Infectious disease exam 1
The Plague enters Europe inthe Sicilian port of Messina
"At the beginning of October, ... 1347, twelve Genoese galleys ... entered the harbor of Messina... In their bones they bore so virulent a disease that anyone who only spoke to them was seized by a mortal illness and in no manner could evade death." +seemed to be airborne- - not, could come from lungs tho
Molecular determinations
"G + C" content (melting temperature of DNA) more G:C base pairs, "stronger" DNA is, more heat needed to disassemble most higher organisms 30-50% G+C, proks (20-90%) vary WIDELY 10% change in G + C content = not closely related; cannot base solely on G + C (not ordered sequence)
Symbiosis
"living together," the close association of two species for the purpose of growth/replication and/or obtaining food (for one or both partners) *Commensalism: "eating at the same table," an association that is beneficial for one partner, does not adversely affect other (+,0) Mutualism: association that is beneficial for both partners (+,+) Parasitism: one animal, "the host", is to some degree harmed by the symbiotic relationship (-,+)
top causes of death in upper middle income countries
#1 cause noncommunicable diseases: -ischaemic heart disease -stroke -chronic obstructive pulmonary disease ... takeaway- noncommunicable diseases number one cause of death slide 12/lec 1
CRISPR
*found from bacteria- -immune system for bacteria, used for sequencing by us *A more advanced bacterial immune system - collects RNA sequences and archives them -This one "remembers" Specificity of cleavage is important -We can "hijack" these systems to study biology Crispr details: Clustered regularly interspaced short palindromic repeats Many, many bacteria and archaea possess functional CRISPR systems Thought to provide phage (virus) resistance to bacteria + Associate proteins cleave DNA (it's broken now!) With previous tools, can synthesize our own guide sequences + Guide sequence (RNA) + Proteins of Cas family +Highly precise DNA cleavage events
Make new DNA
-Coupled with DNA ligase, can synthesize custom DNA fragments -Add to other pieces of DNA that contain origins of replication and selectable elements (drug resistance) -Make new DNA (recombinant DNA)
third: Evasion -- innate immune response
-Extracellular bacteria - Production of a capsule; resists phagocytosis ex+(Streptococcus pneumoniae- causes pneumonia, meningitis) - Production of enzyme to destroy toxic molecules (ROS=reactive oxygen species) Intracellular bacteria- Once inside cell, bacteria prevent attack by intracellular toxic molecules ex+ (M tuberculosis inhibits phagolysosome formation and/or it escapes into the cytoplasm)
The plague in Florence
-In the year of our lord 1348 there occurred in the city and contado of Florence a great pestilence, and such was its fury and violence that in whatever household it took hold, whosoever took care of the sick, all the carers died of the same illness, and almost nobody survived beyond the fourth day, ... --Florentine Chronicle of Marchionne di Coppo di Stefano Buonaiuti (1327-1385) -And it wasn't just men and women: even sentient animals such as dogs and cats, hens, oxen ,donkeys and sheep, died from that same disease, and with those symptoms ... -Those symptoms were as follows: either between the thigh and the body, in the groin region, or under the armpit, there appeared a lump, and a sudden fever, and when the victim spat, he spat blood mixed with saliva, and none of those who spat blood survived. +lump=swollen lymph nodes Sons abandoned fathers, husbands wives, wives husbands, one brother the other, one sister the other. The city was reduced to bearing the dead to burial; many died who at their passing had neither confession nor last sacraments, and many died unseen,... ... pits were dug..., as wide and deep as the parish was populous; and therein, whosoever was not very rich, having died during the night, would be shouldered by those whose duty it was, and would either be thrown into this pit, or they would pay big money for somebody else to do it for them. and seeing finally at the beginning of October(1562) that nobody was dying of that pestilence any more, it was discovered that putting together men and women, children and adults, from March to October, 96,000 had died.
Affinity protein purification
-Recombinant DNA constructs provide "fusion" protein expression -Protein binds a specific functional group (MBP in this case) -No other proteins in cell should have these modifications Specific elution of target Why does this help? -page not found for link so..?
variola virus
-causes smallpox Enveloped, brick-shaped or ovoid virion, 220-450 nm long and 140-260 nm wide. The surface membrane displays surface tubules or surface filaments. Two distinct infectious virus particles exists: the intracellular mature virus (IMV) and the extracellular enveloped virus (EEV) • Linear, dsDNA genome of 130-375kb. The linear genome is flanked by inverted terminal repeat(ITR) sequences which are covalently-closed at their extremities. • Early phase- produces proteins needed to block antiviral response • Intermediate phase - produces proteins needed to replicate genome • Late phase- makes structural components to make more virus • Early-late can take as little as 3 hours Vaccinia virus propulsion in actin tails: -sit outside cell and make projections to infect other cells via actin tails
when smallpox endemic-ness ceased
-last regions effected= Brazil, India, middle east, and many regions in Africa After a global eradication campaign that lasted more than 10years, the 33rd World Health Assembly declares the world free of smallpox in 1980 +who made eradication poster in 1970s
small facts about microbiology
-most life is microbial and prokaryotic ex+ bacteria > 3/4 life circle -archaea are the prokaryotes that eukaryotes likely evolved from on circle model, even many eukaryotes are microbial -microbes important factor to anoxic and oxic produciton of organic matter -environmental microbiology ex- cow gut -microbial communities= live in thermal vents -microbes used for cheese production and Tempeh a fermented soy product microbes cause: staphylococcus aureus= causes staph infrections on skin HSV= coldsores brugei malayai= elephantitis
Hybridization: How much DNA sticks to a known type strain?
