sperm do not tolerate it. Chance of expansion to full is directly related to size of permutation: about 100% chance at 100 repeats, <59 has never expanded to full. Loss of function: gene methylated and turned off, none/low levels of FMRP made. Mosaicism (for size and methylation) frequent in males and may be higher functioning if more FMRP. FMRP mRNA binding protein is important for regulation of synaptic protein synthesis in response to stimuli to produce synaptic plasticity. FXTAS has gain of function- G repeat in mRNA interacts w nuclear proteins, disturbs function. mRNA toxicity mechanism like intranuclear inclusions.

Unstable Trinucleotide Repeats: Huntington's

Inheritance: auto dominant with anticipation CAG repeat in exon 1. 9-26 is normal, 27-35 premutation, 36-39 possible disease, 40+ always disease Transcribed and translated, codes for polyglutamine stretch Earlier/more severe disease with increased mutation size Sex bias is paternal at all sizes. Juvenile form always >60 repeats, always inherited from father Gain of function: polyglutamine stretch leads to abnormal toxic protein interaction, intranuclear and intracytoplasmic inclusions

Unstable Trinucleotide Repeats: Friedreich Ataxia

Inheritance: auto recessive GAA expansion in intron of frataxin gene. 7-22 normal, 40-119 premutation, 120-800 late onset (>20y), 800+ typical FA Increasing disease severity with increasing size of mutation No known sex preference. Cardiomyopathy >500, DM >800 Loss of function: repeat interferes with transcription and mRNA processing in size-dependent fashion, protein levels about zero with both alleles >800 Mitochondrial protein involved in Fe processing

Macrolides

Inhibit bacterial protein synthesis, bacteriostatic Most common SE is GI irritation. Azithromycin given orally QD (t1/2 65-70h), 2 pills day 1 (LD) Spectrum similar to erythromycin with greater activity against gram- organisms Clarithromycin well absorbed orally, same spectrum as erythromycin but more potent. Forms active metabolite after first-pass Dirithromycin prodrug, rapidly converted. Oral absorption inc by food so should be taken with meals Telithromycin is structurally related but technically a ketolide. Similar spectrum and SE but effective against strains resistant to macrolides. URI/LRI mostly Clindamycin is similar, effective against gram+ and anaerobics (major indication). SE usually in GI (diarrhea). Occasionally allows C diff overgrowth.

Classifications of Antibiotics

Inhibition of CW Synthesis: Penicillins, cephalosporins, vancomycin, bacitracin, fosfomycin, carbapenems, monobactams Inhibition of bacterial protein synthesis: macrolides (erythromycin), aminoglycosides (tobamycin, amikacin), tetracyclines, clindamycin , oxazolidinones (linezolid), lincosamines Inhibitors of DNA repair and damage: DNA gyrase (topo2) targeting drugs: fluoroquinolones, ciprofloxacin, levofloxacin, coumarin. RNA polymerase inhibitor: rifampin Inhibition of folate metabolism: DHPR synth inhibitor: sulfamethoxazole. DHPR reductase inhibitor: trimethoprim

Sulfonamides: MOA

Inhibits folic acid synthesis as a structural analog of PABA. Compete for incorporation into folate. Work only on bacteria because mammalian cells absorb folic acid. Usually bacteriostatic, exert effect after a few cell cycles (after folic acid stores exhausted). In media with thymine excess bacterial killing is inhibited (like in a purulent wound), in absence of thymine (urine, blood) may be bactericidal Active against many gram+/-, as well as actinomyces, chlamydia, plasmodia, toxoplasma Many E. coli and N. meningitidis are resistant. May acquire resistance by: alteration in enzyme that uses PABA, increased capacity to destroy sulfa, alternative metabolic pathway, increased production of essential metabolite (like increased PABA)

Bacitracin

Inhibits synthesis of bacterial CW Use: variety of gram+ cocci/bacilli, neisseria, H flu, treponema pallidum (sensitive to tiny concentrations). Actinomyces and fusobacterium susceptible to larger conc. Enterobacteriaceae, pseudomonas, candida, nocardia are resistant Typically seen in derm and ophthalmologic preps to treat furunculosis, pyoderma, carbuncle, impetigo, superficial/deep abscesses Local application in infected eczema and dermal ulcers

Sulfonamides

Initially effective against many gram -/+, but widespread use caused resistance. Some used topically in burns, others for UTI and GI infections. Block synthesis of folic acid, inhibiting bacterial growth (bacteriostatic). Usually oral, can cause N/V/D or crystalluria (more serious). Can produce allergies in skin and mucous membranes: rash, pruritis, photosensitivity. Stevens-Johnson syndrome produces potentially fatal skin reaction Was effective because mammalian cells must take up folic acid and cannot make it, while bacterial cells cannot take up folic acid and must synthesize it themselves

Viral Serology

Involves detection or measurement of ABs generated in infected host as a result of the infection. If agent is suspected of belonging to particular family, assays based on serology can be performed to: 1. ID genus or strain: ABs against certain strain may be cross reactive with other members of same family. Ability of AB to neutralize virus may give info about ID of viral agent. 2. Learn more about course of disease in infected host: assays using paired acute and convalescent sera may give info about titer of ABs, exposure to virus, and timing of disease course

Detection of Viral Antigen

Involves use of reference ABs generated against specific viral proteins. Assays are performed to detect presence of viral antigen in original clinical sample or in infected cultured cells. Tests include immunofluorescence, enzyme linked-immunosorbent assay (EIA), immunoperoxidase staining, and latex agglutination. Tags/labels for detection In original clinical sample, antigen targets can be in cells or can be released virus In culture, antigen targets are viral proteins made during viral replication cycle

Listeria

L. monocytogenes is aerobic but can facultatively replicate intracellularly, so humoral response is useless. Cell mediated immunity is necessary for control and patients where this is impaired are more susceptible Sporadic with focal epidemics and sporadic cases associated with undercooked food, raw fruits/veggies Gram+ rod, non-spore forming, aerobic, narrow ring of b-hemolysis. Positive CAMP test. Motile using tumbling umbrella pattern on semi-solid agar Widely distributed in food and animals Has neurotrophism: #1 cause of CA meningitis in pts on steroids Often present on skin, important to appropriately prepare skin before taking cultures to avoid listeria contamination Fairly rare, but #1 cause of foodborne illness death in US

HSV 1 and 2: Diagnosis, Treatment

Lab Diagnosis: 1. cell culture shows distinctive CPE 1-2d 2. Tzanck smear: micro exam of cells from base of lesions: multinucleated cells- syncytia, Cowdry type A inclusions 3. PCR analysis of CSF for h. encephalitis 4. Tissue biopsy: enzyme immunoassay, immunofluorpescence, in situ hybridization 5. ID specific type: AB, DNA restriction fingerprinting, DNA probe analysis 6. Serology not useful for dx, just for epidemiology Treatment: avoid direct contact. Cesarean section, No vaccine. Potential drug resistance. Drugs: acyclovir, valacyclovir, famiciclovir (nucleoside analogues), foscarnet, trifluorothymidine

Human CMV: Diagnosis, Treatment

Lab diagnosis Cell culture: CPE in human diploid fibroblasts 2-4w Shell vial: immunofluorescence detection of early antigen Cytology: owls eye basophilic inclusion in body DNA detection/quantitation: direct PCR from pt sample (plasma or WBC) Serology: IgM seroconversion (may remain elevated long term). Transplant serostatus Treatment: spread by sexual contact is preventable CMV seronegative or leukocyte depleted blood for transplant and transfusion (match negative recipients and donors) Prophylaxis and treatment with approved antiviral drugs: ganciclovir (IV, oral, ocular), valganciclovir (oral), foscarnet (IV), cidofovir (IV) Vaccine is currently under development

Enterobacteriaceae

Large family of organisms Facultative gram- rods Ferment glucose Generally oxidase negative, reduce nitrate to nitrite, and do not need NaCl for growth (this helps differentiate them from other gram- rods) Prominent organisms: E. coli Shigella Salmonella Yersinia Klebsiella Proteus Enterobacter Serratia Citrobacter Account for almost half of clinically significant isolates in lab, ~80% of gram- isolates

Borrelia

Larger than other spirochetes, makes Giemsa/Wright staining and microscope visualization possible Microaerophilic, difficult to grow in lab. Needs Barbour-Stoenner-Kelly medium B. burgdorferi causes Lyme disease (leading vector-borne disease in US)- 30,000 new cases/yr in US, over 90% on NE coast. Vector is ixodes tick, reservoirs white tailed deer and white footed mouse. Humans accidental host when bitten by ticks that previously fed on mice/deer B. recurrentis causes relapsing fever, humans are only reservoir. Lice feed on infected person. Requires crowded, unsanitary conditions (war, natural disaster). Restricted to Ethiopia, Eritrea, Somalia, Sudan

Human Cytomegalovirus: Structure, Growth

Largest genome of the herpes viruses Replicates in vitro only in human diploid fibroblasts Very slow replication, 2-4 wks for CPE to develop Infects many types of cells in vivo Species-specific so no animal model Lifelong latency, mild or subclinical infection in normal host reactivated by lowered immunity

