Perspectives on Microbiology Study Guide Fall 2022

MGY277 STUDY GUIDE FALL 2022 UNIT 1 PERSPECTIVES ON MICROBIOLOGY • Know what the major contributors to the Germ theory of disease contributed and how they arrived at their conclusions. 1. Akshamsaddin Turkish Scientist in 1400s, claimed "invisible seeds" in plants and animals 2. Van Leeuwenhoek First to see microbes with microscope, magnified things by 300x 3. Semmelweis Proposed idea of washing hands in between patients to limit spread of microbes 4. Bassi Infected silkworms by fungal pathogens --> found if he touched an infected silkworm to noninfected one the non-infected one would catch infection. Recommendation: Clean equipment 5. Koch Developed postulates: If a microbe met all these conditions it is the cause of the disease 6. Pasteur Biggest contributor to germ theory of disease. Developed techniques for vaccine production. Disproved “Spontaneous generation of microbes”. Developed Vaccine for rabies and anthrax. Discovered Staphylococcus aureus, Streptococcus pyogenes, Pneumococcus, anaerobic fermentation by microbes, and new pathogens of silkworms. 7. Lister Added carbolic acid directly to wounds and found it prevented infections. Later developed other methods to exclude bacteria from wounds: Sterilizing instruments before use & Clean operating room. + Koch’s Postulates (conditions for microbe to be disease causing) 8. Jenner Invented smallpox vaccine using cowpox • How did the discoveries of the major contributors to the Germ theory of disease build upon one another? • What is vaccination? An injection of an inactive or weakened form of a virus to create adaptive immunity in an individual • What is variolation? Exposing an individual to a small dose of live virus to trigger a mild immune response, building immunity to the virus • What impact has infectious disease (and the control of infectious disease) has had on the human population? • What are the major categories of microbes? Bacteria, Archaea, Eucarya • How can microbes be useful? Food production, use in biotechnology (E.coli) making insulin, Commercially valuable chemicals, Biodegradation • What are the key differences between Bacteria and Archaea? rRNA sequence, lipids, transcription, ribosomes, no peptidoglycan in cell walls What about the similarities? Single celled, no membrane bound organelles, flagella, binary fission to multiply, DNA packed in cytoplasm • What are the defining features of fungi, protozoa and helminths? Microscopic or macroscopic, single celled, multicellular, rigid cell wall, degrades organic material (Fungi) Microscopic, single celled, motile, no rigid cell wall, ingest organic material (Protozoa) Multicellular parasites, worm-like, 3 types, transmit through either burrowing through skin, consumed, or insect bite (Helminths) • Why are some non-microbes part of the study of microbiology? Since some non-living microbes such as viruses and prions can still cause disease • What is the evidence for the two-domain system? Slide 48 UNIT 2 – BACTERIA • Know the definitions of magnification, refraction, resolution and contrast and be able to apply them when looking at an image Magnification: the increase in apparent size of the object compared to its actual size Resolution: the ability to see objects as distinct, instead of as a blur that combines them Contrast: the ability to see objects against the background Refraction: when light rays change direction when there is a change in the medium • Know the lenses of a bright-field microscope (ocular, objective, condenser) Ocular – lens magnification 10X. Objective – 4 different magnification (4X, 10X, 40X and 100X (oil)) Condenser – Focuses light on specimen (no magnification) • Know how to calculate the total magnification in a light microscope given the power of the different lenses Total magnification: product of the objective and ocular lens power (objective multiplied by ocular) • Know why and when oil is used in a light microscope To avoid refraction while using lens sensitive to light • Know the difference between bright and dark field light microscopy Dark field is a form of microscopy in which the specimen is brightly illuminated on a dark background • Know the fundamental differences between electron and light microscopy and the advantages and disadvantages of each Electron microscopes have a bigger magnification, electromagnets replace glass lenses, resolution is higher, and electrons replace light. Electron microscopes are more expensive and large, complicated, sample must be dead, stains use toxic/radioactive material. • Know the different images obtained from scanning and transmission EM Scanning EM - Type