Microbiology Final Exam Study Guide PDF

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Microbiology Final Exam SG Active Vaccination  Principle o Adaptive immune response initiated following pathogen infection, preventing subsequent symptomatic infection  Develops 7-12 days into infections  Due to memory function o Vaccination allows for an adaptive immune response w/o the harsh side effects  Stimulates immune cells w/ foreign epitopes w/o exposing the host to disease-causing organisms  Vaccine types (3) o Live, attenuated vaccines  Definition  Living organisms that share most/all epitopes w/ a pathogen, but cannot cause disease  May be mutant or wild type (closely related, but not identical to the human pathogen)  Development  Old school: attenuation by selection on unnatural hosts o Labor-intensive o Time consuming New school: recombinant DNA technology used to 1) mutate a wild-type pathogen to attenuate it, and 2) introduce antigens from severe pathogen into more benign organisms Killed pathogen vaccines  Definition  Pathogen is grown in large scale within a lab, killed so that most antigen epitopes are preserved, & injected into the host where an immune response is initiated  Pathogen cannot reproduce or cause disease  Development  Virus is grown in large amount in a medium such as chicken eggs  Virus is the purified, concentrated, & killed using either UV radiation or chemicals  The killed vaccine is then purified again & divided into appropriate doses Subunit vaccines 

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Definition  Antigens derived from the pathogen are isolated or produced in the absence of the pathogen using recombinant DNA technology  Large amounts are produced, injected into the host, and an immune response to the subunits the pathogen, rather than the whole  Subunits cannot reproduce or cause disease o Lacking genome Development  A gene-encoding virus capsid is put onto a plasmid for expression in eukaryotic cells o Requires things such as; start codon, promoter, polyadenylation side  Plasmid is controlled by eukaryotic gene expression sequences  Transcription & translation result in massive # of capsid proteins  Capsid proteins self-assemble into empty capsids that appear like the pathogen from the exterior, but no genome is present [virus-like particle; (VLP)]  The empty capsids are then extracted & purified to make a vaccine

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Live, attenuated vaccines…  May draw a powerful response w/ a single vaccination dose or a dose + single booster  Attenuation allows replication to some degree, amplifying the dose  Attenuation also means the immune system “sees” the pathogen longer  Draws humoral & cellular immune responses Subunit vaccines…  Fastest to produce Live, attenuated vaccines…  Can be expensive to develop & produce  Often requires a cold chain for delivery  Reversion Killed pathogen vaccines…  Often require multiple booster vaccinations to get high-level, lasting immunity  Vaccination dose doesn’t amplify within host, meaning the host sees a low amount of antigen  Antigen is non-replicating, meaning it is quickly degraded & removed by the host  Immunity to intracellular pathogens is often poorer  Proteins don’t have access to cytoplasm Subunit vaccines…  Often require multiple booster vaccinations to get high-level, lasting immunity  Vaccination dose doesn’t amplify within host, meaning the host sees a low amount of antigen  Antigen is non-replicating, meaning it is quickly degraded & removed by the host  Immunity to intracellular pathogens is often poorer  Proteins don’t have access to cytoplasm

Mandatory Vaccinations  Herd immunity o Protects public health o Spread of infection is decreased by # of susceptible hosts  

o Reduces rate at which infection spreads Threshold: % of population that must be vaccinated in order to prevent epidemics through herd immunity o May be so high that mandating vaccine is necessary, such as making it required to attend public school R0: # of people 1 infected person may be expected to pass the disease to in an unvaccinated population o Affected by factors such as public health practices, hygiene practices, etc. o If R0 increases, so does the herd immunity threshold

Vaccine Development & Testing  Stages (5) o Pre-clinical testing  Main concern = safety & efficacy  Setting  Cell culture & animal studies  Expectations  A killed virus vaccine should not replicate  Vaccine should not cause symptomatic disease  An induction of an immune response, such as production of neutralizing antibody and/or cellular immunity should result

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Main concern = safety Setting  Small # (< 20) seronegative volunteers at low risk of infection monitored for weeksmonths o People who have not seen the organism previously

