Microbiology

Bacterial O2 requirements

Aerobes = grow only in the presence of oxygen EX: Pseudomonas aeruginosa Facultative anaerobes = can grow in presence or absence of oxygen EX: E. coli Aerotolerants = indifferent to oxygen - can grow in presence or absence but doesn't matter since metabolism is always fermentation Strict anaerobes = only grow in absence of oxygen Ex: clostridium spp

Prokaryotes

All bacteria are prokaryotes. They are less complex organisms. They divide by the process of binary fission which is a simple division that results in two identical cells. Flagella = used for motility, powered by proton motive force gradient (as opposed to ATP in eukaryotes) Fimbriae/pili = cilia like structures involved in adherence or exchange of genetic material or locomotion in prokaryotes Bacterial cell walls are composed of peptidoglycan! Bacterial cell membranes lack cholesterol Prokaryotes usually have 1 single, circular chromosome without histones/introns DON'T HAVE A NUCLEUS 70S ribosome unique to bacteria

Antigenic variation Antigenic drift vs Antigenic shift

Antigenic variation = a pathogen's purposeful variation of surface proteins to evade the host's adaptive immune response Driven by natural selection! - random mutations occur during replication - mutations that happen to change the surface antigens and help the pathogen survive are selected for! Antigenic drift = gradual, natural small changes - usually caused by natural mutations inside of a host - drift can make things more pathogenic by mutating proteins to make a virus more transmissible, more able to undergo fusion with different cell types, etc Antigenic shift = abrupt, drastic changes that usually occur after mixing of multiple strains in an animal vessel - when 2 influenza viruses are present within the same host cell and exchange RNA segments (reassortment) - shift is like a completely new HA that has never been seen by humans (that comes from a bird or pig virus, etc)

Beta lactam : monobactams

Aztreonam - Usually used against P.aeruginosa but more than 50% of P. aeruginosa strains from UPMC are resistant

Horizontal gene transfer (HGT) background

Bacteria normally reproduce through binary fission so their offspring are clones of themselves (vertical gene transfer - transferring vertically between generations) *Horizontal gene transfer is the transfer of genetic material to other bacteria that are NOT the offspring - transferring horizontally to members of the same generation Basically ~bacterial sex~ *Goal is to transfer novel genes that permit adaptation to the environment (antibiotic resistance, sex genes, etc)

Other mechanisms of resistance

Biofilms - bacteria living in multicellular communities are triggered to produce and coat themselves in a gelatinous secretion (biofilm) that can be nearly impermeable to antibiotics Persistor cells - some bacteria undergo random variations in gene expression which cause them to be metabolically dormant and stress intolerant (almost like spore forming) - they are more resistant to antibiotics and can stick around and re-surge the infection even after most of the other cells are wiped out via treatment

Hepatitis A virus

Biologic characteristics - picornavirus (+RNA), nonenveloped Reservoir and transmission - reservoir = humans - transmitted via fecal oral route, often contaminated food, raw shellfish, or water - more common in developing countries Pathogenesis - virus replicates in gut - less than 50% of ppl develop symptoms after 2-4 weeks - if not enough neutralizing antibodies are present, HAV invades blood, spreads to liver, produces acute inflammatory disease (Jaundice) - liver damage occurs via inflammatory response *Not a chronic, longterm illness (usually resolves after 2 mo) - people are immune after 1 infection - can be fatal in people with existing liver disease Prevention - vaccine given to infants at 12 mo and travelers

Antimicrobial resistance background

By 2050, 10million deaths will be attributable to AMR (more than cancer) MDR = multi drug resistant XDR = extensively drug resistant *These have few (and sometimes none) effective antimicrobial treatments How did resistance arise? *Resistance arose long before conventional antibiotics were developed (in fact, most antimicrobial compounds were not invented by humans) **This is because microorganisms created antibiotics and resistance mechanisms to outcompete each other!** *The reason AMR is such a huge problem today is that the overuse of antibiotics is putting a huge selective pressure on bacteria, so they have to evolve resistance to survive!* *Resistant bacteria can survive better in today's environment of high antibiotic use, and thus pass on their resistance genes, leading to more resistance *The most potent catalyst of AMR is antibiotic use itself - AMR is a genetic trait that can be passed via Vertical gene transfer (binary fission) or Horizontal gene transfer (sex)

Listeria monocytogenes immune evasion

CHARACTERISTICS *Intracellular bacteria, gram pos rod - catalase positive, beta hemolytic RESERVOIR/TRANSMISSION - food borne pathogen found in soil, decaying vegetation, digestive tract of animals (cattle) - can cross placenta & lead to spontaneous abortion, stilbirth, premature labor, neonatal meningitis VIRULENCE FACTORS - Listerolysin O = toxin that allows it to be released from the phagosome and enter the cytoplasm - ActinA = controls host actin polymerization that can propel bacteria into neighboring cell (allows bacteria to spread without encountering immune cells) PATHOGENESIS - common cause of food borne illness - causes meningitis in newborns!

Legionella pneumophilia (Legionnaire's disease)

CHARACTERISTICS - gram neg coccobacillus (small rod) - intracellular bacteria (hard to see on gram stain) - has a single polar flagellum and many pili RESERVOIR/TRANSMISSION - Lives within amoebae and protozoa in water! - is chlorine tolerant so can survive water treatment - organism is transmitted through aerosolized contaminated water - inhalation/aspiration *grows in humidifiers, air conditioners, etc! PATHOGENESIS - Legionnaire's disease = pneumonia caused by Legionella pneumophilia (1-10% of CAP)

Pseudomonas aeruginosa

CHARACTERISTICS - gram negative, anaerobic, motile rod - can make blue/green pigments - oxidase positive - often antibiotic resistant VIRULENCE FACTORS - Exotoxin A = causes necrosis - Proteases/elastases = cause tissue damage - Leucocidin = inhibits/kills WBCs - Endotoxin = promotes shock (but weaker than most) - Capsule = antiphagocytic, important for biofilms - Pili = adhesion TRANSMISSION/RESERVOIR - ubiquitous in the environment - often a normal colonizer of the skin but can be an opportunistic pathogen - mainly causes disease through wounds, incisions, burns, catheters DISEASE - opportunistic pathogen! in healthy patients, WBCs can fight off disease - septicemia leads to shock - particularly important in cystic fibrosis infections, burns, and catheters/IV lines

Category A: anthrax

CHARACTERISTICS - gram pos rod, non-hemolytic - rods form a chain!! (unusual) * obligate aerobe! (requires oxygen) * Forms spores that can last in soil for years! - comet's tail appearance (kind of tear drop shaped) - occurs worldwide - Reservoir = sheep, goats, cattle INFECTION - naturally occurring disease of the skin - Cutaneous (95%), inhalation (5%) - occurs after exposure to infected animals/animal products - spores germinate, bacteria multiply and produce a toxin - causes severe inflammation of the lymph nodes VIRULENCE FACTORS - capsule = protects it from phagocytosis - Exotoxins = Edema toxin increases cAMP and interferes with cellular function / Lethal toxin zinc metalloprotease that cleaves/inactivates kinases and interferes with signal transduction - this causes tissue necrosis and leads to the black eschars -both toxins have to be present to cause disease! Cutaneous anthrax symptoms - spores enter damaged skin - incubation period of 1-7 days - pruritic papule at site, black eschar, - lesion is usually painless!! - enlarged lymph nodes around region of infection Gastrointestinal anthrax (rare) - can come from uncooked meat - 40% mortality - 1-5 day incubation period, followed by nausea, vomiting, fever, severe abdominal pain, hematemesis, ascites, bloody diarrhea Inhalation anthrax (wool sorter's disease) - 45% mortality - incubation period of 4-6 days, followed by flu-like illness with no rhinorrhea, bloody pleural effusions, mediastinal/pulmonary hemorrhage - dissemination can result in hemorrhagic meningitis (usually always fatal) Diagnosis - blood cultures turn positive in 6-24hr - nasal swab culture can be used to test for exposure - PCR/immunohisto/anthrax IgM test Transmission - no person to person transmission - can be spread by contact with open wound - no special isolation required!! Treatment - multiple antibiotics at once (since resistance can be engineered) - antibiotics given for 60 days (due to potential of spores to regenerate) - antibody based therapy - Post exposure prophylaxis (3 doses of vaccine and 60 days antibiotics)

General classification of viruses

DNA VIRUSES - ss DNA - ds DNA RNA VIRUSES - ssRNA --- Plus strand (+RNA = retroviruses) --- Minus strand (-RNA) - dsRNA

How is antibiotic sensitivity tested in a lab?

