Microbio Module 1 Review PDF

Module 1 Review CLASS OBJECTIVES: ENCOUNTERING MICROBES  Define vocab words & use them appropriately  Identify the normal microbiota and where it colonizes  List examples of the role of the normal microbiota (“flora”)  Understand what happens during dysbiosis and the consequences of  Compare...

Module 1 Review CLASS OBJECTIVES: ENCOUNTERING MICROBES  Define vocab words & use them appropriately  Identify the normal microbiota and where it colonizes  List examples of the role of the normal microbiota (“flora”)  Understand what happens during dysbiosis and the consequences of  Compare & contrast probiotic & prebiotic  Identify what is required for tissue tropism  Learn the 6 steps required for the establishment of infectious diseases  Be able to apply some of today’s material to clinical settings  REVIEW OF LAST CLASS  Define vocab words & use them appropriately  Identify the normal microbiota and where it colonizes Common Locations:  Skin: moist areas especially, such as the groin and between the toes  Respiratory tract: nose and oropharynx  Digestive tract: mouth and large intestine  Urinary tract: anterior parts of the urethra  Genital system: vagina Less common locations:  Rest of respiratory & digestive tract  Urinary bladder  Uterus Diagnostically Significant Locations:  Blood  Cerebrospinal Fluid (CSF)  Synovial fluid  Deep tissues  REVIEW OF LAST CLASS  Give examples of the role of the normal microbiota  Keeping out invaders  Role in human nutrition & metabolism  Conversion of ingested compounds (good AND bad)  Immune stimulation  Common source of infection  Understand what happens during dysbiosis and the consequences of  Dysbiosis= microbial imbalance/impaired microbiota. Depends on pathogenicity, virulence, & host response  Compare & contrast probiotic & prebiotic  Prebiotic- Food ingredient that supports the growth of one of more members of the microbiota  Probiotic- live organism that, when ingested, is believed to provide benefit to the host  Identify what is required for tissue tropism  Site of entry  Affinity for host receptors  Temperature of organ  REVIEW OF LAST CLASS  Learn the 6 steps required for the establishment of infectious diseases  Encounter:The agent meets the host.  Entry: The agent enters the host.  Spread: The agent spreads from the site of entry.  Multiplication: The agent multiplies in the host.  Damage: The agent, the host response, or both cause tissue damage.  Outcome: The agent or the host wins out, or they learn to coexist.  Be able to apply some of today’s material to clinical settings  i.e. the question we ended class with CLASS OBJECTIVES: BASIC CHARACTERISTICS OF PATHOGENS  Identify the three domains of life and what they compose  Compare & contrast prokaryotes & eukaryotes (including cell walls)  Understand pros and cons of being prokaryotic and be able to identify ways in which they adapt and survive  Hint: RON  Identify basic differences amongst different types of bacteria (gram+ vs. gram- vs. acid fast)  Define fungi & distinguish how fungi differ from viruses & bacteria  Define what a parasite is and their basic organizational structure  Be able to identify how viruses are classified  REVIEW OF LAST CLASS  Identify the three domains of life and what they compose  Archaea, Eukaryota, Bacteria  Compare & contrast prokaryotes & eukaryotes (including cell walls)  Eukaryotes have nucleus, Prokaryotes do not  Prokaryotic DNA is circular, Eukaryotic is linear  No membrane bound organelles in prokaryotes  Prokaryotes reproduce binary fission, eukaryotes reproduce mitosis/meiosis  Prokaryotes are smaller, eukaryotes are bigger  Prokaryotes 70S ribosome, Eukaryotes 80S ribosome  Prokaryotes are haploid, eukaryotes are diploid (or more!)  