1-genomes chopped up and binds to filler 2-labelled with radioactivity 3- 70% homologous= related / 40%=unrelated
The big 6/ Killer diseases
1.) Lower respiratory infections 3.1 million >2.)Diarrheal diseases 1.5 million >3.)HIV/AIDS 1.5 million >4.)Tuberculosis 900, 000 >5.)Malaria 627, 000 >6.)Measles 145, 000 +Neglected Tropical Diseases Up to 530, 000
Koch's Postulates
1.)The organism must always be present, in every case of the disease. 2.) The organisms must be isolated from a host containing the diseases and grown in pure culture (tricky) 3.) Samples of the organism taken from pure culture must cause the same diseases with inoculated into a healthy, susceptible animal in the laboratory 4.)The organisms must be isolated from the inoculated animal and must be identified as the same original organism first isolated from the originally diseased host
Major sequencing techniques (microbio lec 3 slide 22-25)
16S or 18S rRNA sequencing: useful for easy genus classifications slow to change, essential not subject to lateral gene transfer (important!) genomic fingerprinting: multilocus sequence analysis (MLSA) restriction length polymorphism analysis Needed for SPECIES classifications, follow multiple loci that evolve quickly(why important?) Illumina sequencing High throughput sequencing Can run millions of sequencings at once from pure or mixed populations Relies on SHORT sequences of starting DNA; fragmentation and adapter additions Sequence by synthesis Fluorescently labeled nucleotides are added; 3' ends are "blocked" Addition of nucleotide is read by lasers and measuring fluorescence (1 round) Fluorescent "blocker" is removed, next round begins Repeat (millions of potential clusters, containing thousands of similar DNAs in one area) Relies on sequence overlap to assemble sequences
Smallpox: Through History part 2
16th Century • European colonization and the African slave trade import smallpox into the Caribbean and Central and South America. • Led to the demise of the Aztec Empire • Along with measles, smallpox decimated the population (9 out of every 10 people died) 17th Century • Increased use of variolation. • Smallpox spreads into North America • European colonization imports smallpox into North America. • 20th Century • America in the early 1900s, while Europe and North America have smallpox largely under control through the use of mass vaccination. • The map shows the worldwide distribution of smallpox and the countries in which it was endemic in 1945
Sweden = first to start vaccinating against smallpox
1801 Sweden started vaccinating against smallpox, compulsory in 1816 next was Scotland, Netherlands, Prussia, and Belgium and Austria
Global Health Security Agenda
2014 Partnership between US, World Health Organization (WHO),World Organization for Animal Health (OIE), and Food and Agriculture Organization (FAO) of the United Nations and at least 70 partner countries Aims to strengthen abilities to: Prevent Avoidable Epidemics: including naturally occurring outbreaks and intentional or accidental releases Detect Threats Early: including detecting, characterizing, and transparently reporting emerging biological threats early through real-time biosurveillance Respond Rapidly and Effectively: to biological threats of international concern how?: Prevention Prevent the emergence and spread of antimicrobial drug resistant organisms and emerging zoonotic diseases, and strengthen international regulatory frameworks governing food safety Promote national biosafety and biosecurity systems Reduce the number and magnitude of infectious disease outbreaks through surveillance for zoonotic disease and immunization programs **key = moniter and slow antimicrobial resistance and minimize spillover of zoonotic disease, and immunization Detection: Launch, strengthen and link global networks for real-time biosurveillance Strengthen the global norm of rapid, transparent reporting and sample sharing Develop and deploy novel diagnostics and strengthen laboratory systems Train and deploy an effective biosurveillance workforce Response Develop an interconnected global network of Emergency Operations Centers and multi-sectoral response to biological incidents Improve global access to medical and non-medical counter measures during health emergencies
Smallpox: Through History
3rd Century BCE: • Traces of smallpox pustules found on the head of a 3,000-year-old mummy of the Pharaoh Ramses V 4th Century: • A written description of a disease that clearly resembles smallpox appears in China • In China, people appealed to the god Yo Hoa Long for protection from smallpox. 6th Century: • Increased trade with China and Korea introduces smallpox into Japan. • Drawing of a woman defeating the "smallpox demon" by wearing red. A myth commonly believed around the world advocated that redlight would cure smallpox. 7th Century • Smallpox is widespread in India. Arab expansion spreads smallpox into northern Africa, Spain, and Portugal. 11th Century • Crusades further contribute to the spread of smallpox in Europe with the European Christians moving to and from the Middle East during the next two centuries 15th Century • Smallpox is widespread in many European countries, and Portuguese expeditions to African west coast and new trade routes with eastern parts of Africa introduce the disease into West Africa. • Statue of Shapona, the West African god of smallpox. Smallpox was thought to be a disease forced upon humans due to Shapona's "divine displeasure," and formal worship of the god of smallpox was highly controlled by specific priests in charge of shrines to the god. People believed that the priests themselves were capable of causing smallpox outbreaks