Disk diffusion test = bacteria are plated in a lawn and disks of antibiotics are dropped onto the plate and incubated - diameter of zone of inhibition is measured (the smaller the zone, the more resistance) E-test = a strip that has a gradient concentration of antibiotics - lay it on the plate and zone of inhibition can be read as min inhibitory conc (MIC) of that organism Genetic testing = PCR amplification to identify the presence of known resistance genes or mutations in genes encoding known targets

Beta lactam: carbapenems

Ertapenem Meropenem Meropenem+vaborbactam CRE = carbapenem resistant enterobacteriaceae - predominant mechanism of resistance is production of carbapenemase enzymes (KPC, VIM,) which hydrolyze all other B lactams *CREs are usually resistant to almost all other antimicrobials - vaborbactam is an agent that inhibits KPC enzyme, removing resistance

Hepatitis B/C antivirals

Hepatitis B (B=better) - most acute infections are not treated bc they will resolve on their own - treatment is reserved for chronic HBV (lamivudine, entecavir, emtricitabine, tenofovir) Hepatitis C (C=chronic) - goal of treatment is to reduce mortality, complications related to cirrhosis, and achieve virology cure/undetectable viral RNA - standard treatment used to be interferon and ribavirin for at least 24 weeks (had a lot of side effects and only 50% of patients followed through) - now we use direct acting antivirals which are well tolerated and associated with cure rates close to 100% INDIRECT ANTIVIRALS Interferon = cytokine that inhibits viral protein synthesis. Synthetic form of this can be given as drug but causes flu-like symptoms so ppl don't like it Ribavirin = guanosine nucleoside analog DIRECT ANTIVIRALS - target specific proteins of hep C virus - Protease inhibitors, polymerase inhibitors, etc - Ledipasvir-sofosbuvir (Harvoni) (most commonly used regimen for HCV1 infection)

Integrons / transposons

Integrons = mobile DNA elements encoding an integrase (allows foreign DNA to be integrated into host chromosome) - may carry additional genes such as those encoding antibiotic resistance Transposons (Tn) = a "jumping gene" that can repeatedly insert at many different sites in the genome - transposons generally carry: one or more drug resistance genes, toxins, virulence factors, etc *Transposons are always found as an integrated part of the genome Insertion sequences (smallest) = small (750-1K base pairs) that only carry genes required for their movement Transposons = larger than 5k bp, carry genes required for their movement as well as toxicity genes Composite = transposons that carry insertion sequences at their ends, typically carrying a resistance gene

Structure of a transposon / mechanism of transposition

Mechanism: - can be either replicative or conservative - replicative = semiconservative replication of transposon resulting in duplication of the Tn element - conservative - results in simple insertion of transposon at target site - Transposition can take place within the same genome or between 2 genomes - Many R factors carry many transposons with many resistance genes Structure: - tnpA = gene encoding for transposes protein - tnpR = gene encoding for repressor of transposition - Ampr = gene that encodes B lactamase, making bacteria resistant to ampicillin - inverted repeats = DNA sequence at one end of transposon and repeated at the other in an inverted orientation (sticky ends!) necessary for transposition

LPS

More on LPS **LPS is an inflamm mediator, recognized by TLR4 - LPS is composed of 3 regions: O antigen - (repetitive oligosaccharide making up a chain) - O antigen helps resist compliment Lipid A (connects to outer membrane) - responsible for barrier properties of outer memb - Known as ENDOTOXIN - Unique to gram neg bacteria! **Endotoxic shock core polysaccharide (links lipid a and O antigen) - critical for growth

#3 = decreased permeability of drug

Most common way to reduce permeability: loss of porins - porins are proteins in gram neg bacteria that facilitate transfer of molecules across cell membranes by forming tunnels - many antibiotics enter via these porins, so modification can prevent or slow their entrance into the cell - plays a big role in carbapenem resistance for Pseudomonas aeruginosa

General advice for traveling patients

Most travelers illnesses are self limiting - 60% of travelers with diarrhea are better within 48hr Some expats, immigrants, refugees, and long-term travelers may benefit from a post travel examination to screen for parasites or TB

Antigenic variation of Neisseria gonorrhoeae Antigenic variation of Trypanosoma brucei

Neisseria gonorrhoeae - gram negative diplococci with pili *Pili are an important virulence factor for attachment and can undergo phase and antigenic variation - phase variation = on/off expression of that gene/protein - antigenic variation = mutations in that gene Trypanosoma brucei - causative agent of African sleeping sickness (trypanosomiasis) - is a parasitic organism: flagellated protozoan parasite transmitted by tsetse fly! - parasites survive in bloodstream and must avoid antibodies - do so by having antigenic variations of variable surface glycoproteins (VSGs) - when antibodies are raised against one VSG, new ones are selected for and flourish

Medically important protozoa

Protozoa = single-celled microscopic animals, which include amoebas, flagellates, ciliates, sporozoans, and many other forms Entamoeba histolytica = Amoeba! - microscopic, unicellular - transmitted via feces (contaminated food or water) - Cyst (gets excreted into environment), gets ingested, breaks open in gut to become a trophozoite, attaches to colonic mucosa and can penetrate it, reaching portal circulation and forming an amebic liver abscess - Amebic dysentery (bloody diarrhea) - Treatment: Metronidazole/ paromomycin Acanthamoeba - amoebic infection of the cornea due to contaminated contact solution or swimming with contacts in (A cantha see ya!) Naegleria fowleri - Brain eating amoeba! - found in warm freshwater (lakes, hot springs) and soil (Fow-nd in water) - enters nose when swimming or diving, can reach brain through cribriform plate where it causes a fatal meningoencephalitis *No treatment! Giardia lamblia - causes diarrhea (Gee diarrhea) Cryptosporidium spp - causes diarrhea Microsporidia - mainly causes diarrhea and is mostly a problem in immunosuppressed ppl with HIV Trichomonas vaginalis - one of the most common STIs (men are asymptomatic) - Tranmission is infected female -> male -> uninfected female - large amt of bubbly/foamy vaginal discharge, fish odor - metronidazole treatment (treat partner too!) Plasmodium spp - malaria!! Babesia - infects RBCs like malaria - tested by blood smear - people with functional asplenia are at high risk - part of lifecycle occurs in mice, ticks are vectors! - common in NE (nantucket, martha's vineyard, PA) - treatment = clindamycin and quinine. atovaquone & azithromycin * (RBCs in the hampton's) Leishmania spp - transmitted by sandflies - common in central/south america & middle east/africa - Cutaneous leishmaniasis / visceral leishmaniasis (enlarged liver/spleen) Trypanosoma spp - Causes Chagas disease (transmitted by kissing bugs) - American trypanosomiasis symptoms = esophageal/colon dysmotility + cardiomyopathy - can be transmitted through blood transfusion (1:5000 donations in Florida/california are positive) - transmitted mother to child - African trypanosomiasis is transmitted by tsetse fly and causes sleeping sickness (meningoencephalitis) Toxoplasma gondii - manifests as eye infections (retinitis) through perinatal transmission and also reactivation encephalitis

Common traveler infections

TRAVELER'S DIARRHEA - can be bacterial, viral, parasitic - 50-75% of cases are bacterial, half of which are due to E. coli (followed by Salmonella, campylobacter, shigella, bacillus fragilis respectively) - Viral diarrhea makes up 5-20% (mostly norovirus and rotavirus) - parasitic diarrhea 0-5% (Giardia, cryptosporidium) - common antibiotics = floroquinolones (cipro), azithromycin, doxycycline, rifaximin MALARIA - Africa > SE asia > SA - immigrants may wrongly believe they are immune to malaria (but within years of not being exposed, this protective effect disappears) TYPHOID FEVER - caused by Salmonella typhi - fever, malaise, not often diarrhea - most common in india, SA, asia, Africa - vaccine (injected/oral) has 50-70% efficacy and only lasts 2-5 years respectively - treatment is bacterium, amoxicillin, floroquinolones YELLOW FEVER - rare but often fatal illness characterized by jaundice! - CFR is 20-50%! - occurs within 15degrees of equator - immunization lasts a lifetime

Conjugation

"Bacterial sex" - Gene transfer that requires direct contact between cells via a sex pili known as Factor F An F+ bacteria is said to be male (bc it can encode for the sex pillus) An F- bacteria is said to be female Direction of transfer is always F+ -> F- *At the end of the process, both cells will be F+! The F factor can exist as: - an independent plasmid - an episome (integrated into host chromosome) - an independent plasmid containing host genes *This results in some additional genetic material getting transferred along with the F factor - Donor transfers a single strand of the F factor gene to the recipient

Fungi vs bacteria (main differentiating features)

(see figure) Fungi: - are eukaryotes - are not anaerobic (human pathogens anyway) - are chemotrophic (secrete enzymes that degrade organic substrates into soluble nutrients which they then absorb) - lack chloroplasts - are nonmotile (spread by wind, water, contact) - reproduce sexually(spores) or asexually (mitosis) - have a rigid cell wall , cytoplasmic membrane is made of sterols Constituents of fungal cell wall: - Mannan = mannose based polymer - Glucans = form fibrils which increase strength of fungal wall - Chitin = structural support

4 major mechanisms of antimicrobial resistance

*all mechanisms of resistance arise from random mutation, that is then selected for if it provides a survival advantage 1. Inactivation (destroy or inactivate the drug) 2. Target protection (modifying the drug's target so that it still fulfills its biological function but does not allow the drug to bind) 3. Decreased permeability (decreased ability of drug to enter the cell and reach target) 4. Increased efflux (presence of pumps which remove antibiotics from cell and decrease amt of drug present at site of action)

Virus lifecycle

1. Initiation Phase Attachment - a protein on the virus is recognized by a cell surface receptor (viral receptor) Penetration - movement of the viral particle/nucleocapsid through the cell plasma membrane - For enveloped viruses: the viral lipid envelope fuses with the cell membrane, releasing the nucleocapsid/DNA - Or can occur via receptor mediated endocytosis (for both enveloped or non-enveloped viruses) Uncoating - release of the viral genome from the capsid 2. Replication Phase Genome expression - synthesis of viral proteins via host machinery Genome replication - synthesis of 100K+ copies of viral nucleic acid (DNA/RNA) 3. Release Phase Assembly - viral capsid + viral genome + other associated proteins are assembled (can occur in inclusion bodies in the nucleus or cytoplasm) Release/egress - exiting the cell - Enveloped viruses = all derive their envelopes from the cellular membrane, either exit by budding through plasma membrane OR fusion of secretory vesicles - Nonenveloped viruses = usually exit by cell lysis Each cell produces hundreds of thousands of new viruses which can then go on to infect other cells

General genome replication of viruses

All viruses need host enzymes to synthesize their proteins BUT NOT all viruses need host machinery to synthesize their DNA - they all encode their own polymerases EXCEPT parvovirus (the only ssDNA virus) which uses host DNA pol LOCATION OF REPLICATION - Most DNA viruses replicate and assemble in the nucleus (exception: pox viruses, cytoplasm bc they encode all of the DNA/RNA enzymes needed) - Most RNA viruses replicate/assemble in cytoplasm (exception: influenza (-RNA) replicate their genomes and make mRNAs in the nucleus) *Viral replication has a high mutation rate (essential for evolution - immune evasion/drug resistance) - polymerases are very error prone (especially RNA dependent RNA polymerases which lack proofreading) In viral replication: 1. Genome synthesis - The genome has to be replicated into its original form to provide genetic material for new viruses 2. Protein synthesis - The genome has to be converted into +mRNA so that it can be transcribed by host machinery into viral proteins!