Poxvirus: Characteristics, Mechanism

Largest viruses, complex structure Brick shaped with internal structures Linear, double stranded DNA with covalently fused ends Replicate in the cytoplasm (Important) Encode all proteins needed for mRNA synthesis Encode proteins for DNA synth, immune evasion Assembled in cytoplasmic inclusions- Guarnieri bodies Transmission: smallpox- inhalation or direct contact (rarer) Molluscum: direct contact; zoonoses: direct contact Initial stimulation of cell growth, then lysis Encodes products for immune escape Cell-mediated and humoral immunity for resolution No latency or persistent infection

VZV: Latent and Recurrent Infections

Latent is usually in dorsal root or CN ganglia Recurrent infection is herpes zoster- shingles Activated by trauma, meds, neoplasia, immunodeficiency Severe pain in area of innervation Rash limited to a dermatome unilaterally Lesions small, closely spaced, maculopapular w erythematous base Lesions limited but pain is persistent (post herpetic neuralgia can last years) Ramsay Hunt Syndrome- herpes zoster oticus- intense ear pain, rash around ear, vertigo, hearing loss, resolves on own in days-weeks

Leptospira: Disease

Leptospirosis: Symptoms develop 1-2w after transmission 1. Flu-like symptoms: pt is bacterimic with leptospira and organisms can be isolated from CSF even without neuro symptoms. Symptoms remit after 1 week 2. Phase 2: more severe, sudden onset of HA, myalgia, chills, abdominal pain, conjunctival suffusion. Severe disease progresses to vascular collapse, thrombocytopenia, hemorrhage, hepatic/renal dysfunction Weil disease: hepatic involvement with jaundice seen in very severe cases. Necrosis is not seen and surviving patients do not have permanent damage

Daptomycin

Lipopeptide, binds to bacterial cell wall causing depolarization, rapid death. Large molecule Bactericidal activity more rapid than Vancomycin Use: gram+ infections including sepsis, endocarditis, some VRE IV admin only, renal t1/2 about 8h. Inactivated by pulmonary surfactant so will not work in lungs (pneumonia) Toxicity: Myopathy, monitor creatinine phosphokinase

EBV: Serological Profile, Treatment

Listed as heterophile, VCA-IgM, VCA-IgG, EA-R/D, EBNA 1. Acute primary: +, +, +, +/-, - 2. Chronic primary: - - + +/+ - 3. Past infection: - - _ -/- _ 4. Reactivation: - - + +/+ + 5. Burkitts: - - + +/- + 6. Nasopharyngeal carcinoma - - + -/+ + Treatment: no vaccine or drugs, although acyclovir has in vitro activity and is used for oral hairy leukoplakia Acyclovir decreases viral shedding in oropharynx, but does not alleviate symptoms of disease Ubiquitous and shed asymptomatically which are problems for control Lifelong immunity except for immunocompromised Early exposure is best as early disease is relatively benign

Fasciola Hepatica

Liver fluke, first whose life cycle was solved Life cycle: definitive host- sheep, cattle, goats, humans 1st intermediate: stream/pasture snails 2nd intermediate: watercress, aquatic vegetation, grass Ingestion of plants with encysted metacercariae Disease: Phase 1: metacercariae migrate through liver, cause necrosis: fever, RUQ pain Phase 2: metacercariae larvae migrate to bile ducts and mature to adults. Damage due to mechanical irritation and obstruction: hepatomegaly, eosinophilia Epidemiology: worldwide, most in sheep/cattle raising countries (S France, GB, Cuba, US) Morphology: adults large with cephalic cone, eggs operculate and large Diagnosis: detection of large operculate eggs in stool

Paragonimus Westermani

Lung fluke Life cycle: definitive host: man, other mammals 1st intermediate: snails, 2nd: freshwater crabs/crayfish Infection by ingestion of raw infected crab/crayfish Epidemiology: Far East endemic areas (China, Japan, South Korea, Taiwan, Philippines). SE Asia and parts of CA/SA Morphology: large eggs with shoulders and flattened operculum Diagnosis: travel history/residence in endemic area Detection of eggs in sputum/stool

B. burgorferi: Disease

Lyme Disease- 3 stages (less distinct than syphilis) 1. Transmission in warm summer months, incubation 3-30d, organisms multiply in skin and disseminate in blood. Bulls eye lesion (erythema migrans) forms, fades and disappears in weeks 2. In untreated patients in days-weeks. Severe fatigue, HA, fever, malaise, arthritis, arthralgia, myalgia, erythematous lesions. 60% pts get arthritis (knee), 10-20% get neuro sx (Bell's palsy), 5-10% CV complications (myocarditis). Stage 2 is common, many people were not aware of infection 3. Months-years after initial infection. Arthritis of 1 or more joints intermittently. Chronic skin lesions lead to discoloration and swelling (acrodermatitis chronica atrophicans). Cardiac, neuro complications common

Ganciclovir/Valganciclovir: MOA, Indications

MOA: acyclic nucleoside analogue of guanosine, VGCV is L valine ester prodrug of GCV Oral BA of VGCV 60%, oral GCV 6-8% Hydrolyzed by esterases in intestinal wall/liver to GCV Triphosphorylated intracellularly to active: by TK of HSV/VZV, UL97 kinase of CMV GCV-TP incorporated by viral DNA polymerase into DNA, results in termination of DNA synthesis Indications: treatment and suppression of severe CMV in immunocompromised 10x more active than ACV against CMV in vitro Equal in potency to ACV against HSV, VZV, EBV, with some HHV6 activity

Erythromycin

Macrolide, bacteriostatic, binds at 50S subunit Works mainly on gram+, with additional activity at Campylobacter jejuni, m pneumo, legionella, c. diphtheria, pertussis, syphilis, chlamydia, and many anaerobes Pharmacology: can be destroyed by gastric acid (sterate and ethylsuccinate preps more acid stable). Decreased absorption with food, crosses BBB, t1/2 90m Toxicity: GI, phlebitis (IV), cholestatic hepatitis (mostly in adults taking estolate form, maybe inc in pregnancy), transient hearing loss

Corynebacterium jeikeium

Main characteristics same as diphtheriae, relatively rare Causes bacteremia in cancer patients, can also lead to endocarditis, wound infections, foreign body infections Hallmark is very high antibiotic resistance Susceptible to vancomycin as last line of defense

C. jejuni: Pathogenesis

Main reservoir is intestinal tract of animals (poultry). Adhesins, cytotoxic enzymes, enterotoxins exist but role in disease unknown. GI disease most characterized by histologic damage to mucosal surface of jejunum, ileum, colon. Surfaces appear ulcerated, edematous, and bloody, with crypt abscesses in epithelial glands and infiltration into LP with neutrophils, mono/macro, and eosinophils Inflammation consistent with intestinal tract invasion About 1.5m cases per year in US

Opportunistic Fungal Infections: Pneumocystis jirovecii (and carinii)

Major cause of pneumonia in immunosuppressed, esp those with advanced HIV or chronic high dose steroid use Life cycle is similar to protozoa but grouped with fungi based on ribosomal RNA sequences 1. Ecology: largely unknown. Environmental inhalation? 2. Life cycle: trophozoites and cyst forms found in alveolar spaces of lung, trophs multiply and form mature cysts which rupture, releasing new trophozoites 3. Disease: pneumonia, likely from reactivation of latent infection: fever, cough, dyspnea, hypoxia Leading cause of morbidity/mortality in advanced HIV 4. Diagnosis: morphologic ID of organism in tissue Microscopic exam of bronchoalveolar lavage: fluid or lung tissue for cysts (silver stain) or trophozoites (Giemsa) Culture difficult and rarely done 5. Treatment: tri-sulfa, pentamidine

Babesiosis: Disease

Many asymptomatic, some develop flu-like symptoms (fever, chills, sweats, HA, body aches, LOA, nausea, fatigue) Because they infect/destroy RBCs, can cause hemolytic anemia leading to jaundice and dark urine Can be severe/life-threatening, especially in those without a spleen, those with weak immune system (cancer, lymphoma, AIDS), serious health conditions (liver/kidney disease), or the elderly Complications: low/unstable BP, severe hemolytic anemia, low platelet count (thrombocytopenia), DIC leading to blood clots and bleeding, malfunction of vital organs (kidney, lungs, liver), death

Identification of Fungi: Histopathological

Many fungi are large and can be seen directly in specimens 1. Microscopy direct mount: specimen on slide with 10% KOH to lyse and clear cells but will not lyse yeast CW. Can be paired with parker ink to stain fungal CW. 2. Gram stain: usually not useful, yeast are gram+, molds gram-. Exception: Candida stains as large gram+ cells 3. India ink: stains capsule of cryptococcus 4. Calcofluor white: binds fungal cell wall polysacs, fluoresces under UV light 5. Periodic Acid Schiff: stains cells pink, gomori methenamine silver stains them black. GMS mostly for p jirovecii