of electron microscope that magnifies with a beam of electrons scanned over surface of specimen. It is used to observe surface details and yields a 3-D effect Transmission EM - Type of electron microscope used to observe fine detail of cell structure, also allows to see internal details. Works by directing electrons that pass through or scatter. • Know the steps of a Gram-stain and the basic reason why some cells stain purple while others do not • Know what the acid-fast stain is used for Detects organisms that did not take up the stain --> used to identify clinical specimens • Know the difference between differential and simple staining Simple Staining - One staining agent to determine shape, arrangement, etc. Differential Staining- more than one staining dye to differentiate between samples • Know what fluorescence microscopy is (vs. simple light microscopy) and what makes immunofluorescence techniques so powerful Fluorescence - Microscopy in which sample is fluorescent in order to see things better Immunofluorescence- Fluorescent molecules that are chemically attached to antibodies that can bind to specific cellular components • Know the terms for the shapes and groupings of bacterial cells (cocci, bacilli, etc) Coccus: spherical Rod (bacillus): cylindrical Vibrio: Bent Cheetos Spirillum: Spiral Worm like Spirochete: Spiral very strong zigzag • Know how molecules get across lipid bilayers (diffusion and passive, active, and facilitated transport) Facilitated diffusion- Down conc. No energy Active Transport – Up conc. Energy • Know how molecules get across the outer membrane of Gram-negative bacteria • Know the fundamental structure of a Gram-positive and Gram-negative bacterial cell Purple Gram + Thick layer peptidoglycan + no outer membrane Pink Gram – Thin layer peptidoglycan + inner membrane • Know the basic structure of peptidoglycan (NAG-NAM chains and wall peptides). (NAG) does not have a pentapeptide attached to it while the N-acetylmuramic acid (NAM) has a pentapeptide attached to it- only in bacteria • Know the very basic structure of LPS (Lipid A, core, O-antigen) and its importance Lipid A: - Anchors the LPS to lipid bilayer Core: - Short Stretches of sugar linked to one another, sometimes with unique arrangement O antigen: - Repeating chain of sugar molecules that sticks out from bacteria and contact the outside world Contrast is improved by -ve/+ve staining and dark-field microscopy UNIT 3 – VIRUSES • What are the contributions of Beijerink, Ivanovsky, Loeffler and Frosch? Beijerink - Dutch microbiologist, discovered that the disease causing material (in a tobacco plant) could pass through filters that normally trap bacteria. Ivanovsky - co-discoverer of viruses and one of the founders of virology Loeffler & Frosch - Foot and mouth disease virus • What are the physical and genomic features of viruses? Physical - Protein capsid surrounding nucleic acid & There are enveloped and non-enveloped viruses • How viruses are classified and grouped? Through viral taxonomy 6 orders - Virales 87 families - viridae 19 sub families - virinae 349 genera - virus 2000 species • What makes viruses challenging to study in the laboratory setting? Require a host to divide, must always be cultivated in cells for study • What are the basic structures of enveloped and non-enveloped animal viruses, and what functions do they serve? (helical, icosahedral, complex, spike proteins) Helical- Rod-shaped capsomeres that form a continuous helix around the nucleic acid icosahedral - 3D, 20 sided figure with 12 evenly spaced corners complex - bacteriophages, the viruses that infect bacteria. Take shapes that are not symmetrical • What is the relationship between shingles and chickenpox? Where does the varicella zoster virus reside in the body? Both caused by the varicella zoster virus. *It resides in the spinal cord • Know the difference between acute and persistent infections Acute - Quick infection, symptoms don't last very long Persistent - chronic or latent infections caused by persistent viruses that tend to remain in the host for long periods-from many weeks to a lifetime • How can viruses contribute to cancer? Transformation of host cell to malignant cell Viruses enter cells with onco-genes which can interfere with cells control mechanisms • What is a virion? Nucleocapsid-capsid containing genome (Nucleic acid + the protein coat (capsid)). • Know the five steps of viral infection life cycle. 