Clostridium botulinum

CHARACTERISTICS - gram positive spore forming rod RESERVOIR/TRANSMISSION - found in soil around the world - particularly common in Alaska VIRULENCE FACTORS - Botulinum toxin - enters neuron and causes descending, flaccid paralysis - Spores - heat resistance of bacteria (but toxin is heat sensitive) ENTRY - ingestion of contaminated foods (can be due to ingestion of bacteria itself OR ingestion of the toxin - intoxication) - "infant botulism" - GI tract gets colonized by C. botulinum and the toxin gets made in vivo (can happen to adults too) - Wound botulism - bacteria grows in wound and produces toxin en vivo DISEASE - double vision, swallowing difficulties, descending flaccid paralysis, breathing problems - infants with infant botulism first present with constipation - high fatality rate TREATMENT/PREVENTION - botulinum antitoxin, supportive therapy (fatality rate lowered to 10%) - boiling for 5 mins inactivates this toxin *don't feed infants honey!!

Plasmodium falciparum (malaria)

CHARACTERISTICS - protozoan parasite! 4 species: - P. falciparum = tropical regions, infects RBCs of all stages, causes severe malaria w/ no dormant liver stage - P. vivax & P. ovale = found in more temperate zones, latent liver form - P. malariae = causes few serious cases RESERVOIR/TRANSMISSION - Anopheles mosquito is vector - humans can be reinfected multiple times, immunity builds making severe disease less likely PATHOGENESIS - invades RBCs so hides from immune system - cyclic fever is a hallmark - caused when RBCs lyse periodically to release parasites - Symptoms: cyclic fever, nausea, vomiting, fatigue, headaches - cerebral malaria can occur when parasites invade brain - causes brain swelling (high mortality)

Pathogenic fungi

Candida (yeast) - most common opportunistic fungal infection (candida albicans) - this organism is a normal inhabitant of the mouth, skin, gastrointestinal tract, and vagina (a disturbance can cause overgrowth) - Candidiasis can be superficial (thrush, esophagus, vagina, diaper rash), or deep (bloodstream, liver, brain, heart, kidneys, etc) - invasive candidiasis is usually a disease of the severely ill Cryptococcus neoformans (yeast) *C. neoformans and C. gattii are found in nature and are typically inhaled into the lungs and migrate to the CNS (can cause meningoencephalitis - cryptococcal meningitis) - most typically opportunistic infections seen in patients with AIDS and other immunosuppressive conditions (C. gattii is rarer and usually associated with normal hosts) - polysaccharide capsule protects against phagocytosis and also produces melanin which can prevent oxidative stress - mixing india ink with body fluids (CSF) rapidly identifies the encapsulated yeasts Aspergillus (mold) - ubiquitous in nature and found in large numbers in rotting plants - Mostly respiratory tract infections (sinusitis, airway colonization, allergic bronchopulmonary aspergillosis, invasive pulmonary aspergillosis, disseminated aspergillosis) - Route of infection: inhalation of spores, local lung infection, entry into blood vessels, dissemination to other sites - Diagnosis: growth from respiratory specimens, detection of branching hyphae in resected tissue Mucor, Absidial, Rhizopus, Rhizomucor (zygomycoses) - enter body via respiratory tract and have high affinity for vascular structures, causing thrombosis and infarction - cause infections in patients with immune deficiencies, metabolic disorders (diabetes), and iron rich states (hemochromatosis) - can invade nose -> sinuses -> brain Sporotrichosis - Sporothrix schenckii most commonly occurs in people who have exposure to soil or infected plant products - common presentation is a non-healing, inflamed nodule that doesn't respond to antibacterials - thermally dimorphic fungus that grows as mold at ambient temperatures and small budding yeast in tissue Dermatophytes (mold) - cutaneous fungal infec. - infect the superficial keratin layer of the skin using keratin as a nutritional source - unable to grow at 37 degrees or in the presence of serum (so can only grow on skin) - Zoophilic dermatophytes = ring worm / tinea capitis (microsporum canis) - Geophilic (soil) - Anthropophilic = most common human dermatophytes, athlete's foot/jock itch (trichophyton rubrum) - onychomycosis (fungal infections of the nails) - Treatment = imidazole (topical) or azoles (oral) Pneumocystis jiroveci - common cause of pneumonia in immunocompromised individuals

More details on Capsule, Flagella, Fimbriae/pili

Capsule (glycocalyx) - found on some bacteria (gram pos and neg) - consists of polysaccharides/polypeptides/lipids - Divided into 2 types: capsule & slime layer *Main difference is that capsule is more firmly attached to cell than slime layer is - Capsule = virulence factor, hides most bacterial antigens so it is hidden from host, barrier to phagocytosis by blocking complement, prevents drying out, composed of repeating carbohydrates - Slime layer = exopolysaccharide (EPS), loosely attached to cell surface, slime will drip off, hard to stain since mostly carbohydrate Flagella - long whip like structures responsible for cell movement based on chemotaxis - composed of flagellin protein (aka H antigen) which is recognized by TLR5 Fimbriae aka Pili - Protein based projections used for adherence, locomotion, transfer of genetic material - essential for the formation of biofilms - Sex pilus (F pilus) - Twitching/gliding motility achieved by extension/retraction of pili

Tetanus

Caused by C. tetani (gram pos, spore forming anaerobic rod) - found in soil around the world in the form of spores! Virulence factors - Tetanus neurotoxin (tetanospasmin) inhibits release of inhibitory neurotransmitters resulting in uncontrolled muscle contractions - toxin is produced in wound and then migrates along nerves into the CNS - death results from respiratory failure Entry - enters through a wound or during childbirth via contaminated umbilical stump - spores will germinate if redox potential is low *Can have a long incubation time of up to months while spore waits for proper conditions to grow Treatment/prevention - Treatment = very difficult, give tetanus antitoxin, muscle relaxants, assisted ventilation - Prevention = vaccine against tetanus toxoid, 60k infants die each year due to tetanus, could be prevented if mothers were vaccinated

bacterial shapes

Coccus = sphere Coccobacillus = oval-ish sphere Vibrio = skinny pointed comma shape Bacillus = rod Spirillum = wavy Spirochete = really curly The # of cocci stuck together have different names (streptococci is a long chain, staphylococci is a big clump like a bunch of grapes)

Colonizers / opportunists / pathogens

Colonizers = most occupy the gut and skin - there are more microorganisms than human cells - prevent other more pathogenic bacteria from overtaking our skin/gut - Also ferment carbohydrates, produce essential vitamins (vitamin K) etc Opportunists - normally do not cause harm, but can if they are present in the wrong location - EX: staphylococci normally found on the skin can access the bloodstream via a needle and cause infection Pathogens - organisms that are always harmful - Ex: ebola virus

Concentration/time/exposure dependence of antibiotics

Concentration dependent = higher concs mean more killing *Larger doses given less frequently to maximize peak drug level - ahminoglycosides, daptomycin, metronidazole, fluoroquinolones Time dependent = killing increases with increasing amt of time that antibiotic concentration remains above MIC *Smaller doses given more frequently prolong the time that drug levels remain high - beta lactams, linezolid, trimethoprim, slufamethotoxazole Exposure dependent = area under the curve (aka depends on both time and concentration or total daily exposure) - 100mg given 4x per day or 400mg given 1x per day - All other bactericidal antibiotics (vancomycin)

Endotoxins Exotoxins Enterotoxins Neurotoxins Hemolysins Superantigens

Endotoxin - Endotoxins are produced by Gram-negative bacteria - are cell-associated - part of the actual bacteria that is recognized by host immune system - LPS is an example! - usually heat stable Exotoxins - a toxin that is produced by a bacterium and then released from the cell into the surrounding environment - secreted toxins! - Generally come from gram pos bacteria - usually heat labile Enterotoxins - an exotoxin that acts specifically on the intestinal wall! - usually cause diarrhea, cramps, vomiting Neurotoxins - an exotoxin that affects the nervous system - EX: Clostridium botulinum & Clostridium tetani - Tetanus toxin = causes spastic paralysis, blocks release of inhibitory neurotransmitters - Botulinum toxin = causes flaccid paralysis, blocks release of ACh (no contraction can occur) Hemolysins - a toxin that lyses RBCs (and also WBCs) - most gram positives produce some form Superantigens - cause non-specific activation of the immune system by binding outside of the TCR/MHC synapse, resulting in massive T cell activation and cytokine release! - EX: TSST, staph enterotoxin, strep erythrogenic toxins (scarlet fever) - mostly produced by gram positives

+ and - strands of DNA/RNA convention

Everything is based off of mRNA! POSITIVE STRANDS (sense/coding) (5->3) - mRNA is positive (+) bc it can be immediately translated into protein - that same strand of DNA (will have the exact same order of letters, just Ts instead of Us) is called the positive DNA strand bc if it were mRNA, it would be immediately translated into protein NEGATIVE STRANDS (antisense, template) (3->5) - are the "template strands" - are complimentary to the + strands * Must be copied into + mRNA in order for it to be translated

Growth forms of fungi

Fungi that cause human infections grow as yeasts and molds: Yeasts - round, unicellular organisms 3-10um in diameter - form smooth flat colonies when plated, resemble plated bacteria but are larger and more opaque - reproduce by asexual budding * Candida spp and Cryptococcus neoformans Molds (aka filamentous fungi) - multicellular organisms composed of tubular structures called hyphae (web of hyphae is a mycelium, which makes colonies appear fuzzy!) - grow by branching and longitudinal extension * Aspergillus spp, Mucor, Penicillium marneffei, fusarium, scedosporium Dimorphic fungi - can grow as molds or yeasts depending on environmental conditions - Many human pathogens are thermally dimorphic (grow as molds in ambient temperature and yeasts at or above 37C) EX: histoplasmosis capsulate, blastomyces dermatitis, coccidioides immitis, sporothrix schenckii