Arenaviridae: Lymphocyte Choriomeningitis Virus

Meningitis is actually not typical presentation Normally causes fever with flulike myalgia. In ~10%, progresses to CNS infection with meningeal illness 10d after onset. Most common arenavirus infection in US and considered underdiagnosed. Perivascular mononuclear infiltrates may be seen in neurons of all sections of brain and in meninges. Most pts survive, no chronic infection noted. Mortality <1%. Aseptic meningitis, encephalitis, meningoencephalitis require hospitalization and supportive therapy. Anti-inflammatories (corticosteroids) for severe circumstances

Polyomaviruses: Merkel Cell, SV40

Merkel Cell (MCV): first polyomavirus associated with human tumor. rare primary neuroendocrine carcinoma of skin, integrated into genome of cancer cell SV40: simian virus, unapparent infection in monkeys Oncogenic in hamsters Present in original Salk polio vaccine from cell culture Associated with mesotheliomas, but no definitive link to human disease

Ureidopenicillins

Mezlocillin, piperacillin Piperacillin is a semisynthetic broad-spectrum ampicillin derived drug used for pseudomonas and in combination with other antibiotics. Note for PCNs overall: Used for strep, meningococcal, neuro-syphilis. Usually given IV, t1/2 about 30m means dosing intervals every 4 hours

Togaviridae: Chikungunya

Mosquito-borne alphavirus, transmitted human-human from bites of female Aedes aegypti/albopticus mosquitoes. Africa, Asia, India, recent spread to Europe/Americas. Current outbreak: 2006-2013 28/yr in US, all travelers. Some local transmission in Caribbean and FL in 2014. In 2015, 679 cases in 44 states, all travellers. Signs/Symptoms: Undifferentiated fever with debilitating joint pain lasting days-weeks. Most fully recover, rarely pain can persist for years. Occasional eye, neuro, GI, cardiac complications. Elderly at inc risk for severe disease/death Treatment: supportive, no vaccine. Avoid vectors, use pesticides, long clothes suggested.

Flaviviruses: Dengue Fever: Transmission/Epidemiology

Most common arbovirus in the world. Transmitted by female Aedes aegypti/albopticus mosquitoes. Infected mosquito can transmit virus for rest of its life. Widespread throughout tropics, grown dramatically Infection is 390m per year, 96m with severe disease Rate increasing and spreading to new areas (France, Croatia, 2000 cases in Portugal, Key West, Hawaii) Current outbreaks: Hawaii island (under control but infectious mosquitoes may still exist), Florida (peaked in 2010, 1 case in 2016)

Inhalation Anthrax

Most dangerous form, previously occupational hazard (Wool Sorters) Onset can take 2 asymptomatic months Spores can remain latent in nasal passages or reach lower airways where they are digested by alveolar macrophages and transported to mediastinal LN. Biphasic disease. Initial fever, malaise, myalgia, non productive cough, abdominal/chest pain. CXR shows widened mediastium. Pts begin to recover then quickly succumb to edema, sepsis, shock, meningeal signs (in 50%). Mortality about 80%

Isolation

Most definitive method of determining viral etiology is recovery and growth of the agent In clinical lab, specimen will be inoculated onto battery of cell lines and ability to grow on specific lines provides valuable information Type (appearance) of cytopathology produced gives valuable info If agent suspected of being novel virus and does grow in tissue culture, sample of virus grown should be examined by electron microscopy to visualize morphology Other tests necessary to definitively identify

Parasitology: Pathogenesis

Often it is host inflammatory/immune response against dead parasites that actually causes the damage Sometimes huge parasite burden can impede organ function, use up nutrients, or block blood flow Intracellular parasites can kill infected host cells and induce further inflammatory response Different stages of life cycle may produce different symptoms (example: hepatocyte and RBC stages of malaria)

Aminoglycosides: Structure

Most have 6 membered ring with glycosidic bond to 2+ sugars. Removal of amino or hydroxyl groups results in loss of antibacterial activity and loss of toxicity Very water soluble, don't cross lipid membranes (BBB) well

Adenovirus: Diagnosis, Treatment

Most serotypes grow in cell culture derived from epithelial cells, needs about 6d. Serotypes associated with gastroenteritis do not grow in available cell types PCR used most often, serological assays to ID serotype Diagnosis is mostly for epidemiology Treatment: no approved drugs Live oral vaccine used in military recruits for types 4 and 7, some coverage for serotype 14 Handwashing and chlorination of swimming pools decreases transmission Vector for gene replacement therapy

Parasitology: Transmission

Must know: how is it transmitted, what is infective form? Involves 3 factors: source of infection, mode of transmission, presence of susceptible host 2 Types of vector: mechanical- mechanically move parasite from one organism to another, like eye seeking fly Biological: essential period of growth occurs in vector, like malaria mosquitoes 2 Types of Host: definitive: final host, where adult form of parasite is found or sexual reproduction takes place Intermediate: host harbors intermediate or larval (asexual) form of the parasite

Mitochondrial Inheritance

Mutation in mtDNA (multiple copies in each mitochondria and multiple mito in each cell) mtDNA codes for 13 respiratory chain subunits, 2 rRNAs, all tRNAs, only affecting respiratory chain 1. Sporadic mutations- often not inherited (duplication/deletion)- in KSS/CPEO 2. Maternally inherited point mutation- in MELAS, MERRF, NARP, LHON 3. tRNA mutation or deletion will affect several enzymes 4. Subunit gene mutation affects only protein coded for by that specific gene Heteroplasmy: some mtDNA will have mutation, some do not, symptoms dependent on % of abnormal mtDNA inherited and propagated in specific tissue. Percentages will be very different in different offspring Bottleneck when zygote formed mtDNA mutations more frequent than genomic bc of poor repair Inheritance always maternal: males will never pass to children, all children of mom will inherit it but will be variably symptomatic (tissue threshold for manifesting effects, % inherited, distribution of mutation, etc)

Natural Penicillins and Beta-lactimase resistant PCNs

Natural PCN: For aerobic, gram + organisms Penicillin G is DOC for infections from sensitive S. pneumo Penicillin V preferred for S. pyogenes. Also can be used for Strep viridans endocarditis B-lactamase resistant: resistant to hydrolysis by staph penicillinase> Methicillin, oxacillin, dicloxacillin.

Herpesvirus Simiae (B Virus)

Natural host is Asian monkeys- no disease Transmitted by monkey bites, saliva, tissue culture cells Acute ascending paralysis, encephalitis, usually death No treatment of clinical disease, can treat with herpes B gammaglobulin after exposure Diagnosis by virus culture or serology Concern for xenotransplantation: just one example of virus that is benign in normal host, lethal when it crosses species barrier

Metronidazole and Tinidazole

Nitroimidazoles 1. Metronidazole: used for anerobic and microaerophilic bacteria, bacteroides and clostridium, H pylori, Entamoeba histolytica (not against cyst form), giardia lamblia, trichomonas vaginalis 2. Tinidazole: can be used as a single dose (giardiasis) Better tolerated and maybe more effective than metronidazole Used for giardia lamblia, some metronidazole resistant trichomonas vaginalis, and tissue trophozoite form of entamoeba histolytica

Human CMV: Latent and Recurrent Infection

No apparent reactivation in immunocompetent host Large percentage of T cells reactive against CMV in >50y Seropositive recipients of transplants have reactivated infection of endogenous strain, donor strain, or both Seronegative recipients of transplants have infection from donor strain AIDS pts have high rate of CMV reactivation when HIV viral load is high: when decreased, so is CMV

Epstein-Barr Virus: Structure, Growth

No cell culture system Limited host range- monkey and human cells, limited cell tropism. Human and new world monkey B cells, epithelial cells of oro/nasopharynx Receptor os C3d complement receptor (CD21) Outcome of infection: replication in epithelial cells, latent in B cells, immortalized B cells (lymphoblastoid cell lines) By age 30, 70% of US population is seropositive

Arboviruses: Vectors and Reservoirs

Normally reservoir will develop lasting immunity to virus, but sometimes significant disease produced. Prolonged viremia in reservoir necessary to maintain arthropod-borne virus disease cycle Vectors spread virus, usually via saliva, usually show no disease. Two life cycles: 1. Sylvatic/Jungle: virus transmitted back and forth from arthropod to vertebrates including nonhuman primates. Eventually transmitted to human, a dead-end host 2. Urban: same as above but humans are part of cycle, not dead ends. Yellow Fever and Dengue Fever have both cycles

Flaviviruses: Zika: Transmission/Epidemiology

Not a new virus. Noted in monkeys in 1947, humans in 1952. Transmitted via Aedes aegypti mosquito which bites during the day, esp in early morning and late afternoon. ZIka is unique in that it can also be spread via sexual transmission (vaginal, anal, and oral) from infected males. Virus is active in semen longer than in blood. Can cross placenta, so maternal-fetal transmission in utero and at delivery possible. Before 2015, in Africa, SE Asia, Pacific Islands. In 2016, outbreaks in 65 countries, Florida pending CDC confirmation. Olympics: would not affect spread, but 4 countries at risk bc they did not have significant travel to Zika areas: Eritrea, Djibouti, Chad, Yemen