REVIEW OF LAST CLASS  Understand pros and cons of being prokaryotic and be able to identify ways in which they adapt and survive  R- Resistance – survive damaging agents  Cell wall, NAG & NAM, LPS, Lipid A (endotoxin), periplasmic space  O- Occupancy – habitability of environment  Biofilm & flagella  N- Nutrition – intermittent availability of food  Types of membrane transport: facilitated, active, group translocation  Identify basic differences amongst different types of bacteria (gram+ vs. gram- vs. acid fast)  Gram+ have teichoic & lipoteichoic acid, thick peptidoglycan cell wall surrounding cell membrane, retain dye- iodine stain after alcohol wash  Gram- have LPS outer membrane outside thin peptidoglycan cell wall that surrounds cell membrane, porin channels for transport, & periplasmic space, do not retain dye-iodine stain after alcohol wash, but retain saponin counterstain (red)  REVIEW OF LAST CLASS  Define fungi & distinguish how fungi differ from viruses & bacteria  Fungi (singular: fungus) are a kingdom of usually multicellular eukaryotic organisms that are heterotrophs (cannot make their own food) and have important roles in nutrient cycling in an ecosystem. Fungi reproduce both sexually and asexually  With the exception of yeast (has a nucleus=eukaryotic), most unicellular organisms (like bacteria) are prokaryotes  Viruses are just genetic material, not “living” like eukaryotic fungi  Define what a parasite is and their basic organizational structure  Parasite- an organism that lives on or in a host organism and gets its food from or at the expense of its host 1. Protozoa*- amoebozoa, flagellates, ciliates, and apicomplexa 2. Animalia:  Helminths- nematodes, cestodes, trematodes  Ectoparasites (Arthropods)- Mites, Lice, Fleas, Ticks, etc.  Be able to identify how viruses are classified  Morphology & replication CLASS OBJECTIVES: HOST PATHOGEN INTERACTIONS I  Differentiate between innate & adaptive immunity  Be able to describe components of the innate immune system & their function  Be able to identify different immune cells based on job/role & picture  Be able to describe how the innate immune system activates the adaptive immune response  Differentiate between the different lymphocytes of the adaptive immune response (how lymphocytes are activated & their roles)  Be able to describe what antibodies are and what immunological memory is  Distinguish between MHC class I & II  REVIEW OF LAST CLASS  Differentiate between innate & adaptive immunity  REVIEW OF LAST CLASS  Be able to describe components of the innate immune system & their function  Cellular:  Phagocytic cells (neutrophils, macrophages)- ingest & kill bacteria  Pro-inflammatory cells (macrophages, mast cells, eosinophils, basophils, etc.)- induce host defenses & inflammation  Antigen Presenting Cells (APCs) (dendritic cells, macrophages)- recognize, process & present antigen to lymphocytes; initiate adaptive immune response-  Natural Killer Cells*- kill virus infected or damaged cells (like cancer cells) *also part of adaptive immune system  Neutrophil extracellular traps (NETs)- complexes of DNA, histones, & granule proteins released by neutrophils that “catch” extracellular microbes  Humoral:  Bile, gastric acid, (low pH) mucous, tears (lysozyme), normal microbiota bacteria & fungi, produce antimicrobial peptides- kill & digest microorganisms  Complement- enhance phagocytosis/opsonization, induces inflammation, kills some organisms  Classical- triggered by antigen-antibody complexes  Alternative- triggered by bacterial lipopolysaccharides (LPS)  Lectin- triggered by mannose containing polysaccharides  Cytokines- small secreted proteins released by cells that are involved in signaling (pro-inflammatory, anti-inflammatory, attract leukocytes)  Chemokines- “chemoattractant cytokines” involved in signaling (pro-inflammatory, anti-inflammatory, attract leukocytes)  *Don’t forget the PRRs (the cellular receptors) so technically not cellular  Review inflammation as it’s also a feature of innate immune response BE ABLE TO IDENTIFY DIFFERENT IMMUNE CELLS BASED ON JOB/ROLE & PICTURE REVIEW OF LAST CLASS Be able to describe how the innate immune system activates the adaptive immune response: 1. Microbial antigen appears 2. Dendritic cell recognizes the microbial antigen via pattern recognition receptors 3. Dendritic cell takes up microbial antigen & migrates to lymph node & matures into an antigen presenting cell 4. Dendritic cell processes the antigen and loads it onto MHC class II molecules 5. Dendritic cell presents antigen + MHC class II molecule to CD4+ Helper T cells & activate them 6. Activated CD4+ T cells then activate B cells to differentiate into plasma cells to secrete antibody & eliminate the microbial antigen  REVIEW OF LAST CLASS  Differentiate between the different lymphocytes of the adaptive immune response (how lymphocytes are activated & their roles)  When T cells are