Smallpox: Anti-Vax
Anti-vaccine movement "The Cow Pock-or-the-Wonderful Effects of the New Inoculation!" +by James Gilray from "The Publications of the Anti-Vaccine Society", June 12, 1802 cartoon made fun of people who got the vaccine Correlation vs Causation • Many anti-vaxxers will use correlations to "strengthen" their views on vaccination • Easy to find odd correlations if one wants to for example organic food sales can be correlated with autsim
Antibodies
Attaches to surface of microbe or toxin a.) neutralization- antibodies prevent a virus or toxic protein from binding to target b.) opsonization- a pathogen tagged by antibodies is consumed by a macrophage or neutrophil c.)complement activation- antibodies attached to the surface of a pathogen cell activate the complement system *also view model of antibody dependent cell cytotoxicity (ADCC) 1-antibodies bind to surface target 2-Natural killer call CD16 receptors recognize call-bound antibodies 3-Crosslinking CD16 triggers degranulation intp a lytic synapse 4-infected cell dies by apoptosis
The Three Amigos
B cell - mediators of humoral immunity (antibody mediated immunity) - - secrete antibodies which bind to antigens via the top of the light chains and heavy chains at top of the Y shape (the antigen binding site) CD4+ T cell - helper T cells; prime/coordinate CD8 and B cells CD8+ T cell - mediators of cell mediated killing; CTLs *All 3 have specific antigen receptors
Humoral Immunity (Antibody Mediated Immunity)
B cells secrete antibodies (Y-shaped) Antibodies recognize and bind to specific portions ("epitopes") of antigens* *antigen = molecule recognized by the adaptive immune system
PARASITES
Bacteria Fungi Protozoa Worms and flukes (Helminths) Viruses Prions
Important clinically-relevant microbes
Bacteria (Gram-negative and Gram-positive) Viruses Eukaryotic organisms: Yeasts/Fungi Unicellular parasites Multicellular parasites
first: physical and chemical defense continuation of "the immune system"
Barriers (both physical and chemical) epithelial cell layers (skin and "mucous membranes") cells and small molecules present on mucosal surfaces (respiratory, digestive and reproductive/urogenital tracts)
innate vs adaptive immunity
Born with innate immunity Develop adaptive immunity lag= innate is immediate response and adaptive takes at least a few days adaptive immunity is more specific and diverse than innate immunity adaptive immunity has a memory and induce amplified responses with more exposure unlike innate immunity ***view model for solubility and cells***
third: Attack and Clean-up- -Innate Immune Response continuation of "the immune system"
Cells- macrophages, neutrophils(polymorphonuclear cells; PMNs), natural killer cells Phagocytosis by phagocytes (enclose large particle, becomes active in acidic pH = less than 7), lysis of infected cells, secretion of toxic molecules and cytokines(cell-derived molecules that activate and instruct other cells) *type of endocytosis https://onlinesciencenotes.com/phagocytosis-an-example-of-endocytosis/
Evasion to Antibody Responses
Changes surface antigens by mutation(error-prone replication) - Virus, Plasmodium, Bacteria -Rearranging nucleic acid segments with other strains +Influenza: antigenic "drift" (mutation) and "shift" (mixing up RNA segments)
T cell Responses-Evasion
Changes surface antigens by mutation(error-prone replication) - Virus, Plasmodium, Bacteria Rearranging nucleic acid segments with other strains Influenza: antigenic "drift" (mutation) and "shift" (mixing up RNA segments) No recognition--> no cytokine response--> inadequate cooperation and orchestration of adaptive response
WORMS AND FLUKES
Complex, multicellular organisms (also called helminths) - trematodes(ex. schistosomes) - cestodes (ex. tapeworms) - nematodes (ex. Hookworms (intestinal) and filaria (bloodborne: elephantiasis in humans and heartworm in dogs and cats) Have complex life cycles Transmission in many involves excretory passage and/or ingestion of eggs trematodes involve an intermediate host in water; commonly snails cestodes also involve various intermediate hosts; fish, pigs, dogs, etc. nematodes are directly transmitted via eggs or larvae(intestinal and tissue infections) or via insect vectors (blood infections): Schistosoma, Brugia malayi/Wuchereria brancofti (elephantiasis), Drancunculus medinensis (guinea worm)
PROTOZOA
Complex, single-celled organisms Nucleated, with chromosomes, and organelles Use various means for motility: ameboid movements, cilia, flagella, undulating membrane Most are free-living, but some are obligate parasites - latter are of medical importance Reproduce sexually or asexually Have complex life cycles: live in one or more hosts which harbor the sexual and asexual stages some may also exist in external environment between hosts (commonly as a resistant egg or cyst) important ones: Plasmodium falciparum (malaria), Trypanosoma brucei gambiense and rhodesiense (African trypanosomes)- african sleeping sickness
FUNGI
Complex, unicellular or multicellular organisms Nucleated, with chromosomes, and organelles * Many are saprophytes (live on dead organic matter) or symbionts, but some are obligate parasites - latter are of medical importance Reproduce sexually and asexually - by means of spores or budding (yeast) Common infections are not life threatening (athletes foot). Can cause serious complications and even death in immune compromised (AIDS patients)
microbial cell
Conserved biological processes Easy to grow quickly Foundational discoveries(DNA, central dogma)