 Low doses Expectations  Adverse reactions  Development of immune response (production of antibodies, cellular response) Phase II clinical trial  Main concern = safety  Setting  Larger # (10-100) seronegative volunteers at low risk of infection  Range of doses  May include preliminary  Expectations  Long-term adverse reactions Phase III clinical trail  Main concern = safety & efficacy  Setting  1000s of volunteers (seronegative & those at risk) monitored for months-years  Limited range of doses determined by results in phase II  Expectations  Adverse reactions  Immune response Protection from disease  Where most vaccine candidates fail due to low efficacy or unexpected safety issues Long-term monitoring (may include possible phase IV clinical trial)  Main concern = safety & efficacy  Setting  Evaluation of efficacy under different field conditions  Evaluation of safety for side-effects of potential concern  Expectations  Reporting of suspected vaccine-related adverse events using vaccine adverse event reporting system (VAERS) reporting o Run by CDC & FDA 

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Vaccine Development & Testing—Rotavirus Disease  Rotavirus: upset stomach & diarrhea in children (stomach flu) o Transmitted via fecal-oral route o Resulted in discomfort and lost economic productivity (lost parent work hours due to inability of child to attend day-care) o Killed ~600,000-800,000 children per year o 5 common strains—infection of 1 provides lasting immunity to severe disease arising from that strain  dsRNA, segmented genome  Rota-Shield—an unsuccessful vaccine o Overview  Type: live, recombinant, attenuated virus based on rhesus monkey virus  Administration: 3 oral doses administered at 2, 4, & 6 months of age  Effectiveness: prevents 50-70% of all cases, 70-90% of severe cases  Risk for intussusception (small intestine folding in on itself) = 1 in ever 5,000-10,000 cases

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Pulled from the shelf  Death rate w/o vaccine = ~1/175,000  Death rate w/ vaccine, due to intussusception = ~1/250,000  ~70% efficacy might be expected to save 500,000 children’s lives/year  Due to…  Risk of death from vaccine vs risk of death from the disease were too similar  Company survival (cost of economics and liability) Rotateq—phase III testing vaccine o Overview  Type: live, attenuated hybrid virus vaccine (mixture of cow rotavirus and human rotavirus, resulting in reassortants)  Administration: 3 oral doses administered every 4-10 at 10 weeks of age o Testing data 

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 Subjects: Infants 10 weeks old  Double-blind, placebo controlled  Varied doses  Effectiveness: prevents 74% of all cases, 98% of severe cases Results  Intussusception  Seroconversion (appearance in the blood of antibodies to an antigen of interest)

The Process of Infection  Infection o Host: larger organism that supports the survival & growth of a smaller organism o Infection: microbe growing & multiplying on or within a host

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 May or may not result in overt infectious disease  Varies in respect to severity, location, & type of organisms involved o Infectious disease: any change from a state of health in which part or all of the host is incapable of carrying on normal functions due to presence of a pathogen or its products Pathogenicity o Pathogen: any organism that causes disease  Opportunistic pathogen: pay be part of normal flora & causes disease when it gains access to other tissue or when host is immunocompromised  EX: microbiota of the gut  Doesn’t necessarily cause disease in very host o Pathogenicity: ability of a pathogen to cause disease  Usually related to specific virulence factors o Virulence: degree of harm (pathogenicity) inflicted on the host

Types of Microorganisms  Extracellular pathogens: remain in tissues & fluids but never enter host cells during course of disease  Intracellular pathogens: grow & multiply within host cells o Facultative intracellular pathogens: reside within the cells of the host or in the environment, but can be grown in a pure culture w/o host-cell support o Obligate intracellular pathogens: incapable of growth & multiplication outside of a host cell, cannot be grown in the laboratory  All viruses  Some bacteria

Course of Infectious Disease  Terminology o Signs: objective changes in the body that can be directly observed (EX: fever, rash)  Can be measured o Symptoms: subjective changes experienced by the patient (EX: pain, loss of appetite)  Hard to quantify, broad o Disease syndrome: set of signs/symptoms that are characteristic for a disease  Stages (4) o Incubation period: time between pathogen entry & development of signs/symptoms  Pathogen is reproducing, but has not reached a sufficient level to cause clinical manifestations  Length varies on pathogen type o Prodromal stage: occurs at onset of signs/symptoms that aren’t specific  Host is often contagious o Illness period: when disease is most severe & displays characteristic signs/symptoms o