Gram pos vs Gram neg bacteria

Gram Positive - THICC Peptidoglycan layer (contains teichoic acids covalently linked to PG, which are not found in GN) - Teichoic acids are antigenic - cytoplasmic membrane - can have pili/flagellum - some GP species can form spores!! (GN bacteria can't!) - spores = dormant bacterial form that resists heat, desiccation, and many chemicals Gram Negative - outer membrane (contains porins and LPS) - peptidoglycan layer (thin, 1-2 layers) - cytoplasmic membrane *Periplasmic space = space between outer membrane and inner cytoplasmic membrane (contains peptidoglycan layer) - can have pili/flagellum - outer membrane acts as a permeability barrier - porins in outer membrane act as diffusion channels to allow small molecules

Hepatitis C virus

HEP C VIRUS - +RNA enveloped virus - is present in the blood as heterogeneous quasi species with multiple sequence isolates (high mutation rate due to error prone polymerase) - 80-90% of ppl develop persistent chronic infection - persistent hepatocyte damage eventually results in cirrhosis or cancer due to scarring or hyper proliferation as repair mechanism TREATMENT - no vaccine available - became curable with direct acting antivirals - cure rates = 95% with an 8-12 week treatment

Campylobacter jejuni

IDENTIFYING CHARACTERISTICS - curved gram neg rod - grows best at 42C (campfire) - oxidase positive (blue ring) TRANSMISSION - reservoir in digestive tract of poultry (can contaminate meat during slaughtering) - 1 million cases per year in US VIRULENCE FACTORS - adhesins for bowel attachment - LPS induces intestinal inflammation - some species make enterotoxin which is like cholera toxin (makes person have more diarrhea so more transmission) PATHOGENESIS - after ingestion, C. jejuni attaches to lower small intestine or (more commonly) upper large intestine - invasion of mucosa induces inflammation, which contributes to symptoms - symptoms appear 1 day to several days after ingestion, usually self resolve after 5 days - symptoms include cramps, bloody diarrhea (sometimes with leukocytes), fever - sequelae can include reactive arthritis/ - Guillan-Barre syndrome - autoimmune response that occurs after certain bacterial/viral infections that causes demyelination of peripheral nerves - causes ascending paralysis

#2 = target protection

In order to resist antibiotics, bacteria modify the target protein of the antibiotic in such a way that it is still biologically useful, but the antibiotic can't bind as effectively! EX: alterations in PBPs lead to B-lactam resistance - AA substitutions in PBPs reduce drug binding affinity - this is what occurs in methicillin-resistant S. aureus (MRSA) EX: alterations in peptidoglycan precursors result in vancomycin resistance - Vancomycin binds to D-ala-D-ala repeat in peptidoglycan precursors which inhibits cross linking - Vancomycin resistant Enterococci (VRE) contain an additional set of genes known as the van operon, which reprograms the synthesis of precursor substrates so that instead of having D-ala-D-ala, they have D-ala-D-lac (which vancomycin can't bind to) EX: alterations of DNA gyrase & fluoroquinolone resistance - floros target the DNA gyrase enzyme, but it can have AA substitutions that prevent the drug from binding EX: alterations of ribosomes & macrolide/lincosamide resistance - both of these drugs bind to 50s ribosomal subunit and inhibit translation - ribosomes are composed of protein and RNA, so methylation of the rRNA can block drugs from binding

Epidemiology definitions

Incubation period = time from exposure to development of disease Latent period = period of infection without being infectious (usually right after exposure or late in disease) Infectious period = length of time a person can transmit disease Incidence = number of new cases in a given time period Incidence rate = cases/day Prevalence = total # of cases in a population Attack rate = proportion of exposed individuals who become ill Case fatality = proportion of individuals who will die from infection Virulence - degree of pathogenicity as indicated by CFR (Rabies = 100% CFR, Hep A = .5% CFR) Herd immunity threshold: the fraction of the population that must be immune from a pathogen to prevent an outbreak

Helminths

Intestinal roundworms (Ascaris lumbricoides, whipworm, pinworm, hookworm, strongyloides stercoralis) - Lifecycle: female worms in human gut produce eggs. Eggs are released in poop. Transmission occurs by ingestion of eggs or penetration of skin by larva - common in fecally contaminated soil - pinworm causes perianal itch and is common in US Treatment = albendazole/mebendazole Tissue Nematodes (Loa loa, onchocera, wuchereria) - larva of roundworms are transmitted by mosquitoes/flies - Life cycle = mosquito bites human, larva pass into lymphatics where they mature into adult worms, fertilized females discharge babies into blood - Clinical: skin swellings/eye symptoms (Loaloa), river blindness (onchocerciasis), elephantiasis (wuchereria) come from lymphatic destruction Trematodes (flukes) (schistosoma: hematobuim, japonicum, mansoni) - snail! - approx 200million people are infected with schistosomiasis worldwide!! - Lifecycle: snail is intermediate host, slow moving water where the snail lives allow release of cercariae, humans enter water where snail lives and parasites penetrate skin, migrate to lungs/liver where they mature, worms migrate to veins of bladder/intestine, get released in feces/urine, repeat cycle - found everywhere except north america, europe, austrailia - treatment = praziquantel Cestodes (tapeworms) - Taenia solium = pork tapeworm which can come from contaminated pork or fecal conamination, can grow in the brain causing seizures - Taenia saginata (beef tapeworm) = can cause abdominal symptoms but does not disseminate like T solium - Echinococcus = carried by dogs (eggs transmitted in food/feces) - eggs penetrate intestinal mucosa and enter circulation where they can form cysts in liver

Intracellular vs extracellular pathogens

Intracellular Advantages = nutrients, pathogen is protected from immune system initially, protected from some antibiotics Disadvantages = cells are good at killing invaders, costs a lot of energy/evolution to survive inside cells 2 types of intracellular pathogens - facultative anaerobes - obligate anaerobes How do bacteria get into cells? - Invasins = bacterial proteins that bind to or induce uptake by host cells - Phagocytosis (by macrophages, neutrophils, dendritic cells) - once inside phagosomes, can prevent vesicle fusion, modify vacuole, restrict acidification, or tolerate environment How do they hide from the immune system once in there? - naturally easier for them to hide bc they are inside host cells where immune cells/antibodies can't get to them - BUT CD8 T cells can kill infected cells - some viruses/bacteria down regulate MHC I / II so that immune cells don't see their proteins presented

Ectoparasites

Lice - small insects which can infect scalp hair (nits), body hair (body lice), pubic hair (crabs) Scabies - caused by an arachnid (sarcoptes scabi) whose feces produces an allergic reaction resulting in itch and scaly rash Myiasis -infestation of subcutaneous tissue by larvae of flies (maggots)

Giardia spp

Lifecycle - protozoa that grows either as vegetative trophozoites in duodenum or cyst in colon - cysts are infectious and are secreted in large numbers in stool - once ingested, they are transported to small intestines where they convert back into trophozoite form Reservoir and transmission - zoonotic reservoir = wild animals, farm animals, pets - cysts are very chlororesistant so can be present even in treated water - less commonly spread by contaminated foods Pathogenesis - cysts are very infectious (ingestion of 10 cysts can start an infection) - in most people, no symptoms develop so they can be carriers! - can have acute/chronic relapses - symptoms start 1-3 weeks after ingestion and resolve 1-4 weeks later - symptoms = explosive, sudden onset diarrhea involving a foul smelling, greasy stool devoid of blood or mucus (steatorrhea) - symptoms result from malabsorption of fats and carbohydrates in small intestine Treatment: metronidazole

Inhibitors of DNA/RNA synthesis: Fidaxomicin - only used for 1 type of infection!

Mechanism of action - Inhibits RNA synth by binding to RNA polymerases Mechanisms of resistance - resistance is rare but my occur through mutation Pharmacokinetics/dynamics - Bactericidal - Moderate oral absorption - minimal systemic distribution, stays mostly confined to gastrointestinal tract - Metabolized in liver (CYP450 independent) - Eliminated in feces Adverse events - minor GI side effects Examples and bacterial targets - Only used for treatment of C. diff infection!!