Bacterial Pathogens (Gram-positive)
Contain a single membrane with a thick peptidoglycan layer Peptidoglycan layer attached with lipoteichoic acid Lipoteichoic acid and peptidoglycan recognized by TLR2 for immune activation Some Gram-positive pathogens • Listeria monocytogenes + listeriosis • Mycobacterium tuberculosis +tuberculosis • Clostridium botulinum + botulism
Bacterial Pathogens (Gram-negative)
Contain an inner and outer membrane Outer membrane comprised of lipopolysaccharide (LPS); this is extremely antigenic (TLR4) and called endotoxin (excessive immune response) Lipid A component of LPS is responsible for LPS antigenicity Some Gram-negative pathogens: • Salmonella enterica + salmonellosis + typhoid fever (not typhus) • Legionella pneumophila +Legionnaires' disease • Yersinia pestis + plague
ELISA (enzyme-linked immunosorbent assay) sld 29 lec 3
Detects biomolecules from a complex mixtureCan work in multiple formats 1-capture antibody 2-target antigen 3-enzyme labelled detection antibody 4-subtrate on plate with wells, determine if virus is gram neg/pos and determine if present via diluition? plate has purified spike proteins that target the antibody that will attach to it, the more anibody present the darker yellow the color in the wells
2 pathogen types
Facultative pathogen: Does NOT require host for survival and replication ex-Salmonella, Yersinia, Legionella, Agrobacterium Obligate pathogen: Demands host for replication ex-Chlamydia, Rickettsia ,Plasmodium
microbiology summary
Field of microbiology was driven by disease-causing bacteria Koch's postulates Most microbes are not harmful, however Co-evolution has driven the formation of immune receptors that recognize PAMPs (pathogen-associated molecular patterns) (TLR2/4, fore xample) Pathogens manipulate host biology for survival
herd immunity
How herd immunity works When a person vaccinates against an infectious disease this not only protects that person. The acquired immunity is also beneficial to the rest of population because the immunized person can no longer be a potential transmitter. This cumulative social effect is known as herd immunity. Herd immunity implies that a disease can be eradicated if the fraction V of the population that is immune exceeds a critical value Vc V>Vc
Global Health Security Agenda 2024
In 2018, all member countries committed to the next phase of theGHSA strategic framework, termed "GHSA 2024". GHSA 2024positions member countries to develop the leadership, technical knowledge, and collaborative foundation to sustain health security in the long term: •Develop sustainable financing mechanisms for global health security •Promote multi-sector collaboration to improve GHS capacities •Improve information sharing across member countries •Strengthen accountability to member country commitments -GHSA 2024's target is for countries to take greater ownership of global health security efforts, and for more than 100 countries to improve health-security-related technical areas within five years
Molecular Biology Summary
Increased specificity of tools allow us to manipulate genomes Coupled with the tenants of microbiology, can understand mutant organismal phenotypes and assign activities to genes Total understanding of biological systems (genetic, molecular, biochemical)
What have restriction enzymes and PCR allowed us to do?
Isolating specific genes of interest Creating new genetic constructs (mutants) Rapid DNA sequencing (all current models rely on PCR techniques) Organism detection (important for clinical and environmental microbiology) New biochemistry (protein purification)
Bacterial protein secretion example-legionella
Legionella Type IVb secretion system secretes what? Effectors! ATP-dependent translocation of effectors into host cytosol *Translocation required for pathogenesis IcmS-IcmW important chaperones for delivery view slide 40????
Germ Theory" of disease
Living organisms below the limit of detection cause disease (as opposed to "spontaneous generation") By the time of Robert Koch, bacteria are known, can be isolated in pure culture, and can be attributed to specific diseases
Parasitism
Many organisms rely on others for sustenance and/or propagation an organism that relies on a host for sustenance and/or propagation and, in the process, harms the host Obligate parasite: cannot survive in any other manner but as a parasite: e.g., viruses, malaria parasites temporary obligate: may be occasionally, but not perpetually, "free-living" Facultative parasite: may exist in a free-living state or as a commensal; is an opportunist—if the chance arises, it may parasitize: +e.g., some fungi, Acanthamoeba (causes eye infections)
VIRUSES
Microscopic, pathogenic* packages of DNA or RNA and protein must invade cells within a host to survive and multiply: obligate parasites "A virus is a piece of nucleic acid surrounded by bad news" Peter Medawar, 1960 important ones: Influenza, HIV, Ebola and other hemorrhagic viruses, SARS coronavirus, MERS, Nipah, Variola major (smallpox)
Eukaryotic microbial pathogens
Often not really considered when discussing "microbiology" Examples: • Yeast/fungi (spores infectious) • Aspergillus fumigatus (aspergillosis) • Cryptococcus neoformans (cryptococcosis) * Healthy individuals are rarely infected invasively • Protozoa (unicellular): •Plasmodium falciparum (malaria) • Toxoplasma gondii (toxoplasmosis) • Naegleria fowleri ("brain eating") • Multicellular pathogens (usually helminths, slightly above microscopic): • Brugia malayi (lymphatic filariasis)
How do we know what is even causinga disease? How do we find out? Identification techniques?