Togaviridae: Rubivirus: Transmission, Epidemiology

Not spread by arthropod, but by aerosols. Not vector-borne, humans are only reservoir Once rampant in US and world (pandemic in 1965) but now very rare due to immunization (MMR) Over 90% of adults are seropositive Vaccination rates have decreased in recent years (have had measles and mumps outbreaks) Can be spread transplacentally when mother is viremic. dependent on month of gestation, decreases significantly after month 5- 1st trimester 18%, month 4 6%, month 5 <2% Virus can persist within infant for months to years

Bacteroides Fragilis

Note: gram- anaerobes outnumber aerobes 10-1000 fold Typical gram- cell wall structure surrounded by anti-phagocytic polysac capsule Pleomorphic rod shape, anaerobic Stimulated by bile, grows on bile esculin agar Gentamicin resistant Grows on blood agar Cell wall has LPS but little to no endotoxin activity Grows rapidly in culture

Legionella

Noted at 1976 outbreak of Legionnaire's convention, not seen before because stains and grows poorly L. pneumophilia: small, gram- pleomorphic rod Obligate aerobe, needs cysteine and iron to grow Facultative intracellular bacteria with worldwide distribution Commonly present in bodies of water and cooling towers Disease can follow exposure to aerosolized organism No evidence of person-person spread or animal reservoir L pneumo causes 90% of all infections, fluoribacter bozemanae and tatlokia micdadei cause similar symptoms

Penicillin

Obtained from penicillium mold. Alteration of basic structure, addition of groups provide many preps. Has 4-sided b-lactam ring. Targets constituents of thick peptidoglycan gram+ wall Ring binds to/inhibits bacterial enzymes (PBPs) necessary for CW synthesis. Leads to formation of defective CW by altering crosslink formation, causes bacteria to release autolytic enzymes causing cell lysis and death. Divided into several groups based on spectrum (4 generations) Beta lactamase inhibitors can be given: inhibit penicillinase and allow penicillin to remain active (clavulanic acid, sulbactam, tazobactam) Minor adverse effects: nausea, rash. Diarrhea with oral. Most serious is allergy (highest of any drug). Rashes, fever, inflammation, anaphylaxis

Insertion/Deletion from Unequal Crossover

Occurs at sites where homologous sequences are repeated in DNA near each other on chromosomes When chromosomes line up in meiosis, mispairing so repeated sequence gets shifted up or down Crossover occurs- one chromosome gets an extra piece, the other is missing a piece Chromosomes separate and offspring can inherit either, and each brings a different disease Example: pts with Charcot Marie Tooth 1 or HMSN1 have a duplication of PMP20 gene (3 copies) due to extra small piece Family members may have deletion of corresponding piece (1 copy) and get hereditary neuropathy with pressure palsies (HNPP)

Diagnosis of Genetic Disorders

Once mutated gene is known, can get a DNA test Can be done prenatally DNA tests are NOT chromosome tests If a common mutation (like unstable TNR), easy to get DNA test If not, may need whole gene sequenced: harder and much more expensive

Parasitic Protozoa

One celled organism, facultative anaerobes (free oxygen is often limited in the host). Nutrition is via direct absorption, ingestion, or both Survival depends on reproductive potential (can be sexual, asexual, or both) Transmission of intestinal and atrial protozoa is direct from host to host or through contaminated food/water Blood and tissue protozoa usually involve vertebrate host and invertebrate host that acts as a vector Prevention of infection involves sanitation and hygiene (for intestinal/atrial) and vector control (tissue/blood)

Polyomavirus and Papillomavirus: Common Features

Originally papovaviruses, now two families Icosahedral, no envelope Circular double stranded DNA Groups are antigenically distinct Viruses encode proteins to promote cell growth-- bind to cell growth suppressors, p53, pRB Lytic infections in permissive cells, immortalize non permissive cells

Papillomaviruses: Mechanisms

Over 100 types, 16 groups A-P. Cutaneous/mucosal tissue is susceptible. Highly resistant to inactivation on surfaces MOD: transmitted by close contact through breaks in skin or mucosa, sexual contact. Tissue tropism/disease varies among types Replication dependent on epithelial cell differentiation Benign warts specific for epithelial surfaces (cutaneous): skin, anogenital (condyloma accuminatum), larynx Uncontrolled infection in patients with genetic disorder (epidermodysplasia verruciformis) High risk types (16,18) associated with dysplasia, cervical cancer Cervical Carcinoma: detected on PAP smear, mild dysplasia has 40-70% regression. 16,18 most common types, commercial assay detects 12 others Integration into host genome inactivates E2, causes growth stimulation and neoplasia

Pseudomonas

P. aeruginosa is most important- ubiquitous in nature, also waterborne pathogen Motile gram- rod, usually aerobic Has series of adhesins, endo/exotoxins, and significant resistance Causes: 1. Pneumonia, esp hospital acquired 2. Cellulitis, associated with hot tubs 3. Ear infections- swimmers ear 4. Eye infections

Sulfonamides: PK, Toxicity, Interactions

PK: absorption- well absorbed from GI distribution- enters CSF, pleural, and peritoneal fluids at 80% serum levels, excreted by kindey after acetylation/glucuronidation in liver Protein bound variably and reversibly, bound is inactive Serum levels useful in renal failure, peak should be <120 Toxicity: less soluble (sulfadiazine, sulfathiazole) associated with crystalluria, stones. Acute hemolytic anemia in patients with G6PD deficiency, agranulocytosis, thrombocytopenia. Not used in pregnancy (compete for bilirubin/albumin and cause kernicterus). Stevens-Johnson, erythema mutliforme/nodosum in long acting. Rash, N/V/D, hepatic necrosis Interactions: 1. Displace warfarin, methotrexate, chlorpropamide, tolbutamide from albumin and inc activity 2. Procaine and other local anesthetics derived from PABA can decrease activity

Imprinting: Prader Willi/Angelman Syndrome

PWS: hypotonia, early feeding problems/FTT, later obesity, behavior, mild mental retardation, mild dysmorphisms (small hands/feet) AS: developmental delay, delayed motor skills, ataxia, laughing spells, seizures, severe MR, behavior, dysmorphism Both result from identical deletions of imprinted area PWS from: paternal deletion of gene which is normally turned off (imprinted) on maternal chromosome, or maternal disomy 15 (both imprinted genes on maternal) AS from: maternal deletion of gene normally turned off on paternal chromosome, or paternal disomy 15 (80% cases come from loss of activity of one gene (UB3A) turned off in brain only on paternal chromosome)

Parasitology: Basics

Parasites are eukaryotic organisms without cell walls Can be very large, some have thick outer covering (tegument). Protozoans- single celled, Metazoans-multicelled, includes platyhelminths (flatworms) and nematodes (roundworms) Infection is not synonymous with disease Understanding life cycles is vital

Bunyaviridae: Non-Arthropod-Borne: Hantaan Virus

Part of Hantavirus genus Natural reservoir is mice and other rodents in Asia, E Europe. Transmitted when rodent excrement dries and crystallizes, can then be aerosolized or included in dust that is inhaled by humans, exposing virus to mucous membranes of eyes, nose, mouth. Disease is a hemorrhagic fever. Symptoms in 1-2w, begin suddenly: intense HA, back/abdominal pain, fever, nausea, rash, blurred vision. In viremic period, ABs form and can form immune complexes causing capillary leak, edema, shock, and hemorrhage. Renal disease notable, can lead to renal failure from immune complex deposition in kidneys (Hemorrhagic Fever with Renal Syndrome). Hemorrhagic symptoms in about 1/3, have 5-10% mortality

Bunyaviridae: Non-Arthropod-Borne: Sin Nombre Virus

Part of Hantavirus genus, AKA Muerto Canyon, 4 Corners Spread by dried excrement of deer mice, first noted in 1993 in SW US (at 4 Corners). Disease: emerging disease, relatively rare. Incubation not known, appears 1-8w. Early symptoms: fever, muscle aches, fatigue, dizziness, chills, abdominal pain, N/V/D. 4-10d after initial phase, dyspnea with cough from interstitial pulmonary edema. In 50% leads to respiratory failure and death. "Tight band around my chest and a pillow over my face" Supportive therapy only, no vaccine

Clostridium difficile: Characteristics, Pathogenesis

Part of normal intestinal flora in small number of healthy people and hospitalized patients Overgrowth causes watery diarrhea, exceptionally difficult to kill Gram + rod, anaerobic, spore forming Grows rapidly in culture, very O sensitive Characteristic barnyard smell Enterotoxin (A): binds to brush border of intestines causing inflammation, cell death, watery diarrhea Cytotoxin (B): disrupts cytoskeleton by depolymerizing actin, leads to enterocyte death/necrosis. Yellow/gray exudate forms pseudomembrane on colonic mucosa Disease is associated with Clindamycin use