1) Attachment (adsorption) 2) Penetration and uncoating 3) Synthesis of viral proteins and genome replication 4) Assembly 5) release • Know the basic strategies of replication and how they relate to the type of nucleic acid the virus has (DNA or RNA - single stranded or double stranded - positive or negative sense) DNA- Generally double stranded, replicates in nucleus, host machinery for DNA synthesis RNA- Generally single stranded, replicates in cytoplasm, requires replicase (virally encoded RNA) • Define latent, acute, chronic infections Latent- Spikes of acute infections randomly over time Acute- Quick infection, symptoms don't last very long Chronic- Type of persistent infection that continuously releases low levels of particles for a long period of time like hepatitis • What is a cytopathic effect? How does it manifest? Multiple nuclei in one cell. Can result from viral infections, occurs due to a viruses ability to fuse membranes. UNIT 4 – EUKARYOTIC MICROBES • Know the difference between an opportunistic and primary pathogen. Opportunistic pathogen: cause disease in immunocompromised individuals Primary pathogen: can cause disease in otherwise healthy individuals • Know what differentiates a eukaryotic cell from a prokaryotic cell. Eukaryotic cell: • • • • • Larger Has nuclear membrane No peptidoglycan Membrane-bound organelles Non-extreme environments Prokaryotic/Bacterial Cell: • • • • • A lot smaller NO nuclear membrane Has PEPTIDOGLYCAN Does not have membrane-bound organelles In all environments (extreme or not) • What are the defining characteristics of fungi? Fungi: • • • • • Eukaryote Cell wall has CHITIN Cell membrane composed of ERGOSTEROL (animal cell membranes composed of cholesterol) Can exist in many forms: • single-celled yeast • hyphae or pseudohyphae (multi celled filaments) • spores (many fungal spores everywhere on earth… 10, 000 cells/per meter cubed in the air we breathe); with each breathe, about 5 fungal spores Causes disease in 3 ways: • Allergic/asthmatic reaction • Mycosis (infection; grows on or throughout body) • Produces toxin which causes illness after ingestion • • What unique fungal cell pathways make attractive targets for antifungal drugs? Ergosterol biosynthesis is a major antifungal drug target • What are the defining characteristics of protozoa and how they contribute to human disease? Protozoa: • Microscopic, single-celled eukaryotes • Live in soil and water • No cell well • Usually motile • Exist in multiple forms: • Ex. oocysts (resistant to disinfectants) • Extremely evolutionarily diverse, and not a unified group • Shape bacterial evolution by acting as “training grounds” • Support environmental persistence of several pathogens • Know the three major types of helminths, their differentiating features, and routes of human infection. Nematodes (roundworms): - Ingested - Rob human body of nutrients by feeding on material that enters the digestive tract - Cause choking an pulmonary symptoms when they enter respiratory tract Cestodes (tapeworms): - Ingested (raw and undercooked meat) - Attach to intestines of hosts and absorb pre digested nutrients Trematodes (flukes, flatworms) - Infects through skin - Suckers hold them in place while they suck fluids from hosts • Know the definition of intermediate and definitive hosts Intermediate Host- Asexual expansion of parasite numbers. A temporary host for a parasite Definitive Host- The host in which the sexual reproduction of a parasite takes place. • What is a prion and how does it propagate? Infectious protein, through body fluids like feces, saliva, blood, or urine, either through direct contact or indirectly through environmental contamination of soil, food or water. • What is the prion “species barrier”? If one species is infected by another it will very rarely develop the disease • How can prions be detected? Using Real time quaking-induced conversion (RT-QuIC) • Know the basics of the following eukaryotic pathogens (including risk factors for acquiring, if relevant) • Histoplasma capsulatum • Pneumocystis jiroveci • Cryptococcus gattii • Cryptococcus neoformans • Candida auris • Candida albicans (fungi) • Normally lives as part of our microbiota, but can be disrupted due to underlying health issues or medications • Cause disease by invading deep layers of the skin and subcutaneous tissues • Switch between yeast and filamentous form; if it is locked in one or the other form, then less virulent • Acanthamoeba keratitis • Cryptosporidium • Toxoplasma gondii • Tapeworms (not in 2019 review) • Ascaris • Naegleria fowleri • Schistosoma mansoni UNIT 5 – CONTROLLING MICROBIAL GROWTH • Know the definition and characteristics of psychrophile, psychrotroph, mesophile, thermophile, hyperthermophile, neutrophile, acidophile, alkalophile, halophile, and halotolerant bacteria Psychrophile: Bacteria that prefer cold temperatures, from -5 to 15 degrees C Psychrotroph: Bacteria that thrive at 20 to 30 degrees C Mesophile: Bacteria that thrive at 25 to 45 degrees C Thermophiles: Archaea (usually) that thrive in hot temperatures, from 45 to 70 degrees C Their proteins resist denaturation due to their amino acid sequence Hyperthermophiles: Archaea (usually) that thrive in extremely hot temperatures, from 70 to 110 degrees C Neutrophils: Most microbes are in this pH range, around 7 (neutral) Acidophils: Optimal growth under 5.5 pH Alkaliphiles: Optimal growth over 8.5 pH Halophiles: Microbes that require high salt concentrations Halotolerant: Microbes that withstand high salt concentrations (up to 10%) • Know the differences between facultative anaerobes, obligate aerobes, obligate anaerobes, microaerophiles, aerotolerant anaerobes Facultative anaerobes: Can live with or without oxygen Obligate anaerobes: Only lives without oxygen Obligate aerobes: Only lives with oxyen Microaerophiles: Grow in presence of low concentrations of oxygen Aerotolerant anaerobes: Do not use oxygen but can tolerate it • What is catalase? Enzyme present in peroxisome of almost all aerobic cells. Converts hydrogen peroxide to water and oxygen • What is superoxide dismutase? Produced by almost all organisms growing in presence of oxygen. Inactivates superoxide by converting it to oxygen and hydrogen peroxide • Describe the principles of sterilization, disinfection, pasteurization, decontamination, sanitization, and preservation. Sterilization: Removal or destruction of microbes Disinfection: Elimination of most or all pathogens Pasteurization: Brief heating to reduce number of spoilage organisms, destroy pathogens Decontamination: reduce pathogens to levels considered safe to handle Sanitization: Substantially reduces microbial population to meet accepted health standards Preservation: Process of delaying spoilage of foods and other perishable products • Understand when the following physical methods would be used to control microbial growth: o Pasteurization: Brief heating to reduce number of spoilage organisms, destroy pathogens o Autoclaving: Sterilization using pressurized steam o Dry heat: Hot air ovens or incineration are two common methods: denatures proteins, destroys medical waste o Filtration: Retains bacteria from heat sensitive solutions - Membrane filters = thin - Depth filters = thick o Radiation (ionizing vs ultraviolet): UV- Presence in sunlight - Destroys microbes by damaging their DNA Ionizing- X rays and gamma rays - remove electrons from atoms Destroys DNA and damages cytoplasmic membranes o High pressure (Pascalization): pressure of up to 130,000 psi - destroys microbes by denaturing proteins and altering cell permeability • Understand when the following classes of chemicals would be used to control microbial growth: o Alcohols: Ethyl or isopropyl alcohol kills most bacteria and fungi Denatures essential proteins and damages lipid membranes Common as antiseptic and disinfectant o Aldehydes: Work by inactivating proteins and other nucleic acids Kills bacteria, inactivates viruses, preserves specimens o Ethylene oxide gas: Useful gaseous sterilant that destroys microbes including endospores and viruses by reacting with proteins o Halogens: Oxidizes proteins, cellular components o Peroxygens: Powerful oxidizers used as sterilants Example: hydrogen peroxide, peracetic acid o Phenolic compounds: - Kill vegetative and micro bacteria but not reliable on all virus groups - Phenolics destroy cytoplasmic membranes, denture proteins o Quats: Quaternary ammonium compounds • What important factors are there to consider when selecting an appropriate germicidal chemical? • Compare and contrast chemical preservatives, low-temperature storage, and reducing the available water as methods to preserve perishable products. • What is a biofilm? Organized bacterial community - bacteria or fungi living in organized communities Hard to kill, resistant to antibiotics and disinfectants, accumulations in pipes and drains, involved in tissue infections UNIT 6 – MICROBIAL CLASSIFICATION AND IDENTIFICATION • What is the difference between a strain and a species? Strain: Level of categorization within species Species: Basic unit of taxonomy, group of closely related isolates or strains. Permits identification • Describe how prokaryotes have been/are identified, classified, and assigned names Prokaryote Identification: Microscopy, culture characteristics, biochemical assays, and nucleic acid analysis Prokaryote classification: Three-domain system, five-domain system, phylogenetic trees, Bergey's manual Prokaryote naming: Arbitrary --> generally given to first