activated they divide & proliferate  Helper (CD4) T cells- secrete cytokines & activate other cells (CD8 T cells & B cells)  Cytotoxic (CD8) T cells- kill cells bearing the antigen (i.e virus infected or damaged cells)  Tregs- suppress/regulate immune response  When B cells are activated they divide & proliferate & synthesize immunoglobulins  B cells differentiate into plasma cells which secrete antibody  Be able to describe what antibodies are and what immunological memory is  Immunoglobulin aka antibodies- glycoprotein molecules produced by plasma cells (white blood cells)  Immunological memory- once an infectious organism stimulates an adaptive response, subsequent encounters with that organism produce mild or even unapparent effects because of rapid & enhanced action of antibodies or effector T cell  Tolerance- responses to future exposures can be diminished  REVIEW OF LAST CLASS  Distinguish between MHC class I & II  Glycoproteins found on different cells and upregulated during innate immunity  Used in antigen recognition to activate T cells in adaptive immunity  MHC class I  Presents endogenous antigens (from cytoplasm)  Found on all nucleated cells  Presents antigen to Cytotoxic (CD8) T cells  MHC class II  Presents exogenous antigens (extracellular)  Found on antigen presenting cells (APCs) (dendritic cells, macrophages, B cells)  Presents antigen to Helper (CD4) T cells  CLASS OBJECTIVES: HOST PATHOGEN INTERACTIONS II  Differentiate between the 6 Stages of Establishment of Infectious Disease & 5 Stages (Periods) of Infectious Disease  Define and give examples of virulence factors  Further breakdown RON & learn about transmission to new hosts  Define what is needed for nutritionally compatible niche (i.e. oxygen- aerobe v. anaerobe, facultative v. obligate; & iron)  Identify mechanisms of cell death and how microorganisms perform them  Identify the three types of bacterial toxins & give examples of each  Compare & contrast antigenic drift & antigenic shift  REVIEW OF LAST CLASS  Differentiate between the Stages of Establishment of Infectious Disease & Stages (Periods) of Infectious Disease  REVIEW OF LAST CLASS  Be able to define and give examples of virulence factors  VIRULENCE FACTORS- enable pathogen to replicate and disseminate inside a host by either subverting or eluding host defenses. Ex. Adhesins, capsules, toxins, etc.  Further breakdown RON & learn about transmission to new hosts  R (Resistance)  Defending against complement  Subverting phagocytosis  Surviving inside phagocytes  Becoming intracellular  Other mechanisms of subverting the immune response: latency, immunosuppression, antigenic variation  O (Occupancy)- Surface colonization, adhesins  N (Nutritional Niche)- ex. Oxygen (Anaerobes vs. Aerobes), Iron & how to steal it  REVIEW OF LAST CLASS  Identify mechanisms of cell death and how microorganisms perform them  Lysis- disintegration of cell by rupture of cell wall or membrane  Apoptosis (ahp-op-toe-sis)-Programmed cell death  Differentiate between the three types of bacterial toxins & examples of each  Intracellular: Exotoxins, Type III cytotoxins, Type IV to VII cytotoxins  Extracellular: Endotoxin (LPS), Membrane-damaging toxins, Superantigens  Extracellular matrix: Exoenzymes  To clarify for those that may still be confused, intracellular vs. extracellular toxins is referring to where their damage occurs. Intracellular toxins exert damage INTRACELLULARLY (i.e. inside cell), while extracellular toxins exert damage EXTRACELLULARLY (i.e. cell membrane). Extracellular matrix toxins attack the extracellular matrix REVIEW OF LAST CLASS  Which is not an example of an extracellular toxin? A. Endotoxin B. Exotoxin C. Lipopolysaccharide D. Superantigens  CLASS OBJECTIVES: LABORATORY DIAGNOSTICS  Describe the four diagnostic principles  Assess the performance of different diagnostic tests  Aka apply sensitivity, specificity, PPV, NPV (with math, but I’ll try to pick easy numbers so it’s not difficult math)  Understand when to use tests from each of the 4 diagnostic principles (especially clinically) & the meaning of the results  Be able to diagnose infections by culture (phenotypically)  Describe molecular and genetic approaches to studying bacteria  REVIEW OF LAST CLASS  Describe the four diagnostic principles 1. Microscopic examination of patient samples. 