Old methods (phenetic)-classify based on phenotype Newer methods (phylogenetic/genotypic)- use evolutionary evidence and look for similar DNA to comapare ez technique= isolate table--chart with characteristics of microbe advanced techniques= rapid clinical diagnoses--color changing rapid tests--wells with C&N given to computer and outputs determine organism based on color
Restriction modification in bacteria
One type of primitive immune system in bacteria -Each specific system has an endonuclease and a methyl-transferase - "self" DNA gets methylated at a specific site -Unmethylated DNA gets cleaved(restricted) in example slide 42- phage cannot effect bacteria bc sequnce in orange isn't methylated (the recognition site), once methylatd it can
Phenetic and phylogenetic classification
Phenetic: attempted to order diversity via classification via phenotypes + motility + color + shape Phylogenetic: post-evolution classification scheme; ordered via evolutionary relationships + evolved organisms share many processes and DNA sequence
The Big Killer Diseases of Children
Pneumonia 920, 000 Diarrhea 526, 000 Malaria 306, 000 Meningitis 116, 000 HIV 87, 000 Measles* 74, 000 Pertussis* - Tetanus* - *Vaccine preventable, 5.3mil children under 5, most deaths in sub-Saharan Africa and asia
Robert koch (1843-1910)
Probably the first "real" well-known clinical microbiologist (1843-1910) Grew pure cultures of organisms Experimented with different growth media to grow different cells Attributed specific organisms to specific diseases: Bacillus anthracis = anthrax Vibrio cholerae = cholera Mycobacterium tuberculosis = TB
Manipulating host biology
Reasons for manipulating host machineries? • Evade normal host defenses • Complete central dogma (replication, transcription, translation) • Host nutrient acquisition • All focuses on survival and replication. Disease is a secondary result! (I'm evil, but I don't really know that I'mevil)
The Immune System
Recognizes invading pathogens as foreign and mounts an attack Immunity is critical for protecting us against infection Pathogen evolution has allowed development of a multitude of "escape routes" -->"immune evasion" Host defense is multi-layered, sequential and intercommunicating: first: physical and chemical defenses -the skin, surfacing coatins of tissue such as mucous secretions, tears, acid pH, and surface cleansing mechansims second: frontline defenses -- cell-autonomous, intrinsic defenses -detection of altered cell metabolism, unusual macromolecules made only by invading parasites -protection of cytokines, induction of apoptosis, and interference with early steps of viral replication= role of antiviral proteins Third: attack and clean up - -innate AND adaptive immune defense -direct amplified response by coordinated action of cytokines and lymphocytes -infection cleared by pathogen specific antibodies, helper T-cells, and cytotoxic T-cells *production of maintenance of B-cell and T-cell "memory cells" --"immune host" ,ready to respond instantly to the same infection that induced the memory response
Major tools in the advent of molecularbiology
Restriction enzymes and DNA modification enzymes in the 1950—1960s Polymerase chain reaction (PCR) in the 1980s-critical for rapid progression of microbiology
How do these pathogenic microbes manipulate host biology?/ Host: pathogen interactions (not viruses)
Secreted proteins: + (Exo)Toxins: Proteins directly cytotoxic on cells +.e.g. ADP-ribosyltransferases (cholera toxin), proteases (BoNT), pore forming proteins (pneumolysin) + "Effector" proteins: not cytotoxic by themselves but interact with host pathways to alter cell. Can be toxic by themselves; often work with other effectors Cell surface proteins: stay in pathogen cell wall Other pathogen "parts:" manifestation of disease can result from dead bacteria (immune response to endotoxin, for example)
The 5 immunoglobin (Ig) classes +Ig= type of antibodies
Secretory IgA dimer= transferred to newborn via breastfeeding *view model
BACTERIA
Simple, single-celled organisms * Free-living, commensal (or mutual), and obligate parasitic species - latter are of medical importance Multiply by binary fission (splitting in two) - grow very quickly More complex than viruses single circular chromosome (but no true nucleus or nuclear membrane) have a cell membrane and (most) a cell wall have all the machinery to replicate DNA, transcribe DNA to RNA, and to translate RNA into protein Important ones: Yersinia pestis (plague), Bacillus anthracis (anthrax), Treponema pallidum (syphilis), Mycobacterium tuberculosis (TB)
Microbio-termonology of strains
Species: collection of strains that share properties and are measurably different from other species Strain: descendants of a pure microbial culture (clonal) Biovar: strain variants via biochemical/physiological differences Morphovar: strain variants via morphological differences (shapes) Serovar: strain variants via antigenic properties
total deaths from diseases
TB>Smallpox>malaria>plague>influenza>cholera> AIDS
third: Attack and Clean-up - - adaptive immunity
Unique features of adaptive immune responses: Unlimited specificity Memory Attack and Clean-up
Polymerase chain reaction (PCR)
Utilizes a heat-stable DNA polymerase to synthesize DNA DNA synthesis with most DNA-dependent DNA polymerases cannot occur without a free 3' hydroxyl This 3' -OH is "donated" by a synthetic fragment of DNA(primer) that is directed to the location you want to replicate (amplify) Multiple rounds of heating and cooling greatly amplifies a specific fragment
Viral Disease Eradication
What are the requirements to eradicate a viral disease? • Replication only occurs in one host • Vaccination induces lifelong immunity • Viral diseases that are species specific • Smallpox - humans - SUCCESS • Polio - humans - still survives in human fecal matter • Measles - humans - low income countries • Rubella - humans - virus still persists • Rinderpest - BUT in cattle and even-toed ungulates -SUCCESS (have not found a case since 2001 and was declared eradicated in 2011)
Microbiology
a branch of biology dealing with microscopic forms of life +first printed in 1880 so newish +biochemistry= 1848 and biology=1799
top causes of death in low income countries
death= descending in number and listed #1 cause communicable, maternal, neonatal and nutrition: -lower respiratory infection -diarrheal diseases -HIV/AIDs -malaria -TB -preterm birth compilation -birth asphyxia complication noncommunicable diseases: -ischaemic heart disease -stroke injuries: -road injury takeaway= low income the common factor causing death
top causes of death in middle income countries
death= descending in number and listed communicable, maternal, neonatal and nutrition: -lower respiratory infection -TB -diahorreal diseases -preterm birth complication #1 cause noncommunicable diseases: -ischaemic heart disease -chronic obstructive pulmonary disease -diabetes mellitus -liver cirrhosis injuries: -road injury takeaway- blend of noncommunicable and communicable
Trends and Global Inequality in child mortality
declined by 59% from 93 deaths per 1000 live births About 74% of under-five deaths occurred in two regions in 2018, WHO Africa(52%) and WHO South-East Asia (22%)
Types of Hosts
definitive host (primary host): supports adult stage(s) development; sexual reproduction (i.e., production of offspring) of parasite ex-dog/heartworm & humans and lice intermediate host (secondary host): supports asexual/immature stage(s) growth ex-mosquito and brugei malayai & pigs and tapeworm incidental host (accidental host)*: capable of supporting parasite growth, but not necessary for parasite survival or development; may suffer disease ex-humans and bacteria that causes lyme disease & humans and rabies reservoir host*: maintains a parasite stage that is infectious for humans ensures continuity of transmission; does not suffer disease*if this is an animal host that harbors a parasite that is infectious for humans, then the disease is a zoonosis ex-bats and Ebola virus & ticks and bacteria that causes Lyme disease *view assignment 1!!!!