Minimum inhibitory concentration (MIC)

MIC = the lowest concentration of antibiotic that results in no visible growth of bacteria - the higher the MIC, the higher the conc of antibiotic that is required to inhibit its growth - if the MIC of a bacteria is higher than the concentration that can be obtained by an antibiotic (either bc higher concs would be toxic or bc you can't get the conc that high in a specific compartment without poisoning the patient), the pathogen is considered "resistant" Bacteria are characterized as: - susceptible - intermediate - resistant *Based on their MICs (if it takes a LOT of an antibiotic to inhibit bacterial growth, those bacteria are said to be resistant to that antibiotic) *Important to consider harmful dose level of antibiotic to human (in some cases, in order to reach the concentration in the blood needed to kill the bacteria, you would have to administer so much antibiotic that it would hurt the human) EXAMPLE: - An E.coli strain has an MIC of 32 for cefepime. A safe IV dose of cefepime attains a serum level of 25 and a urine level of 100. So, if E.coli is isolated from the blood (bacteremia), it is reported as resistant to cefepime (bc blood concentrations for a safe dose cannot overcome 32), but if the E.coli is isolated from the urine, it would be reported as susceptible to cefepime (bc 100 is greater than the minimum 32 needed)

Anaerobic bacteria Why are some bacteria anaerobic Predisposing factors to anaerobic infections Locations in body where anaerobes are normally found Most common anaerobic pathogens

Major theory is that oxygen causes oxidative damage to the bacteria and they don't have the enzymes to protect themselves from it - lack catalase (breaks down H2O2) - lack superoxide dismutase (detoxifies free radicals) - may have enzymes that require a reduced environment *Normally, the redox potential of healthy tissue is too high for anaerobes to grow. But they can grow in cases of: - circulatory problems (lower redox potential) - tight orthopedic casts - co-presence of facultative anaerobes which can consume the oxygen - antibiotic therapy - bite wounds - aspiration of mouth flora into lungs - GI perforation and spillage into peritoneum Anaerobes are naturally present on the skin, mouth, vagina, colon

Inhibitors of cell wall synthesis: Glycopepetides

Mechanism of action - Binds to D-ala, interrupting peptidoglycan synthesis (occurs 1 step before B lactam step) Mechanisms of resistance - cell changes peptide to D-alanyl-D serine/lactate to prevent drug from binding - thickened cell wall prevents drug from reaching target site Pharmacokinetics/dynamics - bactericidal, exposure dependent killing - except enterococcus (bacteriostatic) - oral absorption = very low <5% - Distribution = good, moderate CNS penetration - Metabolism = none - excretion = 100% renal Adverse events - Red Man's syndrome = rash and hypotension with rapid IV administration (not a hypersensitivity reaction) - Nephrotoxicity (high doses) - Neutropenia (less common) Examples and bacterial targets Vancomycin PO is used for C. diff infections Vancomycin IV = good for MRSA and strep bacteria, mostly used for GP

Inhibitors of protein synthesis: Aminoglycosides

Mechanism of action - bind irreversibly to 16S rRNA component (part of the 30S subunit) of bacterial ribosomes which leads to protein mistranslation Mechanisms of resistance - bacteria mutate their ribosomes (16S methylation) - also produce amino glycoside modifying enzymes Pharmacokinetics/dynamics - Bactericidal, concentration dependent killing (against gram neg) - minimal oral absorption - Poor distribution - not metabolized, eliminated 100% unchanged in urine Adverse events - Nephrotoxicity (10-15%) usually reversible - ototoxicity (rare) usually irreversible Examples and bacterial targets - Gentamicin/Tobramycin - always used in combination with cell wall agents for Gram Pos infections - good against P. aeruginosa

Beta lactam : penicillins

Mechanism of action - bind to and inhibit penicillin binding proteins PBPs to inhibit cell wall synthesis *Bactericidal against GP and GN Mechanisms of resistance - Gram Pos bacteria = alter their PBPs to have decreased beta lactam affinity - Staphylococcus only = possess an enzyme that hydrolyzes b lactam ring which renders the antibiotic inactive before it reaches PBP target - Gram Neg bacteria = overexpression of drug efflux pumps, beta-lactamases, loss or mutation of porin channels which is what the drug uses to enter the cell Pharmacokinetics/dynamics - bactericidal, time dependent killing - oral absorption = moderate - Distribution = moderate (cefepime, meropenem, impanel best for CNS penetration) - Metabolism = none - Elimination = 80-100% in urine Adverse events - C.diff infection - Hypersensitivity (rash, anaphylaxis) - Seizures (high doses, imipenem in patients with renal impairment) - Hepatotoxicity (oxacillin only - pediatrics) - Interstitial nephritis - most common w nefacillin Examples and bacterial targets - Penicillin - Amoxicillin/ampicillin - Ampicillin + sulbactam (includes B-lactamase inhibitors to avoid resistance) - Oxacillin/nafcillin/dicloxacillin (penicillinase resistant) - Piperacillin + tazobactam (betalactamase inhib)

Inhibitors of cell wall synthesis: Fosfomycin

Mechanism of action - inhibits 1st step of peptidoglycan synth by binding to enzyme which forms NAM Mechanisms of resistance - decreased drug uptake - target site modifications - enzymatic inactivation Pharmacokinetics/dynamics - Bactericidal, exposure dependent killing - oral absorption = moderate (40%) - Distribution = excellent - not metabolized - elimination - renal, unchanged in urine Adverse events - very well tolerated Examples and bacterial targets Fosfomycin = PO - used only for UTIs, very broad activity but not against P. aeruginosa

Beta lactam: cephalosporins

Mechanism of action Mechanisms of resistance Pharmacokinetics/dynamics Adverse events Examples and bacterial targets - cefazolin/cephalexin/cefadroxil (surgical prof) - cefuroxime/cefaclor/cefprozil (sinusitis/otitis) - cefoxitin (added anaerobic activity) - Cefdinir/ceftriaxone/ceftazidimide/ceftaroline (ceftriaxone = non renal clearance, ceftaroline = only b lactam with MRSA activity) - Cefepime (broadest activity, excellent p.aeruginosa) - Ceftolozane + tazobactam (blactamase inhib) - Ceftazidime + avibactam (blactamase inhib)

Inhibitors of protein synthesis: Macrolides

Mechanism of action - Bind to 50S subunit resulting in translocation of peptide rRNA, which inhibits peptide elongation Mechanisms of resistance - ribosomal mutation/modification Pharmacokinetics/dynamics - Bacteriostatic - moderate oral absorption - extensive distribution (but minimal CSF) - metabolized by liver - elimination via feces (azithromycin) or urine (clarithromycin) Adverse events - Nausea vomiting, diarrhea - Erythromycin > clarithromycin > azithromycin - oral erythromycin is used to increase GI motility - QTc prolongation, torsades de pointes (heart rhythm abnormalities) Examples and bacterial targets - Azythromycin = pretty full coverage, commonly used for atypical pathogens of upper respiratory tract

Inhibitors of protein synthesis: Tetracyclines

Mechanism of action - bind to 30S ribosomal subunit and block access of tRNAs to the adjacent ribosomal acceptor sites Mechanisms of resistance - ribosomal mutation - modification of drug efflux pumps Pharmacokinetics/dynamics - bacteriostatic - really good oral absorption (90-100%) - extensive distribution (minimal CSF) - excreted in bile/feces Adverse events Nausea, vomiting, diarrhea, esophageal ulceration - gray/brown teeth discoloration in children (depression of bone development) - photosensitivity Examples and bacterial targets - doxycycline/minocycline = used in outpatient setting for URIs, lyme disease, good for GP and GN - Tigecycline (not appropriate for bacteremia due to low serum levels)

Inhibitors of DNA/RNA synthesis: Fluoroquinolones

Mechanism of action - bind to topoisomerase II or IV leading to double stranded DNA breaks and cell death Mechanisms of resistance - mutations in topoisomerase Pharmacokinetics/dynamics - Bactericidal, concentration dependent killing - Excellent oral absorption - extensive distribution, moderate CNS - Metabolism: Moxifloxacin > Ciprofloxacin > Levofloxacin - opposite order for renal clearance Adverse events - CNS (headache, dizziness, insomnia, mood alterations) - Seizures! - Tendinitis with rupture (especially older patients, achilles tendon) - Heart dysrythmias - C. Diff diarrhea!! (high risk) Examples and bacterial targets - Ciprofloxacin - Levofloxacin - Moxifloxacin *All wildly used for UTIs, prostatitis, respiratory, gastro, bone/joint infections, STDs

Inhibitors of protein synthesis: Clindamycin (macrolide)

Mechanism of action - binds to 50S ribosomal subunit resulting in inhibition of peptide chain Mechanisms of resistance - ribosomal mutation - drug efflux pump modification Pharmacokinetics/dynamics - Bacteriostatic - good oral absorption - extensive distribution (minimal CSF) - excreted in feces/bile - metabolized by liver Adverse events - gastrointestinal effects (nausea, vomiting, diarrhea) - C. diff diarrhea (more common with clindamycin than any other antibiotic!!) Examples and bacterial targets - Clindamycin - only good against Gram pos - often used for oral infections in patients with penicillin allergy - good for MRSA

Inhibitors of protein synthesis: Linezolid - reserved only for treatment of....

Mechanism of action - binds to 50s ribosomal subunit and blocks initiation of protein translation Mechanisms of resistance - ribosomal mutation - efflux pump mutation Pharmacokinetics/dynamics - bacteriostatic - excellent oral absorption (nearly 100%) - extensive CSF distribution - metabolized through oxidation and excreted in urine Adverse events myelosuppression/thrombocytopenia with prolonged use (greater than 2 weeks) - serotonin syndrome when used in combination with MAO inhibitors (SSRIs, TCAs) Examples and bacterial targets - reserved for treatment of resistant Gram Pos infections like MRSA and VRE (vancomycin resistant enterococcus)

Cell membrane damaging agents: Daptomycin

Mechanism of action - binds to cell memb and causes depolarization via potassium efflux - associated with disruption of DNA, RNA, protein synth Mechanisms of resistance - thickened cell wall and altered binding sites Pharmacokinetics/dynamics - bactericidal, concentration dependent killing - minimal oral absorption - limited distribution - minimal metabolism - eliminated unchanged in urine Adverse events - muscle pain/weakness - creatine phosphokinase elevations (CPK) - rhabdomyolysis Examples and bacterial targets - Used for MRSA and VRE

DNA damaging agents: Nitrofurantoin only indicated for...