Aminoglycosides: MOA

Passively diffuse through porin channels of outer membrane O dependent AT across cell membrane, inhibited by low pH and anaerobic conditions and is enhanced by CW active antibiotics like penicillin (synergy) Binding to ribosome inhibits protein synthesis, leads to cell death. Bind between 30S and 50S, (streptomycin at 30S) inhibit protein synthesis or cause misreading and bad protein production. Other antibiotics (chloramphenicol, tetracycline) inhibit protein synthesis and are not bactericidal, so aminoglycoside must have other effects that kill cell 1. Concentration dependent killing (in number and speed) 2. Can act synergistically with other antibiotics 3. Post antibiotic effect- lasts beyond time drug is present. (1) and (3) provide rationale for QD dosing

HHV8: Pathogenesis, Diagnosis, Treatment

Pathogenesis: genome present in tissue from: AIDS related B cell lymphomas (primary effusion/body cavity based lymphoma), Castleman's- polyclonal lymphoid proliferation w vascular hyperplasia (multicentric), KS lesions (skin, visceral organs, spindle cells) Genome in saliva of many AIDS pts may be source of transmission ABs in KS pts, seropositivity in 10% normal population Diagnosis: not usually done, no cell culture. Immunohistochemistry and PCR used Treatment: Localized cutaneous lesions treated with cryotherapy, topical immunotherapy, surgical excision Widespread cutaneous or internal disease needs chemo or immunotherapy Anti-retrovirals for HIV induce disease regression so thus are therapy for KS

Tetracyclines: Pharmacology, Toxicity, Interactions

Pharmacology: well absorbed from GI, half life: tetracycline 8h, doxycyline 18h, minocycline 16h. Renal excretion (except doxycycline), cross BBB and placenta (can accumulate in fetal bones and teeth), found in breast milk Toxicity: hypoplasia of tooth enamel, dark staining of teeth (do not give to kids <8), GI irritation (esophageal ulcers after capsules), renal disease (inc azotemia in pts with renal failure, Fanconi), Vertigo (minocycline) Interactions: decreased absorption if taken with Ca, Mg, Al, antacids, milk, sodium bicarb, iron Dilantin and barbiturates decrease half life Methoxyfluorine anesthesia can cause nephrotoxicity

Chloramphenicol: Pharmacology, Toxicity, Uses

Pharmacology: well absorbed from GI, increased levels after po vs IV (because IV must be hydrolyzed to active). Metabolized (conjugated with glucuronic acid) by liver and excreted by kidneys. Wide distribution (CSF, tears, placenta) Reduce dose in liver failure Toxicity: Hematologic: bone marrow suppression (dose related, reversible) or aplastic anemia (idiosyncratic, irreversible, in about 1/20-40k) Gray syndrome: neonate with abdominal distension, flaccidity, cyanosis, can lead to death. From dec ability to conjugate drug in liver Optic neuritis Uses: brain abscess, meningitis (PCN allergy), typhoid, Rocky Mountain Spotted Fever

Aminoglycosides: Pharmacology

Poorly absorbed from GI, Vd=ECF volume, little protein binding Poor concentrations in CSF and eye (so if used must be injected directly here), about 50% of serum concentration in pleural, pericardial, ascitic fluids Crosses placenta Excreted unmetabolized by glomerular filtration, t1/2 2-3h with normal reneal function, can inc to 100h+ with anuria Must monitor serum levels and renal function Usually given in 2-3 equal doses/day if normal renal function. QD dosing is advantageous but not proven

Malaria: Approach To Treatment

Preferable to wait until diagnosis established Treatment guided by 3 factors: 1. Infecting species: falciparum and knowlesi more serious, vivax and ovale have dormant hypnozoite, falciparum and vivax have resistance patterns 2. Clinical status of patient: uncomplicated malaria generally oral therapy, severe need parenteral 3. Drug susceptibility of infecting parasite- includes knowledge of area as well as species Must report to CDC

Togaviridae: Rubivirus: Diagnosis, Treatment

Presence of virus can be detected with RT-PCR. ABs can be used to confirm in unvaccinated people. ABs assayed early in pregnancy to determine immune status of mother and is required in most states. Treatment: None. Highly effective live vaccine as part of MMR or MMRV.

Beta-lactamase Inhibitors

Prevent destruction of b-lactam antibiotics that are substrates for these enzymes Most active against plasmid encoded b-lactamases including the enzymes that hydrolyze ceftazidime and cefotaxime Inactive against type I chromosomal b-lactamases induced in gram- bacteria (like enterobacter, acinetobacter, citrobacter) by treatment with second and third generation cephalosporins

Human CMV: Immunocompromised

Primary infection severe in transplant recipients (pneumonitis, GI disease, retinitis) Recurrent infection in transplant recipients- less severe than primary Recurrent infection in pts with AIDS (low CD4 count): retinitis, GI disease, pneumonitis

VZV: Structure, Growth, MOD

Primary isolation in human diploid fibroblasts, can grow in others. CPE is similar to HSV but longer to develop, up to 2w. No extracellular virus Smallest genome of herpes virus, all proteins have HSV homologues MOD Respiratory spread Syncytia and cell-cell spread Viremic stage leads to infection of skin, lesions Establishes latent infection in neurons of dorsal root and CN ganglia Recurrent infection is herpes zoster- shingles Disseminated disease in immunocompromised

HSV 1 and 2: HSV2 Infection

Primary: classical spread by sexual contact-- genitalia, oropharynx, anorectal tissue Onset later than HSV1, development of lesions similar. Infections of infants in utero or at birth from infected mother- generalized infection of brain and visceral organs Meningitis in neonates, resolves without damage but can be recurrent Latent: asymptomatic, viral DNA in sensory cells of sacral nerve gamglia Recurrent: virus replicates, down sensory nerve fiber. Infects epithelial cells in genital area. Symptoms usually milder. Source of infection with severe effects in neonate

Clavulanic Acid

Produced by streptomyces clavuligerus Poor intrinsic antimicrobial activity, but is a suicide inhibitor that irreversibly binds beta-lactamases produced by lots of gram+/- bacteria. Well absorbed by mouth. Combined with amoxicillin (oral augmentin) and ticarcillin (parenteral timentin) Augmentin effective in vitro and in vivo for b-lactamase producing staph, H flu, conococci, E coli. With ciprofloxacin is effective for low-risk neutropenic patients from chemo. Effective in acute OM, sinusitis, bite wounds, cellulitis, DM foot infections. Timentin extends spectrum so that it resembles imipenem: inc gram- bacilli, s aureus, bacteroides, but no inc activity against pseudomonas. Must adjust dose for RI. Very useful for nosocomial, usually with aminoglycoside

Clostridium tetani

Produces a neurotoxin like c botulinum Results in rigid paralysis, second most potent toxin Large, motile, gram+ rod, anaerobic Spore forming Looks like tennis racket or drumstick Difficult to grow because of O sensitivity Spores ubiquitous, found in soil and organism found in GI of many animals

Physical Structure of Viruses

Proteins, nucleic acid, sometimes lipids, no organelles Genome is RNA or DNA, single or double stranded, linear (all RNA) or circular (some DNA), segmented (some RNA) or unsegmented (all DNA) Single strand can be positive or negative sense 5-200 genes Proteins are structural: capsid- helical or icosahedral structure, matrix (scaffolding), replicase (transcribe mRNA), envelope (insert into lipid envelope derived from host cell membrane); or nonstructural Unique features: do not grow in nutrient media, pass through filters that retain bacteria, damage host by multiplication in cells (no toxins)

R. prowazekii: Pathogenesis, Immunity, Disease

Prowazekii and R. typhus cause epidemic or louse-borne typhus. Humans are reservoir, vector is human body louse. Epidemic typhus happens in crowded, unsanitary conditions Typhus: 2-30d after exposure, initially nonspecific but within 1-3d get high fever, severe HA, myalgia. Possible pneumonia, arthralgia, neuro (stupor, confusion, coma). Centrifugal petechial rash starts in trunk, spreads to extremities. Untreated mortality 20-30%, may be higher if poor health. Uncomplicated disease: recovery takes 2w-3m Can remain dormant for years and reactivate, causing recrudescent epidemic typhus (Brill-Zinsser)

Malaria Drugs: Quinolone Derivatives

Quinine, quinidine, chloroquine, mefloquine, amodiaquine, primaquine MOA: concentrated in acidic vacuoles in intra-RBC parasites, inhibits heme polymerase that normally protects parasite from toxic heme byproduct Parasite ingests hemoglobin, which is then degraded to heme- toxic to the parasite

Togavirus

RNA+ virus Many of arthropod-borne viruses discussed later Nucleocapsid is icosahedral, virion has lipid envelope 2 mRNAs, genomic and one subgenomic are translated into polyproteins Genus alphavirus: Western equine encephalitis Rubivirus: rubella (German measles) Infectious before rash, can cause abortions, stillbirths, congenital rubella syndrome Controlled by live attenuated vaccine

Norovirus

RNA+ virus Member of calcivirus family, has no envelope Causes gastroenteritis Can survive in environment for relatively long time Fecal-oral or fomite transmission Highly contagious