person to work with that isolate or to an inventory system • Describe how phenotypic characteristics—including microscopic morphology, culture characteristics, metabolic capabilities, serology, and fatty acid analysis— can be used to identify prokaryotes. Microscopic morphology: Size, shape, staining characteristics Culture characteristics: colony morphology gives us initial clues that can help identify an organism or culture Metabolic capabilities: Biochemical tests provide more certainty of identification -> Catalase tests, pH inhibitors Serology: The use of antisera (antibodies) from an animal that is currently fighting off a pathogen can allow for the diagnosis of a specific pathogen Fatty acid analysis: Identification of fatty acid composition in prokaryotes. They differ in the types and quantities of fatty acids found within their membranes. • Understand the differences between strategies used to distinguish different strains – biochemical, serological, molecular typing, phage typing, antibiograms • What methods can be used to classify species and strains and how do they work? When are they appropriate to use? Advantages/disadvantages? (including those listed above) o 16S rRNA/rDNA sequencing o Serological typing: Looking at the surface capsule, flagella, and LPS differ from one another in that they have protein/carbohydrate variance among strains which can be used as markers MLST o RFLP: o - Different RFLPs indicate different strains - PulseNet tracks RFLPs of certain bacterial foodborne pathogens DNA hybridization: Take the genomic DNA of microbes and heat to modify them to be labeled and to be separated for further identification. We then mix and cool each of the DNA strands to see if there are any types of annealing/hybridizing back together. o Biochemical tests/API tests: Pathogenic vs. non-pathogenic strains have differences in metabolism. This allows for detection of certain variants within a given species. o MALDI/TOF MS: used to speed up culturing process of the bacteria and will allow for rapid identification of microorganisms o Real-time PCR: RT-PCR is a very rapid and cheap way of diagnostic testing of a sample and does not require culturing o WGS: Genome sequencing can be done for microbial identification, strain typing, outbreak investigations, and antimicrobial resistance surveillance -Fast and reliable -Costly, requires strong lab infrastructure o UNIT 7 – ANTIMICROBIALS AND RESISTANCE • What species of microbes produce antibiotics? Bacteria and fungi • Define selective toxicity; antimicrobial action; spectrum of activity; tissue distribution/metabolism/excretion; effects of combinations; adverse effects; and resistance to antimicrobials. Selective toxicity: Use of drugs that will only cause greater harm to its target rather than the host itself Antimicrobial action: The way the drug can inhibit, prevent, and destroy microbes 2 different forms of antimicrobials: Static and Cidal Spectrum of activity: Type of bacteria that will be targeted by a specific treatment There are broad and narrow spectrum microbials Tissue distribution, metabolism, and excretion: Antimicrobials can alter their behavior when found in different parts of the body/tissues Effects of combinations: Antagonistic - Drugs that interfere with each other when combined Synergistic - Drugs that enhance each other when combined Additive - Drugs that are better independent Adverse effects: Toxic effects, allergic reaction, suppression of microbiotal • What is a “cidal” drug? What is a “static” drug? Cidal drug: Drugs that kill microbes Static drug: Drugs that inhibit microbial growth • Why use combination therapy? What are the benefits? More effective in general Used to prevent development of resistant mutations • What is a “therapeutic index”? How toxicity of a given drug is expressed High TI = less toxic Low TI = patient blood monitored for toxicity • Describe the ß-lactam drugs and other antimicrobials that inhibit cell wall synthesis Drugs that target cell wall synthesis as a result of binding to essential penicillinbinding proteins (PBPs) • Describe the antimicrobial drugs that: o inhibit protein synthesis: Penicillins and cephalosporins, vancomycin, carbapenems and monobactams o Inhibit nucleic acid synthesis: Fluoroquinolones - inhibit topoisomerases and are bacteriocidal Rifamycin - blocks prokaryotic RNA polymerase o inhibit metabolic pathways: Folate inhibitors are the best drug to take to prevent any microbial infections because they produce their own folate by taking precursors -Sulfonamides -Trimethoprim o interfere with cell membrane integrity: Causes bacteria to leak ultimately leading to cell death -Daptomycin -Polymyxin B • Describe how the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) are determined. MIC - Smallest concentration of drug that visibly inhibits growth MBC - Lowest concentration of an antibacterial agent required to kill a particular bacterium • Compare and contrast the Kirby-Bauer disc diffusion test with commercial modifications of antimicrobial susceptibility testing. The test to determine the efficacy of antibiotics or the antibiotic resistance of bacteria. • Describe four general mechanisms of antimicrobial resistance 1. Destruction of drug 2. Change target 3. Keep drug and target away from each other 4. Stop growing or slowed growth • Describe how antimicrobial resistance can be acquired to specific drugs 1. Drug-inactivating enzymes 2. Alteration in target molecule 3. Decreased uptake of drug 4. Increased elimination of drug 5. Spontaneus mutations • What is the difference between intrinsic and acquired resistance? Intrinsic resistance - Some microbes naturally resistant to certain antibiotics Acquired resistance - Resistance that develops through mutation or acquisition of new genes • Describe how the emergence and spread of antimicrobial resistance can be slowed 1. Global cooperation 2. Physician responsibility 3. Patient responsibility 4. Educate public 5. Global impact of use of microbial drugs UNIT 8 – EPIDEMIOLOGY AND DISEASE TRANSMISSION • You should know the definition of: o communicable vs. non-communicable and why Legionella and tetanus are infectious diseases considered to be “non-communicable” o prevalence: Total number of cases at any time or for a specific period in a given population o incidence: the number of new cases at a time/population/case rate and will measure the risk of an individual contracting the disease o case-fatality rate: The percentage of the population that dies from a specific disease o morbidity: The burden of diseases in a population that is at risk o common/single-source vs propagated types of epidemics or outbreaks o epidemic/ pandemic/ endemic o outbreak o reservoir o vector: The main host for transmission of the disease o contact tracing o vertical transmission vs horizontal transmission o mechanisms of spread including - fomites, droplet transmission, and droplet nuclei Fomites: Inanimate objects that serve as reservoirs for microbes o natural host/ transmission host/ terminal host o prospective study/ cross-sectional study/ retrospective study • Explain how characteristics of a pathogen or of a host can influence the epidemiology of a disease. Pathogen: Virulence factors, minimum number of pathogens required for that disease, incubation period • Understand the commonalities and differences between descriptive studies, analytical studies, and experimental studies. Descriptive: Collect data that can characterize occurrence (time, place, and individuals infected) of an outbreak Analytical studies: Determine the relevance of risk factors from the descriptive study Experimental studies: Where researchers will introduce a intervention to a study to impose an outcome • Describe how a common-source epidemic can be distinguished from a propagated epidemic. Common - When a group of persons are all exposed to an infectious agent or a toxin from the same source • Describe the zoonotic origin of many emerging human infectious diseases. Diseases that are constantly emerging are typically originating from zoonotic transmission 60-80% of diseases coming from animals • Know the three main factors that contribute to the emergence of a disease 1. Microbial agent 2. Human host 3. Human environment • Be able to classify scenarios by the factors that contribute to the emergence of a disease UNIT 9 – IMMUNITY AND VACCINES • Know the difference between first-line defenses, innate immune responses, and adaptive immune responses • Know the various ways in which first-line defenses protect our bodies from microbial invasion • Know how the immune system distinguishes between self and non-self • Know the three pathways by which the complement cascade can be activated, where these pathways converge, and the three major outcomes of complement activation 1. Classical = activated by an antibody bound to microbe 2. Lectin = bind to mannose of microbial cells and interact with complement proteins 3. Alternative = Triggered when C3b binds to a foreign cell surface • Describe the major immune cell subsets and their functions (neutrophils, macrophages, dendritic cells, T cells, B cells) 1. Opsonization - C3b can bind to bacterial membranes and allow phagocytes to engulf more easily 2. Inflammatory response - C5a will attract phagocytes to inflamed area; c3a and c5a can increase permeability of blood vessels and induces mast cells to release cytokines. 