2. Cultivation and identification of microorganisms from patient samples. 3. Measurement of a pathogen-specific immune response in the patient. 4. Detection of pathogen-specific macromolecules in patient samples  REVIEW OF LAST CLASS  Assess the performance of different diagnostic tests  Aka apply sensitivity, specificity, PPV, NPV (with math, but I’ll try to pick easy numbers so it’s not difficult math)  True positive- pathogen positive, test positive  True negative- pathogen negative, test negative  False positive- pathogen negative, test positive (Type 1 Error)  False negative- pathogen positive, test negative (Type 2 Error)  Sensitivity- ability of test to correctly identify those with disease (true positive rate)  Specificity- ability of test to correctly identify those without the disease  Positive predictive value- probability that subjects with a positive test will truly have the disease  Negative predictive value- probability that subjects with a negative test truly don’t have the disease  REVIEW OF LAST CLASS  Understand when to use tests from each of the 4 diagnostic principles (especially clinically) & the meaning of the results  Refer to the doc, “Diagnostic Principles Overview for Notes-1.docx” posted in the Microbiology Asynchronous Announcement on 1/15  You should know what a positive or negative result means, e.g. if you see color on immunofluorescence, it means the antibody bound and the antigen of interest is present, or if bacteria grows on a selective media, it has been selected for & is present  Interpret macconkey & emb agar or antibody sensitivity agar  ELISA color changes, latex agglutination & agglutination assay clumping  REVIEW OF LAST CLASS  Be able to diagnose infections by culture (phenotypically)  Blood culture or selective media can also be used, but the only specific examples we discussed in the lecture were EMB & MacConkey agar  REVIEW OF LAST CLASS  Describe molecular and genetic approaches to studying bacteria  Blood culture or selective media can also be used, but the only specific examples we discussed in the lecture were EMB & MacConkey agar  If you need to fully sequence bacteria, PCR is the gold standard!  Microarrays for sequencing large samples!  Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation  CLASS OBJECTIVES: PREVENTION STRATEGIES FOR I.D.  To be able to educate yourself and your patients on how to prevent infections  Differentiate endemic, epidemic, and pandemic  Elaborate on and be able to identify the types of transmission and an example of each  List and give examples of the Standard Precautions for clinical settings  Describe which standard precautions for clinical settings (& PPE) would be best for different types of threats, e.g. blood-borne, vs. inhalation/respiratory, etc.  Define the following terms and give three examples of each: sterilization, disinfection, and antisepsis  Define the three levels of disinfection and give examples of each. When would each type of disinfectant be used?  REVIEW OF LAST CLASS  To be able to educate yourself and your patients on how to prevent infections  Vaccinations, hand-washing, covering coughs & sneezes, staying home when sick, using disinfectants & antiseptics, etc.  Differentiate endemic, epidemic, and pandemic  Endemic- presence of infection is maintained at constant level within area or group aka “baseline”  Epidemic- rise in disease cases above area/group “baseline”  Pandemic- epidemic spread across multiple countries/continents  REVIEW OF LAST CLASS  Elaborate on and be able to identify the types of transmission and an example of each A. General Transmission 1. Abiotic environmental factors  Fomites are inanimate objects that transmit pathogens  Soil & water harbor pathogens 2. Animal/Insect Vectors  Arthropods  Other animals including farm animals B. Human-to-Human Transmission 1. Vertical transmission- infectious agents are passed from mother-to-offspring during pregnancy (transplacental transmission), childbirth, or breastfeeding i.e. ZIKA 2. Horizontal transmission- other human-human transmission  Direct contact- i.e. HIV, Herpes  Indirect contact- i.e. norovirus  Droplets (i.e. bodily fluids)- i.e. HIV  Respiratory/Airborne- i.e. influenza  Fecal-oral- i.e. norovirus  REVIEW OF LAST CLASS  List and give examples of the Standard Precautions for clinical settings 1. Good