Global # of smallpox reported cases
dove to zero around ~1977
Serovars- antigen properties diff in strain
ex Salmonella enterica serovar Typhimurium Typhi Dublin LPS- - lipopolysaccharide: -o-antigen - in O-polysaccharide, attempts to fool immune system + lipid A (includes glucosamine-phosphate dimer and fatty acids) allows the lipopolysaccharide to exist in the membrane
Biovar- biological/chem diff in strain
ex Chlamydia trachomitis biovar Trachoma and biovar LGV Trachoma: limited, localized ocular or genital infections LGV: systemic infections
Common theme for microbialpathogens: hijacking host biology
ex-legionella -bacteria that lines the inside of our cells -our cells use lyssosome to degrade it -legionella dumps proteins into host to disable the cell's machinery to recognize it and it lives inside cells
crispr example- - Incredible power in "recalcitrant" biological systems, including us
in the model part A the Cas9 nuclease targets the gene and repairs it
Global Health Security (GHS)
is the existence of strong and resilient public health systems that can prevent, detect and respond to infectious disease threats, wherever they occur in the world The Center for Disease Control and Prevention (CDC) works 24/7 to protect the health, safety, and security of the American people and fight global health threats worldwide. Why GHS Matters: GHS means safer nations and more stable economies Disease threats can spread faster than ever before with increased global travel and trade The vitality of the global economy is only as secure as the collective health of our people - 11 years ago SARS cost $30 billion in only 4 months - The anthrax attacks of 2001 infected 22 people, killed 5,and cost more than $1 billion to clean up - The 2009 H1N1 influenza pandemic killed 284,000 people in its first year alone - AIDS spread silently for decades
PRIONS
protein or "slow" virus - still quite undefined cause fatal brain disorders: "transmissible spongiform encephalopathies" transmitted via brain/spinal material - bovine spongiform encephalopathy ("mad cow disease") and scrapie in livestock kuru, Creutzfeldt-Jakob disease, and new variant Creutzfeldt-Jakob disease (mad cow disease in humans)
Adaptive Immunity
review sld 17-21 the ability to recognize and remember specific antigens and mount an attack on them Common feature: antigen presenting cells (APC) chop antigen into small pieces (peptide) load them on Major Histocompatibility Complex (MHC)/T-lymphocyte(slide 17) and transport to cell surface model sld 18 -B cell releases antibodies bind and inactivate virus -CD4+ T cells mediate immune response interacting with CD8+ T cells and with B cells leading to the virus specific antibody protection -CD8+ T cells recognize the viral peptides on the cell surface and eliminate the infected cell sld19-21 *** review TCR (t-cell receptor, on T cell) see/or dont see antigen presented by MHC (major histocompatibility complex) which is on APC (antigen presenting cell) which then causes the T-cell to activate/ or not +thousands of TCR on one T-cell, TCR recognizes specific chopped antigens -CD8+ T-cells cells then kill the infected cell thus neutralizing the infection +MHC class 1 -CD4+ T-cells trigger the body's response to infections and gets cytokines to attack +MHC class 2
model slide 24 lecture 2
shows innate vs adaptive immunity
specificity and memory in immune response
slide 12 lecture 2 takeway= generally within a weeks time, the adative immune response (third stage) is triggered
multidisciplinary approach
slide 5/ lec 1 Doctors and scientists: understanding of disease and development and implementation of prevention and control strategies Business persons and economists: making control and prevention strategies affordable and sustainable Architects and engineers: designing physical tools for prevention and control Sociologists and anthropologists: understanding social, cultural, gender, generational biases and attitudes of disease Mathematicians: understanding patterns of disease to allow predictions Geographers/ecologists: understanding how land use patterns affect disease transmission, especially contact between humans and vectors or reservoirs Climatologists: understanding how climate and climate change impact disease transmission and persistence
Mpox vs Covid-19
view model
viruses are diverse
view model slide 14 lecture 3 2121112 Group1-dsDNA genome ex-adenovirus (common cold) or herpes virus (herpes) Group2-ssDNA genome ex-parvovirus (canine parvo) Group3-dsRNA viruses ex-burnaviridae (infectious bursal disease in chickens) Group4- sense-strand ssRNA viruses ex-coronaviridae (sars/mers) Group5-antisense-strand ssRNA viruses ex-rhabidovirus (rabies) Group6- ssRNA viruses w/ reverse transcriptase ex-retroviruses like HIV Group7-dsDNA viruses w/ reverse transcriptase ex-hepadnaviridae (hepatitis B)
Molecular "cloning"
• "clone" gene onto stable, replicating, extrachromosomal DNA molecule(plasmid) • all regulatory information present on plasmid (we can transcribe and translate it) • allow for expression of genes at places other than the chromosome (say, incase of a mutant)
Last Cases of Smallpox