Mechanism of action - drug gets reduced inside bacteria to form DNA damaging free radicals Mechanisms of resistance Pharmacokinetics/dynamics - bacteriostatic - moderate oral absorption - poor distribution - minimal metabolism - eliminated via urine (urine concs decrease with renal impairment) Adverse events - GI effects - pulmonary (ranging from acute cough to pulmonary fibrosis with chronic use) Examples and bacterial targets - Nitrofurantoin = only indicated for UTIs (do not use in patients with creatinin clearance less than 50ml/min)

Inhibitors of DNA/RNA synthesis: Trimethoprim-sulfamethoxazole

Mechanism of action - drugs act synergistically to inhibit nucleic acid synthesis Mechanisms of resistance - structural changes in enzymes targeted by drugs Pharmacokinetics/dynamics - bactericidal (in combination), time-dependent killing - excellent oral absorption - extensive distribution (including CSF!) - sulfa metabolized in liver, trimethoprim is not - elimination in urine (unchanged mostly) Adverse events - skin reactions (3-4%) can be mild to severe epidermal necrolysis - Renal effects - inhibits secretion of creatinine and may lead to mild Examples and bacterial targets - Many clinical uses: UTIs, skin soft tissue infections from MRSA, Pneumocystis treatment, toxoplasmosis, nocardiosis

DNA damaging agents: Metronidazole

Mechanism of action - prodrug undergoes anaerobic nitro-reduction to form radical metabolites that bind to/inhibit DNA function Mechanisms of resistance - rare Pharmacokinetics/dynamics - bactericidal against anaerobes - also used to treat giardia - excellent oral absorption - extensive distribution, including CSF - extensive metabolism - minimal renal elimination Adverse events - metallic taste in mouth - peripheral neuropathy Examples and bacterial targets - Used for treatment of anaerobes - second line drug for C. diff

Atypical bacteria

Mycobacteria - possess a unique impermeable envelope - do NOT stain with gram stain (use acid fast stain) - envelope provides resistance to desiccation and phagocytosis EX: M. tuberculosis, M. leprae Spirochetes - very thin bacteria only visualized by dark field microscopy or immunofluorescence EX: Borrelia burgdorferi, treponema pallidum Rickettsiae spp - obligate intracellular bacteria transmitted by fleas, ticks, lice, etc - have Gram neg envelope but are too small to stain EX: R. ricketttsii (rocky mountain spotted fever) R. typhi (endemic typhi) Chlamydiae and Chlamydophilia spp - Obligate intracellular bacteria with complex lifecycle - energy parasites (use cellular energy) - Too small to see on gram stains EX: Chlamydiae trachomatis (blindis, urethritis, pneumoniae) - Chlamydophila psittaci (psittacosis = a form of pneumonia) - Chlamydophilia pneumoniae = pneumonia Mycoplasma app - small, lack cell wall, have sterols in plasma memb - slow growing on media - lack of cell wall makes them not susceptible to b lactams EX: M. pneumoniae (atypical pneumonia)

Clostridal vs nonclostridal anaerobic infections

Nonclostridal (not endotoxin mediated) - Often involved in abscess formation - abscesses are often polymicrobic, composed of facultative anaerobes + anaerobes (facultative consume the O2 lowering redox) - these bacteria are usually highly antibiotic resistant - difficult to treat bc abscesses don't have blood supply for antibiotic delivery - abscesses must be surgically drained often and treated with multiple antibiotics - Usually have a low virulence (takes a lot to start an infection) but can be fatal - often slow growing and produce fermentation gases (odor can be a clue of anaerobic infection) Bacteroides-like bacteria = most important nonclostridal anaerobes - Gram neg, anaerobic rods found as normal flora in colon, vagina, mouth - Other members of this family include porphyromonas and prevotella - Some species make an antiphagocytic capsule - all species make proteases which help them spread through tissue, some strains make enterotoxin - B. fragilis is the most frequently isolated anaerobe from intra-abdominal and bloodstream infections - Prevotella bivia = found in vagina and can cause pelvic inflammatory disease and infertility - P. melaninogenica P gingivalis found in mouth and can cause respiratory tract infections Clostridial - Histotoxic Clostridia * All are Gram pos anaerobic spore forming rods, some are present as normal GI flora, some in soil Virulence factors = exotoxins (proteins made and secreted outside the cell) - most common is C. perfringens (involved in 90% of HC infections) - Exotoxin = alpha toxin which is a lecithinase which disrupts phospholipase C and thus disrupts mammalian plasma membranes - C. septicum is common in patients with cancer of GI tract Common infections: - Gas gangrene (clostridial myonecrosis) - bacteria are present in the muscle, toxins kill cells to form necrotic tissue with low redox allowing progressive spread of infection. Toxins enter circulation and damage distant organs. Fatal --Treatment = removal of affected tissue by surgery (often amputation). Antibiotics, hyperbaric oxygen (increases redox potential of tissues) - Anaerobic cellulitis = infection of cutaneous and subcutaneous tissue - Simple wound infections = only involves cutaneous tissue - Organ infections (uterine infections from bad abortions), septicemia/bacteremia - C. perfringens type A food poisoning = 3rd most common food poisoning, exotoxin causes diarrhea and abdominal cramps

Fungal diseases (aka mycoses)

Normal defense mechanisms against fungi: - phagocytosis by neutrophils and macrophages is the most important resistance factor *most patients with invasive fungal infections have deficiencies in neutrophils and T-cell mediated immunity! Fungal allergies - fungal spores are potent allergens and continuously enter the respiratory tract - hypersensitivity reactions may present as allergic rhinitis, bronchial asthma, allergic alveolitis Fungal toxicoses - aflatoxins are toxins produced by Aspergillus spp - Aflatoxin B1 is one of the most potent carcinogens and can cause hepatitis/liver cancer - comes mostly from contaminated grains/nuts

Antivirals for Herpesvirus and Cytomegalovirus (CMV)

Nucleoside analogs Acyclovir - drug must first be phosphorylated by viral thymidine kinase (TK) to become active (mutations in TK can cause resistance) - drug does NOT become active in uninfected cells (bc uninfected cells don't contain TK) - acts as a chain terminator - competes with GTP in DNA synthesis - has a 100 fold greater affinity for viral DNApol than human DNApol (minimal toxicity) - as a suppressive therapy, reduces recurrences by 80%, reduces subclinical viral shedding by 50% Valacyclovir - prodrug of acyclovir that is better absorbed Famciclovir - similar but does not irreversibly terminate DNA replication Ganciclovir - has 50x more activity against CMV, used in immunocompromised patients to prevent CMV Valganciclovir - prodrug of ganciclovir with good bioavailability Nucleotide analog Cidofovir - requires phosphorylation by cellular enzymes - inhibits both cellular and viral polymerases (but higher affinity for viral) - the fact that it does not require a viral kinase makes it good for HSV strains that are resistant to above drugs due to mutation in viral kinases - nephrotoxicity is common and can be irreversible Pyrophosphate analog Foscarnet - reversibly blocks pyrophosphate binding site of viral DNA pol - directly toxic to renal tubules, leading to electrolyte abnormalities and renal insufficiency - very selective for CMV dnapol (Fernet megaly fs up your liver) Terminase complex inhibitor Letermovir - new medication against CMV - prevents cleaving of viral DNA and packaging of genome into capsids - does NOT have activity against other herpes viruses

#4 = Increased efflux of drug

Occurs through upregulation/modification of efflux pumps which remove antibiotics from cells - this removes antibiotics before they are able to bind to their targets

General virus information Virus structure

On their own, viruses are considered inert biochemical complexes (since they cannot replicate on their own) - once inside the cell, they can use host machinery to generate virions Viruses attach to host cells by binding to receptors expressed on the host surface Viruses are nonmotile STRUCTURE - viral genome is always enclosed within a protein shell (capsid) - most viral capsids are either: helical/rod shaped capsids OR spherical capsids with icosahedral symmetry - Virus particles can be nonenveloped or enveloped (capsid is surrounded by a lipid envelope) Virion = intact, infectious particle Capsid = protein shell surrounding nucleic acid Nucleocapsid = basically the capsid+viral genome of enveloped viruses

Peptidoglycan

Only found in bacteria! good drug target - like a cell wall in plants, gives structure and protects from lysis - very porous, does not restrict diffusion STRUCTURE - Composed of polymerized disaccharide monomer subunits consisting of NAM and NAG (nam nag repeat in alternating sequence to form a chain) - Glycan strands are crosslinked by a pentapeptide attached to NAM **The 2 terminal AAs on the pentapeptide are D-Alanine (important to remember for antibiotics!) PEPTIDOGLYCAN SYNTH - NAM/NAG synth in cytoplasm - they attach to a carrier which translocate them across the cytoplasmic memb (antibiotic bacitracin interferes with this step) - Now in the periplasmic space, monomer is linked to growing glycan strains - strains are cross linked to each other by penicillin binding proteins PBPs - PBPs have 2 roles: Elongating glycan chains (transglycolase activity) AND Crosslinking glycan chains (transpeptidase activity) - terminal D-ala residue is cleaved upon crosslinking **B-lactam antibiotics are a structural mimic of the D-ala,D-ala peptide sequence on the pentapeptide, and thus block the crosslinking step - without the peptidoglycan layer, the cell may burst and die! **Lysozyme hydrolyzes bond between NAM/NAG in glycan chains - important against GP bacteria (but not so much GN bc outer memb blocks lysozyme access to peptidoglycan) - present in tears, saliva and phagocytic cells

Parasites vs Bacteria Parasite lifecycle

Parasites are EUKARYOTIC (like fungi) - they have a nucleus - they have an 80S ribosome - they may have mitochondria - they do not possess a cell wall - reproduce sexually Lifecycle - many parasites require 2 or more host species to complete their lifecycles - Definitive host = where the parasite reaches sexual maturity - Intermediate host = harbors the larval stage of parasite - fecal oral route (undercooked food) is most common means of parasite transmission - skin penetration (schistoma) - vectors (malaria, filariasis)

Pharmacokinetics & pharmacodynamics of antibiotics

Pharmacokinetics = how the drug manipulates the body (ADME) Absorption = amt of drug that reaches systemic circulation (IV drugs have a bioavailability of 1) - Fluoroquinolones = nearly 100% - Vancomycin = poorly bioavailable (0-5%) Distribution = if the drug stays in the bloodstream or gets distributed to the tissues Metabolism = enzymatic transformation of the drug into another active/inactive substance Elimination = total renal and non-renal clearance of antibiotic (function of kidney function) - patients with renal failure require lower doses to avoid toxicity Pharmacodynamics = how the drug affects body/organism Bactericidal = antibiotic kills the bacteria - penicillins, cephalosporins, ahminoglycosides, vancomycin, fluoroquinolone, monobactams, daptomycin Bacteriostatic = inhibits bacterial growth - tetracyclines, macrolides, clindamycin, linezolid, tigecycline