hand hygiene includes washing with soap and water or hand rubbing with alcohol-based products before and after direct contact with patients, devices, and other objects 2. Personal protective equipment (PPE) includes gloves, masks, and gowns that create a barrier between the medical professional and infected individuals or contaminated objects 3. Respiratory hygiene and cough etiquette means that individuals, including patients, should cover their mouths when coughing or sneezing 4. Proper patient placement requires that patients with infectious diseases should be separated from non-infected patients 5. Maintenance of a clean environment means that the facility and commonly used objects are routinely cleaned and disinfected 6. Careful handling of laundry calls for precautions be used to protect mucous membranes from exposure to infectious agents 7. Safe injection practices include careful handling and cleaning of injection paraphernalia; syringes and needles should never be re-used 8. Sharps safety ensures that needles and other sharp tools, such as scalpels, are used and disposed of properly  >1,000 healthcare professionals are injured by needles or other sharp devices every day  REVIEW OF LAST CLASS  Describe which standard precautions for clinical settings (& PPE) would be best for different types of threats, e.g. blood-borne, vs. inhalation/respiratory, etc.  Blood-borne:- Good hand hygiene, PPE, Clean environment, careful handling of bloody laundry, safe injection practices, sharps safety  Inhalation- PPE, Respiratory hygiene & cough etiquette, proper patient placement, maintenance of clean environment, careful handling of laundry  Sexually transmitted- PPE, etc.  REVIEW OF LAST CLASS  Define the following terms and give three examples of each: sterilization, disinfection, and antisepsis  Antisepsis: Use of chemical agents on skin or other living tissue to inhibit or eliminate microbes; no sporicidal action is implied  Alcohols- all groups of organisms except spores  Iodophors- similar to alcohol, but more toxic to skin  Chlorhexidine- broad antimicrobial (kills at a slower rate than alcohol)  Parachlorometaxylenol (PCMX)- primarily gram+ bacteria  Triclosan- bacteria, not safe for humans?  Disinfection: Use of physical procedures or chemical agents to destroy most microbial forms; bacterial spores & other relatively resistant organisms (e.g., mycobacteria, viruses, fungi) may remain viable  Quaternary ammonia, alcohols, iodophors, phenolic compounds, glutaraldehyde, etc.  Sterilization- total destruction of all microbes, including the more resilient forms such as bacterial spores, mycobacteria, nonenveloped (nonlipid) viruses, & fungi using physical, gas vapor, or chemical sterilants  Steam under pressure- widely used, inexpensive, nontoxic, reliable (autoclave)  Ethylene oxide gas- sterilize temp or pressure sensitive items  Hydrogen peroxide vapors- sterilization of instruments  Chemical sterilants- peracetic acid & glutaraldehyde  REVIEW OF LAST CLASS  Define the three levels of disinfection and give examples of each. When would each type of disinfectant be used?  Disinfection: Use of physical procedures or chemical agents to destroy most microbial forms; bacterial spores & other relatively resistant organisms (e.g., mycobacteria, viruses, fungi) may remain viable  Level used is determined by relative risk surfaces pose as reservoir for pathogens  Low-level disinfectants- used to treat noncritical instruments & devices (e.g. blood pressure cuffs, electrocardiogram electrodes, & stethoscope)  Ex. i.e., quaternary ammonium compounds  Intermediate-level disinfectants- used to clean surfaces or instruments on which contamination with bacterial spores & other highly resilient organisms is unlikely (e.g. semicritical instruments & devices like laryngoscopes, vaginal specula, anesthesia breathing circuits, etc.  