• 1975 - naturally acquired variola major: -discovered by 8yr old who was paid to report • 3yr old Rahima Banu, in bangladesh - isolated at home with guards posted 24-7 until all scabs fell off • Used a house-to-house ring vaccination strategy, ensuring all people within a 1.5 mile radius were protected • Everyone within a 5 mile radius was monitored • 1977 - naturally acquired variola minor: • Ali Maow Maalin - hospital cook in Merca, Somalia • First diagnosed with malaria and then chickenpox, only correctly diagnosed 14 days after fever onset • Made a full recovery from Smallpox • Died in 2013 of malaria he contracted while working in the polio eradication campaign • 1978 - research related exposure • Janet Parker - last person to die from Smallpox • She was a medical photographer at Birmingham University Medical School in England. • Worked one floor above a lab working on Smallpox • She became ill, took 9 days to correctly diagnose • She died September 11, 1978 • Her mother who had taken care of her also came down with Smallpox, despite being vaccinated
Smallpox: Eradication
• After WWII, the World Health Organization (WHO) was founded • WHO introduced standards to smallpox vaccine manufacturing • Focused smallpox vaccination to a global effort • In 1959 - World Health Assembly passed a resolution to eradicate smallpox globally • They did not provide any funding until 1966 • This was a time when air travel was becoming more common place, increasing global interaction at a time where they wanted the virus to stay put *wanted vaccine to bream the skin so special needle was used in place of interdermal needle, shaped like sharp tuning fork -DA henderson - led international effort to eradicate smallpox -1947- 6Mil people vaccinated in under a month after single case reported in manhattan
Cost of Eradication of smallpox
• Before eradication it was estimated that active smallpox outbreaks were costing countries $1 billion per year in 1960s dollars • Eradication effort was completed with a $300 million budget • While international donors provided 1/3 funds • Countries with endemic smallpox provided 2/3 funds
Variolation vs Vaccination
• Both used to prevent Smallpox disease which typically killed 30% of those infected. Survivors were frequently scarred Variolation vs Vaccination: variolation: -Weak smallpox virus (isolated from a patient with a mild case) -Used in China and Africa for thousands of years, brought to Europe by Lady Montagu in 1721 -Still causes smallpox, hopefully a mild case. 1-2% of variolated people died from Smallpox. Able to spread to others Vaccination: -Coxpox - originally Vaccinia virus - widely used form -Edward Jenner and others developed in 1798, spread through Europe -Coxpox infection was safer than smallpox. Still some side effects and occasional deaths, but better than variolation.
Smallpox
• Caused by the Variola virus • Symptoms - fever and vomiting followed by skin rash + Rash turned into fluid filled bumps with dent in the center + 1/3 of patients would end up blind • 3 out of every 10 people with the disease dies • Permanent scarring was common • Scarring on the face and eyes led to blindness • Last naturally occurring smallpox case happened in the USin 1949
Other famous people who supported variolation
• George Washington was scarred from smallpox, but ensured his wife was variolated to prevent her from getting sick • 1775 George Washington ordered the whole Continental Army to be variolated • James Madison had his whole family variolated during a smallpox outbreak • John Adams was variolated before going to Boston which had an ongoing outbreak • Benjamin Franklin did not have his family variolated, but after his 4 year old son died from smallpox, he became an advocate
Smallpox :Variolation
• Measures to control infectious diseases started long before infectious diseases were identified • Variolation was developed in China around 1000 BC A method to induce immunity by purposefully infecting a human with the less virulent smallpox Variola isolate, which usually caused only a mild clinical disease Find someone with a mild case of smallpox, scrape the scabs and pus from the pox, grind the material and this was either blown up the nose or rubbed into the small scratches in the skin Became common in China and Africa • 1721 - Onesimus (O-nes-imus) African slave forced to come to the US in the late 1600s Was purchased for a Puritan church minister named Cotton Mather in 1706 in Boston Onesimus told Mather about the centuries old tradition of inoculation practiced in Africa When a smallpox epidemic hit Boston in 1721, Mather convinced Dr. Zabdiel Boylston to experiment with the procedure, and over 240 people were inoculated 6 died, or 1 in 40 1 in 7 of the non-variolated Bostonians died The practice was also used to inoculate American soldiers during the Revolutionary War • 1721 -Lady Mary Wortley Montagu Lost her brother to smallpox and had severe facial scars from her pox infection While traveling in Turkey witnessed variolation and had her 5 year old son inoculated Brought him and daughter to England and had her daughter inoculated at the royal court A group of prisoners were inoculated and then exposed to smallpox -they survived and Europe began variolation as standard practice Produces a characteristic pox lesion on the hand or arm It is possible for a human to die from variolation 1 to 2% of those variolated died as compared to 30% who died when they were exposed to the disease Because vaccination was thought to be safer
Mpox Outbreaks