Acute infection: Poliovirus

Picornavirus 3 strains (WPV1-3) - small, non enveloped, +RNA Life cycle - enters cells via poliovirus receptor (endocytosis) - uncaring, replication, assembly in cytoplasm - exits cell via lysis Transmission - humans are sole reservoir - spread by fecal oral route in contaminated food/water - has to survive GI tract where it mostly replicates in mesenteric lumen of small intestine - virus is excreted in stool - spread by viremia (entry into blood) with secondary replication in liver/spleen - can spread to CNS (99% of this is prevented by antibodies-vaccination!) - intraneural spread Symptoms - 10% experience fever, vomiting, diarrhea - 90% asymptomatic but still infectious - once in CNS, can cause: - meningitis, encephalitis (fever/headache lasts 2-14 days) - infection of brainstem/spinal cord results in Paralytic poliomyelitis (acute flaccid paralysis) due to motor neuron/muscle damage = occurs in 1/200 people with disease - post polio syndrome (rare) = paralysis and muscle wasting over time (FDR) Vaccines - injectable killed vaccine (Salk) - oral live vaccine (Sabin) - has the potential to mutate and become an active form of the virus that CAN infect people ;0

Bacterial plasmids

Plasmids = small, extrachromosomal elements that have the ability to confer new genetic properties to the cell - circular, DS DNA molecules, very stable - frequently contain antibiotic resistance genes and are the main reason for the spread of antibiotic resistance!! - all plasmids carry genes that allow them to replicate independently of the bacterial chromosome - require host machinery for replication Plasmid replication - Plasmid consists of ORIGIN (Site of initiation of replication), REP GENE (encodes initiator protein for replication), COPY CONTROL GENE (controls replication and copy number of plasmid) - Copy number = the number of plasmids per chromosome, it is a fixed number - Large plasmids have a low copy number (usually 1-2 per chromosome) - small plasmids have a high copy number (more than 10 per chromosome) *A host cell can contain several different plasmids at the same time (compatible plasmids) - other plasmids can be incompatible Types of plasmids - Resistance plasmids (R) - can transfer between different bacterial species!! - R plasmids often contain the F gene so that they can be transferred by conjugation! - Virulence plasmids = carry genes that encode toxins/virulence factors (pXO1 = anthrax toxin)

Ro (R naught)

Ro = reproduction number aka the avg number of people one sick person infects - useful for calculating potential spread of disease Ro = attack rate x number of potentially infectious contacts the avg person has x duration of infectivity of an infected person If Ro < 1 : every new generation of infection will affect fewer individuals and disease will die out (vaccination) If Ro = 1 : approx the same # of ppl are infected with every generation, causing endemicity! (west nile) If Ro > 1 : every new generation will affect more individuals, creating an epidemic or pandemic (flu) Suspect an outbreak when: - there are 2 or more cases of a similar illness linked by time, location, or contacts. You must determine: - reservoir - transmission mode - incubation time - value of Ro

Antifungal medications

Polyenes (amphotericin B, nystatin) - bind to sterols in fungal cytoplasmic membrane to increase membrane permeability - can cross react with cholesterol in human cells (toxicity) - Fungicidal - Frequrent side effects: nephrotoxicity, fever, hypokalemia, hypomagnesemia - resistance is rare Azoles (fluconazole, itraconazole, voriconazole, posaconazole, isavuconazole) - disrupts enzyme that converts lanosterol into ergosterol, forming defective cytoplasmic membranes - usually well tolerated, liver toxicity with elevation of transaminases may occur - oral or IV - Fluconazole = primarily active against yeasts Echinocandins (caspofungin, micafungin, anidulafungin) - inhibit synthesis of glucan of cell wall - Active against candida & aspergillum (used for serious infections) - minimal toxicity Antimetabolite (5-flucytosine) - interferes with fungal DNA/RNA synth - used as combination therapy with amphotericin (if used alone is very prone to resistance) - most common side effect is bone marrow suppression Allylamines (terbinafine) - inhibition of ergosterol biosynthesis Griseofulvin - disrupts mitotic spindle formation - used for superficial mycoses (skin) - response is slow and prolonged therapy is required

#1 = mechanisms of drug inactivation

Prime example: B-lactamase enzymes that cause B-lactam resistance - Normal target of B-lactams is PBPs, which are the enzymes that crosslink peptidoglycan precursors to form cell wall - B-lactamases are encoded on plasmids or the chromosome of resistant bacteria, and function to cleave the B-lactam ring, rendering it useless - these enzymes are very common Narrow spectrum B-lactamases = may only inactivate 1 antibiotic type (ie, penicillins but not cephalosporins) Extended spectrum B-lactamases (ESBLs)= can inactivate multiple antibiotics - most frequently produced by E.coli and Klebsiella pneumoniae Specific examples of ESBLs - AmpC B-lactamase = found in many gram neg bacteria, usually increase in presence of antibiotic - can hydrolyze penicillins and cephalosporins - only B-lactams they can not cleave are cefepime and carbapenims - Carbapenemases = B-lactamases can hydrolyze virtually ALL B-lactam antibiotics ;0 *Beta-lactamase inhibitors also exist and can be given with these antibiotics in order to make them functional* Other example of drug inactivation: - Enzymes that add a functional group to aminoglycoside antibiotics, making them unable to bind to bacterial ribosome, rendering them useless - common enzymes are ACC, ANT, APH which add an acetyl, adenylate, or phosphate group directly to the aminoglycoside drug

5 types of antibiotic therapy

Prophylaxis - giving antibiotics while a person is healthy to prevent infection - Perioperative prophylaxis (cleaning the surgical wound/ giving antibiotics before incision is made) - endocarditis prophylaxis (used to prevent infections of heart valves in procedures that produce bacteremia) - Travel prophylaxis (used to prevent endemic disease like malaria) - Opportunistic infection prophylaxis (taken by immunocompromised patients) - HIV prophylaxis (PrEP, PEP) Preemptive therapy - the use of antibiotics in an asymptomatic infection that is likely to become symptomatic unless treated (cytomegalovirus) Empiric therapy - giving antibiotics when you think someone has an infection, even if you don't know what bacteria/pathogen is causing the disease - if someone has signs of fever, meningitis, etc giving them a broad spectrum antibiotic is better than wasting time finding out what it is Pathogen-directed therapy - treating when the infecting organism is known, but its antibiotic susceptibility is being awaited. Susceptibility guided therapy - when the organism and antibiotic susceptibility are both known *This is the best approach!

Types of parasites

Protozoa - unicellular, free-living, eukaryotic cells - divided into 4 groups based on their locomotion: flagella, cilia, pseudopods, microtubule complex Helminths - worms! - can be divided into roundworms (nematodes) and flatworms (which are divided into tapeworms (cestodes) and flukes (trematodes)) Ectoparasites - lice, scabies, fleas, ticks - part of their lifecycle depends on animals as a host - parasite products can cause an allergic reaction OR parasites can deposit bacterial, viral, or protozoal infections

Microbiologic tests

Qualitative culture - reserved for analysis of sterile body sites (blood, CSF) - place sample into a nutritive broth and see whether something grows or not (pos/neg) - false positives from contamination are common Semi-quantitative culture - plating a specimen on 4 quadrant agar plate and seeing how many quadrants show growth - sort of shows how concentrated the organism is in the sample Quantitative culture - a specimen of known volume is plated on agar and CFUs are counted Blood culture collection - used to test for bacteremia or fungemia (infection of bloodstream) - skin is cleaned and blood is collected into 2 tubes containing liquid media (one for aerobic and one for anaerobic) - should be collected from 2 sites to rule out contamination *Blood may also be drawn to check for antigens, viral RNA/DNA, or antibodies against the organisms that are in the bloodstream Urine - To distinguish a UTI from contamination, look for symptoms, presence of WBCs, more than 100,000 bacteria/mL urine (higher conc means infection), only one kind of bacteria on urine culture CSF - tapped by a lumbar puncture - cloudy suggests presence of leucocytes (inflamm response to infection) - gram stain can identify bacterial infection, CSF can be cultured, PCR can detect viral genomes, india ink is used for fungus Respiratory tract - culturing sputum (contamination potential) - nasopharyngeal swabs - Bronchoaveolar lavage (BAL) most invasive but limits contamination Stool - can identify parasites, bacteria - using selective media can differentiate abnormal flora from commensals - PCR can detect virus/bacteria genomes

Other determinants of choosing an antibiotic

Route of administration - most are IV (good if patient is too sick to swallow a pill) - some antibiotics with good GI absorption can also be pill form Anatomic site of infection - bacteremia is usually treatable bc all IV antibiotics reach blood - if infection is in CSF, is often hard for drug to reach it bc of BBB (so you need high doses) - other poorly perfused sites include: abscesses, necrotic bone, infected tissue Combination therapy - like with HIV, using multiple drugs to reduce likelihood of resistance Toxicity - you should always prescribe the least toxic drug that will treat the causative microorganism and its susceptibilities - EX: ahminoglycosides are more toxic than cephalosporins Drug cost - EX: nafcillin is much cheaper than daptomycin, so the latter should only be used in specific circumstances

Common emerging infectious diseases SARS Avian Influenza Metapneumovirus West Nile Virus Spongiform Encephalopathies Norovirus Zika TB/Polio/salmonellosis