Rotavirus

RNA+ virus Member of reovirus family Double stranded RNA virus Double protein coat with no envelope Causes gastroenteritis More harmful to infants

Flavivirus

RNA+ virus Some transmitted by mosquitoes, some by ticks Yellow fever, Dengue fever, St. Louis encephalitis, Hep C Genome only mRNA, translated into one polyprotein Virus has lipid envelope

Coronavirus

RNA+ virus Strains normally infecting humans are another cause of common cold Some animal strains jumped to infect humans- limited epidemics but can be fatal (SARS, MERS) Nucleocapsid is helical, virion has lipid envelope

Picornavirus: Symptomology

Range from Asymptomatic to paralytic 1. Polio: asymptomatic (mostly) to meningitis/paralytic disease (rare). Flaccid paralysis when virus reaches anterior horn cells of spinal cord or motor cortex of brain and replicates. If medulla involved, bulbar poliomyelitis (paralysis of respiratory muscles) 2. Coxsackie: respiratory infections, fever/rash, aseptic meningitis, paralysis Coxsackie A: herpangia, hand-foot-mouth Coxsackie B: pleurodynia, myocardia, pericardia Most infections not distinctive enough to be diagnosed clinically 3. Rhinovirus: common cold 4. Hepatitis A virus: hepatitis

Poxvirus: Smallpox: Eradication, Bioterrorism

Reasons for eradication: exclusively human disease with no latency. Single serotype, vaccine is protective for all strains Shared antigenic determinants with animal poxviruses used as basis for stable, inexpensive vaccine Worldwide program of quarantine and vaccination resulted in eradication in 1978. Controversy around remaining lab stocks Bioterrorism: large unvaccinated population High mortality associated with infection Virus is easy to propagate and relatively resistant to environmental conditions Could be rapidly disseminated in a susceptible population

Parvovirus: MOD of Bocavirus

Recently discovered, emerging viral pathogen Name comes from bovine/canine, which share genetic and structural characteristics Acute respiratory infections in children Infants and children under 2y most frequently symptomatic, from mild to severe disease Cough, wheezing, fever, rinorrhea, diarrhea, vomiting, pneumonia Diagnosis by in-house PCR Mode of transmission and disease association not yet known- assumed to be respiratory, also found in blood and stool

Genetic Interactions: Recombination, Reassortment

Recombination: two viruses infect same cell, can (rarely) produce virus that is a genetic recombinant New virus is genetically altered, progeny breed true Coronavirus, HSV, HIV Reassortment: two segmented viruses infect same cell, make progeny with genes from either parent Influenze, rotavirus, reovirus

B. recurrentis: Disease

Relapsing fever, begins after 1w incubation Abrupt onset shaking, chills, fever, myalgia, arthralgia, HA Splenomegaly and hepatomegaly common Symptoms resolve in 3-7d Bacteremia and fever return in 1w with milder and shorter course, as many as 10 relapses can occur Mortality highly variable In louse-borne disease can be as high as 70%, caused by cardiac failure, hepatic necrosis, cerebral hemorrhage

Titers

Relative measure of levels or concentrations of AB or virus in sample Tests usually involve dilutions of starting sample, first dilution is arbitrary depending on assay AB titers used to determine if infection is new or old Number of infectious particles is a virus titer (not all new particles released are infectious) Example: plaque assay

B. cereus: Reservoir, Diagnosis, Treatment

Reservoir: exists in almost all environments, almost all infections originate in environmental source (contaminated oil) Diagnosis: Can be readily cultured from clinical specimens from pts with emetic form. Implicated food must be cultured for confirmation of foodborne disease. Treatment: supportive to control symptoms (anti-nausea, rehydration). Prevention: proper food prep and storage. Boiling rice does not kill spores. Germinate when rice is held warm, but low temps will kill bacteria. As they grow on rice, produce emetic toxin. Food must be kept cold to prevent growth or kept hot enough to kill bacteria when they try to grow

R. rickettsii: Disease

Rocky Mountain Spotted Fever 2-14d after tick bite (pts may not remember bite)- high fever and HA with possible malaise, myalgia, N/V, abdominal pain, diarrhea Petechial rash in 90% of patients on day 3. Rash is centripetal (begins on extremities, spreads to trunk) Fatality as high as 20% in kids, averages 10% if untreated

Nematodes

Roundworms: abundant, widespread, serious effects on human health Tube within a tube: outer is body wall, inner is digestive system Separate sexes, males have special copulatory organs at posterior end Can be up to 15cm long Eggs hatch and larvae undergo series of molts at each of 4 stages. L1 is rhabtidiform, L3 is filariform (infective) Both larvae and adults found in man. Life cycles can be direct or indirect and sometimes involve arthropod vectors

One Step Growth Curve

Set up so all cells in culture exposed to at least one infectious virus (high multiplicity of infection) Eclipse: most starting viruses disappear into cells Synthesis: virus components made in cell, self-assemble Maturation/release: infectious virus appears inside cells, then outside

Haemophilus Ducreyi

Sexually transmitted infection- chancroid Painful papule develops several days after infection, ulcerates, leads to regional lymphadenopathy (ulcer-node). More common in men but women may have asymptomatic infections or less visible lesions. Lesions are usually on external genitalia or perirectal. Any time STI is diagnosed/suspected, check for others Difficult to grow in lab- must alert microbiologist that you suspect H ducreyi

Pasteurella Multocida

Small coccobacilli, facultative anaerobes, normal flora of respiratory tract of animals and birds Humans can become infected, esp following animal bites (dog, cat) P. multocida is main pathogen, P. canis causes disease too Most common syndrome is cellulitis, more compromised patients can develop pneumonia or bacteremia

Vibrio cholerae: Pathogenesis/Immunity

Small curved gram- rod, fermentative facultative anaerobes (require salt). Cholera toxin mediated disease, multiplies freely in water Grow naturally in estuarine/marine environment and flourish in shellfish. 3-5m cases, 120k deaths each year Susceptible to stomach acids so need large inoculum for disease unless gastric acid reduced/neutralized (h pylori). Polar flagella for motility, toxin pilus. Cell wall has LPS with an endotoxin lipid A and antigenic O polysac side chain O side chain used to serogroup (O1 and O139 associated with epidemics). Two subunits to toxin, takes A-B structure of E coli, B anthracis, C diphtheriae Ring of 5 identical B subunits binds to intestinal epithelium Active A subunit internalized, interacts wth G proteins that control adenylate cyclase, leading to conversion of ATP to cAMP leading to loss of water, electrolytes Adhere to mucosal cell layer via toxin coregulated pilus

Propionibacterium acnes

Small gram+ rods in short chains or clumps Normal flora of skin, conjuctiva, external ear Stimulates inflammatory response as it attracts WBCs to phagocytose bacteria in sebaceous follicles, produce hydrolytic enzyme Disease: 1. Acnes vulgaris- major cause of acne especially in teens/young adults. Development unrelated to effectiveness of skin clearing because lesion is in sebaceous follicles. Tx is topical benzoyl peroxide, antibiotics 2. Opportunistic infections of prosthetics: inc valves, joints, catheters, CSF shunts

Brucella

Small, gram- coccobacillus, aerobic Grows slowly in culture, takes 1 week or more so must keep blood cultures at least 2 weeks Species: B. abortus, suis, melitensis, canis Pathogenesis: intracellular pathogen Granuloma formation Acute and chronic disease- fever (intermittent or undulant), liver/spleen involvement, CNS, bone

Campylobacter jejuni

Small, spiral or comma shaped gram- bacteria Microaerophilic growth (low O, increased CO2) Unable to ferment or oxidize carbohydrates Grows best at 42C Has lipooligosaccharides instead of LPS, contributes to pathogenesis Oxidase positive, slow-growing, and zoonotic

Polyomaviruses

Smaller, less complex than papilloma Similar structure, organization for BK, JC, Merkel Cell, simian virus SV40 Multifunctional T antigens: transcription control, DNA binding protein- binds to p53, p105RB

Mycoplasma and Ureaplasma

Smallest free living bacteria, do not have a cell wall Cell membrane contains sterols This makes them resistant to cell wall inhibitors (penicillins, cephalosporins, vancomycin) Atypical bacteria, pleomorphic shapes vary between cocci and rods Able to pass through many filtration systems that normally remove bacteria Facultative anaerobes except M. pneumo, a strict aerobe Grow very slowly M. pneumo: reservoir: humans, vector: ticks M. hominis/U. urealyticum: reservoir: mucosal flora, vector: STI What to know: extracellular, lack a cell wall, and are not mycobacterium!