 Immune response has been triggered Convalescence: recovery stage in which signs/symptoms being to disappear, pathogen cleared out

Events in Infection & Disease 1.) Transmission from previous host or reservoir to new host a. Varies due to virulence, abundance of pathogen, & presence of adhesion & invasion factors 2.) Organism outcompetes the resident microbiota for resources & survives host defense mechanisms 3.) Disease occurs (damage of host cell, host immune response stimulated, host genome altered) Transmission & Entry into The Host  Sources: location from which the pathogen is transferred to the host o May be animate (humans or animals) or inanimate (water or food)  Reservoir: natural environmental location in which the pathogen normally resides  Site in which a source acquires pathogen or where direct infection of the host may occur  Zoonoses: a disease in which infectious agents are transmitted from animals to humans  Vector: organisms that spread disease from one host to another (EX: mosquitoes, ticks, fleas)  Types of transmission (5) o Airborne: pathogen is suspended in the air in droplets, droplet nuclei, or dust  Droplets: produced when liquids are placed under pressure & expelled  Direct transmission  2mm in diameter, require close proximity for transfer (1 m)  Droplet nuclei: small particles that result from the evaporation of larger droplets  Indirect transmission  1-5 µm in diameter, remain airborne for hours-days, travel long distances  Dust: carries pathogens that can survive for long periods outside of a host cell  Indirect transmission o Contact: coming together or touching of the source of the pathogen & the host  Direct: physical interaction w/ the infectious source (person-to-person)  EX: kissing, touching, sexual contact, through the placenta, during birth  Indirect: an inanimate object (fomite) transfers the infectious agent between hosts  EX: utensils, bedding o Vehicle: inanimate materials that transmit pathogens indirectly  Vehicle transmission spread the pathogen to multiple hosts (EX: food, water, air) o Vector-borne: living vectors (mostly arthropods) directly transmit pathogen while often benefiting the pathogen by permitting extensive reproduction & spread within the host  Vectors are left unharmed o Vertical: unborn child acquires a pathogen from an infected mother  Not as frequent as horizontal infection  Babies born w/ infectious disease are said to have congenital infection

Infection Dose  Rate at which an infection proceeds correlates w/ initial inoculum & virulence of the microorganisms, as well as the host’s ability to combat infection  Types (2) o Infection dose 50 (ID50): # of microorganisms required to cause disease in 50% of the inoculated hosts  The lower the infectious dose, the higher the risk of infection o Lethal dose 50 (LD50): # of microorganisms required to be lethal to 50% of the inoculated hosts  Highly virulent pathogens kill at a lower dose than less virulent organisms Adhesion & Invasion Factors Initiate Disease  First steps in disease are entry & adhesion to establish colonization o Portal of entry: site at which access to the host is gained (EX: skin, respiratory system, GI tract) o Adherence: attachment of the microorganisms to a target cell  Mediated by adhesions (bind to host sites, facilitate infection, & contribute to the virulence) o Colonization: establishment of a site of microbial replication on or within a host  Doesn’t necessarily result in tissue invasion or damage  Invasion disseminates pathogens o Pathogens described based on infectivity & invasiveness

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 Infectivity: ability to create a discrete point of infection  Invasiveness: ability to spread to adjacent tissues Pathogens can actively or passively penetrate the host’s surfaces  Active penetration: occurs through lytic substances that alter host tissue by…  Attacking extracellular matrix & basement membranes of integuments & intestinal linings  Degrading carbohydrate-protein complexes between cells or on cell surfaces  Disrupting the host cell surface  Passive penetration: not related to the pathogen itself, takes advantage of already-existing barrier disturbances (EX: skin lesions, insect bites, wounds) Pathogen disseminates to deeper tissue once tissue is penetrated  May enter circulatory system  Bacteremia: presence of viable bacteria in the bloodstream  Septicemia: presence of bacterial or fungal toxins in the bloodstream Invasiveness varies among pathogens  Noninvasive pathogens don’t spread from one tissue to another, but produce a toxin that becomes blood-borne  Some microbes use actin-based motility for cell-to- cell spread

Overcoming Host Defenses  Successful pathogens overcome competition & elude host immune response o Produce Type III & IV secretion systems o Find shelter to avoid recognition by defense cells o Survive & replicate inside host cells o Squeeze between host cells o Make capsules to avoid phagocytosis o o o o 