SARS (coronavirus) - Enveloped RNA virus - mainly respiratory transmission but also through aerosolized feces and urine (1-4 days) - 10% mortality rate!! - bats are thought to be main reservoir. Their droppings can fall under fruit trees and be eaten by pigs/civet cats MERS (middle eastern respiratory syndrome) - novel coronavirus identified in Saudi Arabia, Jordan, Qatar - 40% CFR!!!!! - reservoir = camels Avian Influenza - H5N1 has been predominant strain since 2004 - 650 human cases, 400 deaths (CFR 60%!!!!!) - expanding host range includes birds, tigers, cats, humans - this virus is now endemic in asian fowl Metapneumovirus - common cause of respiratory infections in children & elderly - prevalent for decades West Nile Virus - widespread in Africa, middle east, eastern Europe, also cases in US - only symptomatic in 1/5 people, causes meningoencephalitis in 1/150 ppl - reservoir is birds and transmission occurs through mosquitoes - dead crows in New York parks Spongiform Encephalopathies - not caused by microorganisms but by abnormal proteins or prions! - Kuru - Gerstmann Straussler Schnieker disease (GSS) - Fatal familial insomnia FFI - scrapies (sheep), bovine spongiform encephalopathy (BSE), chronic wasting disease (elk/deer) - Sporadic Creutzfeldt Jakob disease (CJD) = human form of bovine spongiform encephalopathy (BSE) aka mad cow disease *prion (PrP) is found in high quantities in brains - CFR of CJD = 100%!!!! (230 cases in UK) Norovirus - self-limited acute gastroenteritis lasting 24-48hr - symptoms = nausea, vomiting, abdominal pain, diarrhea - very contagious and causes outbreaks in schools, cruise ships, hospitals - reservoir = humans - transmission = oral/fecal route & fomites Zika - flavivirus - causes symptoms in 1/5 patients - symptoms = rash, fever, joint pain, conjunctivitis *similar to mild dengue but with rash! - rare complications (microcephaly & guillain barre syndrome) - sexual transmission is possible - virus discovered in Uganda in 1947 - endemic in brazil in 2015 TB/Polio/salmonellosis - re-emerging infections! due to immigration, HIV immunocomp, drug resistant TB

Treatments of parasitic infections

Since parasites are eukaryotes, their cells are similar to humans so they are harder to kill without damaging our own cells! Metronidazole = trichomonas, guardia, amebiasis Ivermectin = intestinal roundworms, also lice/scabies Clindamycin, quinine atovaquone = babesiosis Malaria treatment - chloroquine (mostly ineffective due to resistance) - quinine - primaquine - artemisinin - Mefloquine - Atovaquone/proguanil (widely used as prophylaxis)

Diagnosis of fungal infections

Staining - calcofluor white stains chitin and fungi appear brilliant white under fluorescent microscope - Candida albicans can be gram stained (GP) - Silver stains Culture growth - is often slow - bacterial media can be used but there are special media (like Sabouraud's agar) which select for fungi and eliminate bacteria - grow best at 25-30C Immunoassays - detect target antigens including Cryptococcus neoformans polysaccharide antigen test - histoplasmosis capsulate surface antigen test

Transduction

Transduction = gene transfer mediated by a bacterial virus (bacteriophage) Process: - donor cell is infected by a phage - phage replicates in the cell and degrades host bacteria's DNA - phage particles assemble and contain small pieces of bacterial DNA (can come from main genome or plasmids) - upon reinfection of a new bacterial cell, the DNA from the original cell is integrated into the recipient chromosome by homologous recombination

Transformation

Transformation = uptake of naked DNA from environment (ie chromosomal fragments or plasmids released from dead neighbors) In order to incorporate this new DNA into their existing DNA, bacteria must be "competent" Competent = able to incorporate foreign DNA into their own DNA Some Gram Pos bacteria are naturally competent (by natural production of protein called competence factor) - most need to be induced to competence via heat shock, chemicals, etc (standard method of gene cloning in lab) Process: - a single strand of DNA enters recipient cell - SS DNA is integrated into recipient DNA by homologous recombination mediated by RecA protein - the recipient DNA is replaced by the donor DNA

Naming conventions for infectious agents Types of pathogens

Types of infectious agents - bacteria - viruses - Fungi - Parasites - Prions - Bacteria, Fungi, and parasites are all written in italics (Staphylococcus aureus) - Genius is capitalized, species is not - Spp = species (abbreviation) Diseases, viruses, and genus general term (ex enterococci) are NOT italicized

Koch's postulates

Used to establish that a given microorganism causes an infectious disease *Koch's postulates prove the etiology of many but not all infectious diseases 1. The organism is found in abundance in all hosts suffering from the disease, but NOT in healthy people 2. The organism must be isolated from a diseased host and grown in pure culture 3. The cultured organism should cause disease when introduced into a healthy host 4. The organism must be reinstated from the inoculated, newly infected host and be identified as the same original causative organism EXCEPTIONS - C. diff and salmonella typhi can colonize some hosts without making them sick (carrier state - typhoid mary) - postulate 1 - Viruses/prions violate postulate 2 (cannot be cultured on cell free media) - it is hard to test postulate 3 if no animal model is available (HIV)

Virulence

Virulence = the number of organisms needed to start an infection (quantified by LD50 or ED50) Virulence factors = qualities of infectious agents that make them better at infecting - toxins, adhesions, capsules, etc - the set of virulence factors an organism produces determines what type of disease it causes 2 kinds of infections: Infection vs Intoxication - Infection - introduction of microorganisms to the body which replicate and cause disease - Intoxication - ingestion of food containing toxins formed by bacteria (live microorg does not have to be consumed) Disease = results from damage caused directly by pathogen factors (toxins, etc) or by host immunopathologic responses General lifecycle of infectious disease 1. Pathogen enters into body 2. Pathogen adheres to target and colonizes 3. Evasion of host defenses 4. Cell/tissue damage 5. Dissemination of pathogen to infect new host

Why do we need a new flu vaccine every year? Background on influenza antigens

Why do we need a new flu vaccine every year? - the quadrivalent flu vaccine is composed of 2 influenza A strains and 2 influenza B strains chosen based on the previous year's circulating strains - vaccine is 60-70% effective if there is a good match between viral strains and new season's strains (will usually overlap IF dramatic antigenic shift hasn't occurred) *The flu virus mutates every year and different strains can be more or less prevalent - we need an updated vaccine to protect us against this different virus TYPES A, B, C Type A = can cause annual outbreaks - only type that causes epidemics and pandemics! - can infect birds, humans, swine - classified as H#N# Type B = can cause annual outbreaks - humans are only reservoir - classified as Victoria or Yamagata Type C = usually mild and not associated with seasonal outbreaks Pandemics = when a new virus appears to which the population has no immunity Pathogenesis of flu: virus attacks respiratory epithelium and causes death of cells! - targets ciliated columnar epithelial cells - attracts phagocytes and releases lots of interferon (causes systemic symptoms) HA protein = Hemagglutinin - binds to sialic acids on host cells & causes fusion - cleaved to form HA2 which allows release of viral RNA once inside cell - main target for antibodies and vaccine NA protein = Neuraminidase - important for release of new virions TREATMENTS - Neuraminidase inhibitor (Oseltamivir) = prevents viral exit - Baloxavir = interferes with viral RNA transcription *both work best if given within first 2 days of illness

Types of viral polymerases

____ dependent _____ polymerase DNA -> DNA (DdDp) - found in cells & viruses RNA -> RNA (DdRp) - found in VIRUSES ONLY RNA -> DNA (RdD) - found in VIRUSES ONLY DNA -> RNA (DdRp) - found in cells & viruses RNA -> protein - found in CELLS ONLY

Bacterial growth

bacteria reproduce asexually by binary fission Growth is logarithmic and divided into 4 phases: 1. LAG PHASE = adaptation to new environment - cells synthesize enzymes, use new nutrients, adjust to PH/temp 2. EXPONENTIAL (LOG) PHASE - cells exhibit max growth rate for a given environment *Time when bacteria are most sensitive to drugs - preferred time for differential staining 3. STATIONARY PHASE - results from carrying capacity (nutrient depletion/toxic waste accumulation) - sporulation initiated in spore forming species - stationary phase cells have elevated resistance to antibiotics bc they are metabolically inactive 4. DECLINE/DEATH PHASE Biofilms - complex aggregation of bacteria encased in a protective/adhesive carbohydrate matrix - Most bacteria grow in biofilms, involved in 80% of all infections EX: plaque, catheters, cystic fibrosis, UTIs, ear infections - can be a source of recurrent infections - promote resistance to antibiotics and phagocytosis Nutrient requirements for growth - Type of metabolism/food sources can be used for identification - Prototroph = synthesizes all of its own metabolites (Ecoli, Salmonella, pseudomonas) - Auxotroph = has lost ability to synth certain substances required for growth (chlamydia, neisseriae) *Iron = essential for growth - host defense is to limit amt of available iron using iron binding proteins (lactoferrin and transferrin) - bacteria have evolved mechanisms to get iron (lactoferrin/transferrin transporters, iron binding compounds, cytotoxins to release intracellular iron)

DNA viruses

dsDNA = hepadna, herpes, adeno, pox, pap ova, irido ssDNA = parvoviruses DNA Virus Replication - all dsDNA viruses encode their own polymerases (they are more efficient at replicating viral DNA) - follows the same pattern as host DNA replication/translation (DNA->DNA for genome, DNA -> mRNA -> protein for protein) - Viral polymerases are important targets of antiviral therapy!! Early viral proteins = are made prior to DNA replication to help alter the host cell for the genome replication Late viral proteins = made after DNA replication and are important for viral structure and assembly

Bacterial endospores

most resistant, only extreme heat or chemical treatment destroys them *can survive for more than 100 years before germinating into a new cell! Endospores are only formed by: - Bacillus (aerobic or facultative) - Clostridium (anaerobic) Why so resistant? - they are very low in internal water - rich in DNA stabilizing proteins - in a state of "suspended animation" bc no water means no metabolism Important spores: - Anthrax (bacillus anthracis) - Tetanus (clostridium tetani) - Infections caused by histotoxic clostridia - C. diff