Yersinia Pestis

Special organism, causes ulcer-node syndrome Short, gram- rod, bipolar staining. Is not fastidious in growth requirements. Capsular antigen (F1), type III secretion system helps it resist phagocytic killing Animal reservoir, natural disease of wild rodents (sylvatic plague), spread by fleas Pathogenesis of plague: 1. After flea bite, transported to regional LN, makes them enlarged and tender (buboes- bubonic plague) 2. Organisms entering from bite have no F1 capsule or v/w anti-phagocytic antigens 3. If phagocytosed by PMN, destroyed 4. If phagocytosed by macrophage, grow and at 37C synth F1 and v/w, leave cell fully virulent, phagocytosis resistant 5. From LN, disseminated via blood to spleen, liver, lungs, may cause subcutaneous hemorrhages 6. If hits lung, can be spread human-human by respiratory: pneumonic plague

Environmental Modifier Mechanism

Specific genetic abnormality predisposes to disease Disease is triggered by specific environment interaction Usually rapid onset of disease despite genetic abnormality present whole life with no prior issues Examples: 1. Adrenoleukodystrophy: most with mutation get nothing or adrenomyeloneuropathy AMN is chronic toxicity of VLCFAs on axons/myelin ALD appears suddenly and rapid course after years of normal development Immune response in white matter suggests set off by virus or autoimmune mechanism 2. Narcolepsy: certain HLA type very predisposed, loss of hypocretin neurons in brainstem where disease develops Thought to be AI reaction to virus in genetically primed person, much like diabetes

Flaviviruses: West Nile: Transmission/Epidemiology

Spread by Culex mosquitoes. Humans mostly dead end, major reservoir is birds. First isolated in West Nile in 1937, now almost worldwide First appeared in US in NY in 2000, spread to DC and 27 states in 2001 with 149 cases 2002: 4,000 confirmed cases, 284 deaths Illinois led nation, esp Skokie: 774, 52 deaths Remains a serious concern in US and worldwide

Virus Spread

Spread in Host: initial site is portal of entry Initial replication takes place there, new virions released to infect neighboring cells (some spread by cell-cell fusions or bridges between cells to protect themselves) Target organ May or may not be same as portal, may be reached by blood or nerves Incubation period is time between implantation and symptoms: short if portal is target, longer if generalized infection, very long if persistent

M. pneumoniae: Pathogenesis/Immunity

Strict human extracellular pathogen. 2m cases/yr in US Colonizes nose, throat, trachea, LRT, spread through aerosols, not part of normal human mucosal flora 1. Adheres to respiratory epithelium by sialated glycoprotein receptors at base of cilia on epithelial cell surface, causing stasis of cilia, destruction of cell 2. Cell death inhibits clearance of upper airway, allows bacteria to spread to LRT 3. Causes persistent cough, functions as superantigen stimulating cells to infiltrate and release inflammatory triad (IL1,IL8,TNFa?)

C. trachomatis

Strict human pathogen with many serotypes (A-L) Different serotypes correlated with different disease Blindness (trachoma): A, B, Ba, C Urogenital tract disease: D-K Lymphogranuloma venereum: L1, L2, L2a, L2b, L3

HSV 1 and 2: Structure, Growth, Mechanisms of Disease

Structure/Growth: prototype viruses for herpes family Genome encodes for up to 100 proteins Viruses share 50% sequence homology Culture in vitro in lots of cells of different species Release high level of infectious extracellular virus Animal models for infectivity, pathogenesis MOD: HSV1 infection earlier, more common than HSV2 Transmission from direct close contact Infection causes cytopathology Avoidance of immune system (cell-cell spread, latency) Reactivation from latency: stress, immunosuppression Cell-mediated immunity: resolution of infection, immunopathology

Acyclovir/Valacyclovir: Structure, Mechanism, Indications

Structure: requires triphosphorylation for activity. Initial phosphorylation needs viral thymidine kinase, next two from cellular kinases. VACV is L-valine ester prodrug of ACV Mechanism: ACV-TP is incorporated into viral DNA by viral DNA polymerase and terminates DNA synthesis VACV is hydrolized by VACVase to ACV (>99% conversion) Once converted has all same properties, 60% BA compared to 10-20% for oral ACV Indications: Treatment of HSV and VZV infection Suppression of recurrent HSV infections Prophylaxis against HSV for transplant recipients, against CMV for stem cell transplant recipients

Enterobacteriaceae: Structure, Antigens, Virulence

Structure: single double stranded chromosome, ribosomes, inner cytoplasmic membrane with phospholipid/protein structure, peptidoglycan layer with periplasmic space, and complex outer layer with LPS, lipoproteins, porins, and organelles (flagella, fimbriae, adhesins, sex pili) Antigens: O- somatic antigens H- flagellar antigens K- capsular antigens VI- subtypes of capsular antigens Virulence Factors: 1. cytotoxins/hemolysins destroy cells 2. Enterotoxins associated with watery diarrhea 3. Endotoxin- LPS of outer membrane of gram- organisms 4. Capsules- protects from antibiotics 5. Plasmids- can code for drug resistance or enterotoxins

Fluoroquinolones

Synthetic antimicrobials, broad spectrum bactericidals Especially against gram- MOA: inhibit DNA gyrase (topo2), essential for synthesis of bacterial DNA. Di/trivalent ions (Zn,Fe,Mg,Al,Ca) decrease absorption and should be avoided around dosing Ciprofloxacin most active against gram-, including pseudomonas. Fluoroquinolones are also effective against gram+ staph and strep and some penicillinase producers, but not MRSA. Indicated for urinary, respiratory, abdominal, bone, soft tissue infections. Newer drugs (gemifloxacin/moxifloxacin) have increased activity against gram+, anaerobic, and resistant bacteria SE include HA, dizziness, GI, and rash (some related to photosensitivity). Not for children or pregnant women. Tendonitis, ruptured tendons, joint pain can occur.

Piperacillin/Tazobactam

Tazobactam is penicillanic acid sulfone b-lactamase inhibitor with poor chromosomal b-lactamase activity in enterobacteriaceae but good activity against plasmid b-lactamases, including extended spectrum class. With piperacillin (Zosyn) does not inc activity of piperacillin against P aeruginosa because resistance is due to chromosomal b-lactamases or to decreased permeability of piperacillin. Current dose is less than piperacillin dose alone so some concern that might be ineffective against some pseudomonas piperacillin can handle on its own. Same spectrum as Timentin

Treponema

Thin, spiral, gram-, unable to be cultured Microaerophilic or anaerobic, extremely O sensitive T. pallidum is causative agent of syphilis, found worldwide, third most common bacterial STI (chlamydia, gonorrhea) Infections had been going down since PCN invention in 40s, increases observed during changes in sexual practices Rate has steadily increased since 2000, with 50k new cases in 2012 (15k highly infectious). Humans only reservoir

B. anthracis: toxins, protein capsule

Three proteins assemble in binary to create 2 distinct toxins A is active component, B is binding component, B has no toxic activity but is necessary for delivery of A to cell Anthrax symptoms from toxins, need both A and B A: Lethal Factor: Zn metalloproteinase binds to/cleaves MAPK, leading to cell death. Induces IL1B and TNFa from macrophages Edema Factor: adenylate cyclase, produces elevated cAMP causing fluid and electrolyte loss (edema). B: Protective Antigen: binds to a receptor on cell surfaces in brain, heart, intestine, lung, muscle, pancreas, macrophage. Allows for endocytosis of toxin via pore in vesicle. Immunogenic, ABs stop toxin by preventing attachment. LF+PA=LT, EF+PA=ET Protein capsule- made up of poly D-glutamic acid, found in clinical specimens but not made in vitro. Anti phagocytic.

Picornavirus: Pathogenesis

Transmission: aerosol or oral-fecal Target cells: primary- mucosal, lymphoid in tonsils/pharynx secondary: anywhere, depends on tropism Generally have viremic phase (rhinoviruses do not as they can only replicate at 33C) Disease caused by: destruction of host cell during replication (little contribution from immune response) Pathogenesis enhanced by protein capsid, fast replication

C. diphtheriae: Lab diagnosis, Treatment

Treatment initiated without lab diagnosis as they are not definitive for at least 1w. ID based on Elek's test which detects exotoxin Vaccination: toxoid part of DTaP for children and Tdap adult booster (needed every 10y) Diphtheria Anti-Toxin: early admin essential to neutralize toxin before it is bound by cell. Once cell internalizes toxin, cell death is inevitable Antibiotics: penicillin, erythromycin Isolation recommended, even though person-person transmission rare. Closely monitor those in close contact

Acyclovir/Valacyclovir: Treatment, Dosage, Interactions

Treatment: HSV- genital or orolabial: oral or IV ACV, oral only VACV. VZV same concept, but higher doses Dose modifications: excreted via glomerular filtration and tubular secretion, dose modification necessary with RI (dec dose or interval, much like aminoglycosides) Interactions: none

Flaviviruses: Yellow Fever: Treatment, Prevention, Control

Treatment: none, only supportive therapy Prevention: live attenuated Theiler 17D vaccine is effective and affordable. Single dose gives 10y protection. Coverage is low in high risk areas, so prompt recognition and control of outbreaks using mass immunization is critical to prevent epidemics. Pregnant women and infants only vaccinated if epidemic. Severe egg allergies and severe immunodeficiencies should not be vaccinated Control: general mosquito control

Flaviviruses: Zika: Treatment, Prevention, Control, Diagnosis

Treatment: supportive, no vaccine. Safe sex should be strictly followed. Couples who have previously tested positive should wait 6m before trying to conceive. If you have travelled to area with active infections should wait 8w before unprotected sex. Diagnosis: RT-PCR within 14d of illness onset or serology of IgM ABs up to 12w after onset. Largely performed in US at CDC. Recommended for symptomatic people living in or with recent travel to Zika area, also for people who have had unprotected sex with man confirmed to have virus. Nationally notifiable condition

Sulfonamide Combination Therapy

Trimethoprim-sulfamethoxazole (Septra/Bactrim) has broad spectrum antimicrobial action. Trimethoprim inhibits DHFR which interferes with further synthesis of folic acid to active form Together they are synergistic and very effective against broad spectrum of gram -/+ bacteria. Used as alternative to penicillins and cephalosporins for respirator, urinary, GI, and systemic infections DOC for p jiroveci, and ear/sinus/pneumonial infections from h flu.