• Mpox (formally known as monkeypox) is a close cousin of smallpox • Actually a disease carried by rodents and is endemic in parts of Africa + Endemic - regularly occurring within an area or community • Once we stopped vaccinating for smallpox, occasional cases of Mpox were identified in regions where the animal reservoirs live • Periodic outbreaks in US typically associated with exotic pet trade • 2022 largest outbreak of Mpox
Smallpox Disease Course
• Once exposed, there was a 7-19 day incubation period -time frame before a person showed symptoms, luckily *Smallpox was not contagious during this time frame • First symptoms (lasted 2-4 days): • High fever, head and body aches, • sometimes vomiting • Early Rash (lasted 4 days): • Most contagious • Rash started in the mouth and tongue, when they would break open spread the virus to the throat and skin • Rash mainly on the outer extremities (hands, feet, face, arms and legs) • By the forth day, the sores would fill with a thick opaque fluid, usually fever would spike during this period • Pustular Rash and Scabs (lasted 10 days) • Still contagious • Sores becomes pustules • Round, firm, like peas under the skin • After 5 days, the pustules begin to crust and then scab • Takes about 14 days for all sores to scab over • Scabs fall off (lasted about 6 days) • Still contagious• Scabs fall off, leaving marks • No scabs • Once all scabs have fallen off the person is no longer contagious, usually take 4 weeks from start of rash
Smallpox Research
• Research is still being done on Smallpox • Only at 4 locations in 1981 • USA• England• Russia• South Africa • By 1984, virus was only actively in USA and Russia • CDC in Altanta, GA, USA • VECTOR in Koltsovo, Russia • Working to make antivirals and understand pathogenesis • BSL4 lab
Ring vaccination
• Smallpox does not readily transmit between people, so you cannot contract it by simply being in public. • There was not enough resources to vaccinate everyone(money, people, or vaccine) • They searched for cases • Vaccinate to provide a "ring of immunity" around each case • Remember the smallpox vaccine was not 100% safe, so this helped minimize adverse events • Most efficient use of vaccine supplies and people-power • Requires people to trust the system and help identify cases -MPXV 1st exposure and the people exposed to those people were vaccinated
Smallpox: Vaccination
• Some people observed dairymaids in close contact with cows with cowpox would get lesions on their hands, but survive Smallpox outbreaks • Vacca means cow • Rather than using a Smallpox lesion to Variolate, they used a Cowpox lesion to "Vaccinate" • Benjamin Jetsy (a farmer) -inoculated his wife and 2 sons with cowpox virus from the udder of an infected cow in attempt to control smallpox (1774; one of ½ dozen persons who's work pre-dated Jenner's) • Edward Jenner recognized that dairymaids infected with cowpox virus were resistant to infection by smallpox virus • 14th of May 1796, used cowpox-infected scab material obtained from a milkmaid to vaccinate 8 year old James Phipps (son of his gardener) • He then exposed Phipps to people acutely ill with smallpox, which Phipps failed to contract • He repeated the experiment on other children, including his own son • Concluded that vaccination provided immunity to smallpox without the risks of variolation *Jenner's findings were published in 1798 and was given the title of father of vaccination In the 1800s, cowpox virus used for smallpox vaccination was propagated by infecting different farm animals • Somehow, cowpox changed to become vaccinia virus • Vaccinia virus is in the poxviridae family, but is genetically unrelated to cowpox and smallpox viruses, but still protects humans against smallpox virus infection (most similar to a horse pox virus) -vaccine made by infecting and skinning cows
Smallpox: Transmission and Spread
• Spreads mainly through direct and fairly prolonged face-to-face contact between people • A patient was contagious once the first sores appeared in their mouth and throat and stayed contagious until their last scabs fell off • Virus could be spread through coughs or sneezes • The pustules and scabs were also full of virus and bedding and clothing would become contaminated and could spread the virus • Only infects humans, so no animal reservoirs or insect spread
The Black Death
• The 1347 invasion of the 1347 invasion of Black Death into Messina (Sicilian port in Italy) and its long lasting grip on Europe • The plague epidemic in 19th century China and what we have learned since then about the disease (epidemiology, pathology and molecular pathogenesis) • Was Yersinia pestis really the causative agent of the medieval Black Death?-yes and caused many varieties of the plague
plague sweeps through europe
• The initial epidemic sweeps through central Europe within 3 years killing what some sources estimate to have been up to 1/3 europe's population • Epidemics flare up in various regions of Europe for the next 4 centuries
Top Global Health Security Risks
•Emergence and spread of new infectious diseases •Ever-increasing globalization of travel and trade, enabling disease to spread •Rise of drug-resistant, disease-causing pathogens •Potential for accidental release, theft or illicit use of dangerous pathogens CDC Strengthens Capabilities: •Surveillance systems to quickly catch outbreaks before they spread •Laboratory networks to accurately diagnose diseases and identify new pathogens •Workforce development of frontline staff to identify, track, and contain outbreaks at their source •Emergency Management systems to coordinate response efforts when crises occur