3. Cell lysis - membrane attack complexes (MAC) will be formed by the C5b → c6, c7, c8, c9 molecules assembling in the membranes of gram negative bacteria. • Know what PRRs and PAMPs are, and what type they can recognize PRR- Allow body to see microbes by detecting PAMPs on microbes, MAMPs on microbes, and DAMPs on host cell damage Pamps - Include anything that a microbe produces or possesses and includes cell wall components (i.e LPS, PPG, lipoteichoic acid, lipoproteins), flagellin, viral RNA molecules MAMPS: • Know what an “inflammatory response” is; know what causes inflammation, which processes are involved, and the consequences of inflammation • Know how adaptive immunity differs from innate immunity • Understand the key differences between humoral immunity and cellmediated immunity • Understand the terms “antigens” and “epitopes” • Know the characteristics of a primary and secondary antibody response • Describe the functions of antibodies • Understand the concept of antigen presentation • Know the principles of active and passive immunity • Know what a vaccine is, and characteristics of effective vaccines • Understand the terms “sterilizing immunity” and “herd immunity” • Distinguish between attenuated vaccines and inactive vaccines; know the advantages and disadvantages of each • Understand the terms used to describe different types of vaccines (i.e. toxoid, recombinant, subunit, etc.) and know which types are used for which diseases • Understand the terms “seropositive” and “seronegative” UNIT 10 – PRINCIPLES OF PATHOGENESIS • Define the terms primary pathogen, opportunist, and virulence. • Describe genomic islands and pathogenicity islands • How do these islands explain why O157:H7 is deadly and strain HS is not? • Describe conjugation, competence/transformation, and transduction • Know about how Vibrio cholera evolved to cause disease • Describe how prophages can contribute to disease and evolution • Compare and contrast acute, chronic, and latent infections. • Describe the requirements for adherence and colonization. • Explain the role of type III secretion systems in infection. • Describe the mechanisms pathogens use to penetrate the skin and mucous membranes. • Describe mechanisms that bacteria use to avoid complement system proteins, antibodies, and destruction by phagocytes. • Describe the general role of cytokines • Describe how various bacteria penetrate the mucous membrane • Describe the difference between exotoxins and endotoxins • Compare and contrast neurotoxins, enterotoxins, and cytotoxins, giving two examples of each. • What is the difference between an effector, an exotoxin, and an endotoxin? • What are the basic functions of AB toxins and their subunits? • How does “scalded child syndrome” occur? • How do superantigens work? What is the S. aureus example we covered? • Explain how inflammation and antibodies can cause damage. • Describe how various bacteria avoid host defenses • Know terminology related to pathogenesis: ID50, incubation period, prodromal, convalescence, carriers, virulence, virulence factors, opportunistic infections, symptoms, signs, infection vs. colonization, primary pathogen, primary infections, secondary infection. UNIT 11 – HUMAN MICROBIOTA • Relate the objectives of the Human Microbiome Project • Describe the microbial load of the gut • List the 5 bacterial phyla (and some of the predominant families within) that dominate the gut microbiota and how they shift in response to environmental cues • Describe the factors that contribute to the distribution of microbiota in the gut • Describe the 3 major metabolites produced by the gut and their functions • What are the main roles of the 3 main short chain fatty acids? • How does the gut microbiota contribute to food digestion? • Discuss how our gut microbiota become colonized and change with age • How does the gut microbiota impact the host immune system? How does it aid in the development of the host immune response? • Define and identify commensals, symbionts, pathobionts and pathogens • Define gene richness, gene diversity, metabolism, catabolism anabolism • Describe colonization resistance, indirect and direct colonization and their major mechanisms • Explain how factors like smoking, antibiotics and diet alter the microbiota • Describe the study that showed the role of the gut microbiota in obesity • Define dysbiosis and identify what it is associated with • Explain how fecal microbiota transplant is used to treat gastrointestinal disease. • How are germ-free mice used in the study of the microbiota?