Burrow under mucus Secrete exopolysaccharides to form communal shelters within biofilms Produce enzymes that inactivate innate resistance mechanisms Excrete specialized proteins to selectively kill host cells

Example o Biofilms: bacteria are protected from nutrient deprivation, predators, environmental shifts, antimicrobial agents, & host immune cells  Bacteria may exchange plasmids, nutrients, & quorum-sensing molecules  Less sensitive to antibiotics & more resistant to host defense mechanisms

Damage to The Host  Pathogenicity islands: large segments of bacterial chromosomal & plasmid DNA that encode virulence factors o Increase bacterial virulence o Absent in nonpathogenic members of the same genus or species o Can be spread through horizontal transfer of virulence genes to bacteria 

Toxingenicity: pathogen’s ability to produce toxins o Toxins: substances that disrupt the normal metabolism of host cells with deleterious effects on the host o Intoxications: disease that results from entry of a specific performed toxin into the host  Don’t require the presence of the pathogen, just its toxin o Types (2)  Exotoxins: soluble, heat-labile proteins released into host tissues as the bacterial pathogen metabolizes  Characteristics o Travel from the site of infection to other tissues o Usually synthesized by specific bacteria that have toxin genes in their plasmids or prophase DNA o Among the most lethal substances known  Types o AB toxins: named for its 2 subunits—A subunit (responsible for toxic effect) and B subunit (binds to host cell receptors, triggering endocytosis)  A subunit exerts the deleterious effect  B subunit determines the cell type the toxin will affect o Membrane-disrupting exotoxins: pore-forming toxins that insert themselves into cell membranes, disrupting it, & causing cellular components to leak Superantigens: stimulate as many as 30% of host T cells to overexpress & release massive amounts of pro-inflammatory cytokines from host immune cells in the absence of antigen  Excessive concentration of cytokines causes host organs to fail, allowing time for pathogen to disseminate  Cytokine storm: superantigens cause fluid loss, fever, low BP—resulting in shock & death Endotoxins: heat stable toxin presented inside a bacterial cell, released when cell disintegrates  Characteristics o Requires a higher dosage than exotoxins to become toxic o Weakly immunogenic o Cause general system effects (fever, shock, damage to the lining of blood vessels, weakness, diarrhea, inflammation, etc.)  Types o Lipopolysaccharide (LPS): outer membrane of Gram-negative bacteria, which is toxic to humans  Endogenous, bound to the bacterium & released when the microorganism lyses or during multiplication  Lipid A = toxic component  Trigger biochemical events that lead to serious complications such as septic shock o

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Epidemiology  Science that evaluates the occurrence, determinants, distribution, & control of health & disease in a population  Determines… o Causative agent, source or reservoir of disease agent, mechanism of transmission, host & environmental factors that facilitate development of disease within a population, & best control measures

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Terminology o Outbreak: sudden, unexpected occurrence of disease, usually within a limited segment of a population o Sporadic: occurs occasionally & at irregular intervals o Endemic: maintains a steady low-level frequency at a moderately regular interval o Hyperendemic: gradually increase in frequency beyond endemic level, but not to epidemic level o Epidemic: outbreak affecting many people at once, sudden increase in occurrence above expected # o Pandemic: increase in disease occurrence within a large population over 2+ countries around the world Measurements o Incidence: # of diseased people during a defined time period, as compared to total population o Prevalence: total # of individuals infected in a population at a specific point in time, no matter when the disease began  Total # in cases in population / total population  EX: looking at flu cases in the month of November? o Morbidity: frequency at which a disease appears in a population  # of new cases of a disease during a specified period / # of individuals in the population o Mortality: relationship between the # of deaths from a given disease & total # of cases of the disease  # of deaths due to a given disease / size of the total population w/ the same disease

Infectious Disease  Communicable disease: infectious disease transmitted from person to person o Not all infectious diseases are communicable 

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Types of epidemics (2) o Common source epidemic: characterized by reaching peak level within a short period of time (1-2 weeks), followed by a rapid decline in # of infected patients  Usually results from a single, common contaminated source o Propagated epidemic: characterized by a slow & prolonged rise, followed by a gradual decline in the # of individuals infected  Usually results from a single infected individual into a susceptible population Herd immuni...