Quinolone Derivatives: Primaquine

Used for elimination of exoerythrocytic (hepatic) forms of parasite Toxicity: hemolysis in G6PD deficient people, primaruly Africans and Caucasians of Mediterranean descent Methemoglobinemia in NADH-methemoglobin reductase deficient people Used as a radical cure of vivax and ovale

F. Tularensis: Disease

Tularemia 1. Ulcero-glandular is most common form, through direct contact with infected animals. Primary lesion at point of entry, reaches LN and they become swollen/tender. Spread via blood to cause lesions in other organs, esp liver/spleen, and sometimes lungs. Primary lesion usually small ulcer, making this an ulcer-node syndrome like plague 2. Pneumonic tularemia if reach lungs, can spread person to person 3. Typhoidal from ingestion of contaminated food/water 4. One of most virulent organisms known to man 5. Virulence from ability to grow and survive in monocytes, making antibiotic treatment difficult

Picornavirus: Vaccines

Two kinds of vaccines against poliovirus 1. Inactivated virus (Salk): IM, elicits no duodenal IgA, requires boosters 2. Live attenuated (Sabin): oral, 5 times Vaccines infect contacts- a booster effect Induces duodenal IgA, may be inhibited by other enterovirus replicating in gut Rare mutations in vaccine virus result in revertant that can cause poliomyelitis Immunocompromised should not receive any live vaccine Both vaccines induce antibodies against all 3 serotypes of poliovirus

Genetic Interactions: Complementation

Two mutant viruses with different mutant genes infect same cell, can complement each other's defect Each makes the protein the other lacks Results in higher virus yield Each single particle still contains only one or the other genome Complementation occurs between mutants in different genes Analysis can determine functions of different viral proteins, used in engineered applications like delivery of genes for gene therapy

HHV6: General, Infection

Two variants based on sequence differences of up to 25% in some areas (A and B) In vivo isolation from peripheral blood lymphocytes In vitro in cord blood lymphocytes and T cell line Infection: infects lymphocytes, monocytes, epithelial cells, endothelial cells, neurons Can replicated when cell is activated, controlled by cell-mediated immunity Establishes latency in T cells and monocytes

Benzimidazoles

Used for Nematodal infection 1. Albendazole: for luminal and tissue nematodes except those causing filariasis, also C. philippinensis, toxocara, T. spiralis. Toxicity minimal in short term, mild reversible hepatotoxicity in long term 2. Mebendazole: not available in US, not as well absorbed as (1). Effective for nematodes: trichiuris trichiura, enterobius vermicularis, trichinella spiralis, ascaris lumbricoides, capillaria philippensis, necator americanus, ancylostoma duodenale. Transient abdominal pain/diarrhea in pts with large parasite burden 3. Thiabendazole: side effects in 50%, used topically for cutaneous larva migrans from ancylostoma 4. Triclabendazole: fasciola hepatica infections

Quinolone Derivatives: Chloroquine

Used for sensitive falciparum and all other forms Resistance: mediated by chromosomal mutation that allows parasite to transport drug out of intraparasitic compartment Widespread resistance to falciparum, some to vivax Toxicity: very well tolerated HA, dizziness, blurred vision, local GI intolerance, confusion, fatigue Rare: exfoliative dermatosis, permanent retinal damage with prolonged use, exacerbation of psoriasis Relatively contraindicated with psoriasis, retinal disease, porphyria

Malaria Drugs: Artemisinin Derivatives

Used in Chinese medicine, re-discovered on archaeological dig, 2015 Nobel for application to malaria Clears parasite rapidly, 10-100x more potent than other drugs Activity against all steps of life cycle MOA: incompletely understood, maybe activated by cleavage of endoperoxidase by heme, leading to free radicals, leading to susceptible protein damage 124 artemisinin binding protein targets identified

Quinolone Derivatives: Mefloquine

Used in treatment of all types except knowlesi, prophylactic agent for travelers Toxicity: Dose related GI (nausea) and neuropsych (HA, seizures, disturbed sleep, acute psychosis) side effects Avoid with quinine, beta blockers (cardiac arrhythmias, cardiac arrest), history of seizures, psych disorders

Moraxella Catarrhalis

Used to be Neisseria catarrhalis Respiratory tract pathogen, associated with tracheobronchitis (especially in pts with chronic lung disease), sinusitis, and OM Increasing incidence of penicillin resistance

Multiple Additive Genes for Same Disease

Usually located in different chromosomal areas Need some total number of mutations to get disease Example: Bardet-Biedl Pigmentary retinal degeneration, obesity, mental retardation, and progressive spastic ataxia 6 genes, need mutation on both chromosomes for 1 gene and a third mutation on one of the others Many combinations exist and some people will get disease with mutations in only one gene

T. pallidum: Disease

Usually via sexual contact, can be transfusion or placental 1. Primary syphilis: one or more painless skin lesions (chancres) at site of penetration within 3w. Organisms multiply locally to create chancre, can also disseminate in blood. Chancre colonized by active infections spirochetes and heals on its own in 2-6w 2. Secondary: 2-24w after chancre heals. Flu-like symptoms (ST, HA, myalgia, fever, anorexia, lymphadenopathy, maculocutaneous rash covering skin inc palms/soles). Raised lesions (condylomata) on genitalia, these and rash are highly infectious. Resolve within 6w and pts either go into remission, enter latent stage, or progress to tertiary 3. Tertiary: 1/3 untreated patients. Asymptomatic period can be years-decades. Devastating destruction of any tissue. Gummas (granulomatous lesions) found in bone, skin, brain, etc. Neurosyphilis, CV syphilis, and other destruction

Togaviridae: Equine Encephalitis

Venezuelan, Western, Eastern Major reservoir is birds, Culex mosquitoes are vectors. Humans and horses are both dead end hosts. All 3 viruses are rare. EEE mostly in SE US, 15/yr. WEE mostly W of Mississippi River, 200/yr. VEE in CA/SA/TX, several thousand per year mostly outside US Signs/Symptoms: disease in 25% infected children, 2% infected adults. Encephalitic phase often fatal. Initial systemic phase: fevers, chills, aches for 1-2d. Severe encephalitic phase: drowsiness, tremor, seizures. EEE especially severe in children (70% mortality). WEE less severe (10%) Treatment: diagnosis by virus recovery in blood or brain or CSF of fatal cases, can also be made by serology. Tx is supportive, no vaccination.

Bordatella

Very small coccobacilli, gram-, strictly aerobic B. pertussis: causes whooping cough Solely human illness. Vaccine effective but still problem worldwide. Used to be a pediatric illness but now many cases in adults who sometimes get chronic illness lasting months Very difficult to grow, so diagnosis usually via ELISA testing for antibodies, or via nucleic acid amplification assay Syndrome: 7-10d incubation, 1-2w catarrhal phase, 2-4w paroxysmal, 3-4w convalescence B. parapertussis causes similar, milder illness

Francisella Tularensis

Very small, gram- pleomorphic rod Strictly aerobic, needs high concentration of cysteine Animal reservoir is mostly rabbits: transmitted animal to animal by fleas and ticks. In ticks, passed via ovaries to eggs and through larvae/nymph stages to adult tick, which transmits the disease Causes tularemia Usually diagnosed serologically because of the innate danger to lab workers

Enterobacteriaceae: Niche, Disease

Widely distributed in soil, plants, intesinal flora of animals Some are part of normal intestinal microflora (E coli), colonization of humans inc with illness, hospitalization Most common gram- rods in lab. Diseases include: 1. Diarrhea (salmonella, shigella, yersinia, some e coli) 2. Abdominal abscess (e coli, klebsiella, enterobacter, others can colonize gut- rupture of intestine with fecal contamination and abscess formation. Usually polymicrobic) 3. UTI- over 70% of UTIs from this family (e coli, proteus) 4. Pneumonia- frequent causes in hospitalized pts. Klebsiella pneumoniae may be a CA process in debilitate pts, eg alcoholics 5. Wound infection, bacteremia, meningitis possible

Anticipation

Worsening of disease manifestations with earlier onset and/or inc frequency over generations Basis for anticipation is unstable trinucleotide repeat Only noted in man, and man is only organism to have unstable TNR sequences All unstable TNR cause neurological diseases, cause disease by all different mechanisms