Ex. alcohols, iodophor compounds, & phenolic compounds  High-level disinfectants- used for items involved with invasive procedures that cannot withstand sterilization procedures (e.g., certain types of endoscopes & surgical instruments with plastic or other components that cannot be autoclaved)  Ex. Moist heat & use of liquids such as glutaraldehyde, hydrogen peroxide, peracetic acid, & chlorine compounds CLASS OBJECTIVES  Understand why vaccines are important  Describe the origination of variolation & vaccination  Describe the different type of vaccines  Identify characteristics of vaccines  Define adjuvants and provide an example  Be able to have a discussion with an anti-vax or on-the-fence patient/patient's parent about vaccination, why it's important, and debunk some common vaccine myths  Learn where to find out more information on vaccines if you don’t remember, or want to learn more  REVIEW OF LAST CLASS  Understand why vaccines are important  Vaccines save lives & prevent illness  Describe the origination of variolation & vaccination  Edward Jenner (1796)- intentional inoculation with material from individuals with cowpox (Variola minor, a related virus that infects cattle, but causes mild disease in humans) protected against smallpox  Variolation- deliberate inoculation of an uninfected person with smallpox virus (e.g. contact with pustular matter) that was widely practiced before era of vaccination as prophylaxis against severe form of smallpox  Vaccination- The act of introducing a vaccine into the body to produce immunity to a specific disease  REVIEW OF LAST CLASS  Describe the different type of vaccines  Live-Attenuated vaccines- based on living organisms but had virulence & ability to replicate reduced by treatment with heat, chemicals, etc. Typically cause only subclinical or mild forms of disease, but do carry possibility that mutation might enable organisms to revert to wild type. Booster shots not usually needed.  Inactivated (killed) vaccines- organisms that are dead because of treatment with physical or chemical agents, or inactivated toxins (toxoids- diphtheria & tetanus vax). Difficult to guarantee that every organism in a preparation is dead. Incapable of infection, replication, or function but still provokes immunity. Booster shots sometimes needed.  Subunit, recombinant, polysaccharide, and conjugate vaccines- use specific pieces of the germ—like its protein, sugar, or capsid (a casing around the virus). Some can infect host cells but cannot induce disease; Booster shots sometimes needed; adjuvants often used  DNA vaccines- naked DNA extracted from pathogen & engineered to remove some of genes critical to development of disease. Host cells to take up DNA & express the pathogen gene products. Typically lasts longer than other methods where vaccine is rapidly eliminated from host  RNA vaccines- RNA vaccines work by introducing an mRNA sequence (the molecule which tells cells what to build) which is coded for a disease specific antigen; faster & cheaper to produce than “traditional” vaccines  REVIEW OF LAST CLASS  Identify characteristics of vaccines  Vaccines must fulfill several criteria to be effective in protecting large numbers of individuals: 1. Effective protection against intended pathogen must occur without significant danger of actually causing the disease or of producing severe side effects 2. Protection that is provided must be long lasting. 3. Vaccine must induce immune responses most effective against intended pathogen across a broad range of individuals 4. Neutralizing antibodies must be stimulated in order to minimize reinfection 5. Vaccine must be economically feasible to produce 6. Vaccine must be suitably stable for storage, transport, & use  REVIEW OF LAST CLASS  Define adjuvants and provide an example  An adjuvant is an ingredient used in some vaccines that helps create a stronger immune response in people receiving the vaccine  Help produce a stronger immune response  However more likely to experience “side effects” like injection site soreness, redness, & swelling  Some vaccine components themselves can serve as adjuvants  Ex. Pertussis component (from Bordetella pertussis) in DTP (Diphtheria-Tetanus-Pertussis) vaccine  Other adjuvants include alum  Aluminum salts (aluminum hydroxide, aluminum phosphate, and aluminum potassium sulfate)  Safety review of aluminum salt pharmacokinetics in vaccines: https://pubmed.ncbi.nlm.nih.gov/22001122/  REVIEW OF LAST CLASS  Be able to have a discussion with an anti-vax or on-the-fence patient/patient's parent about vaccination, why it's important, and debunk some common vaccine myths  No they don’t cause genetic mutations or insert into DNA  They are clinically tested in many phases  FDA licenses vaccines only if they are safe, effective, and benefits outweigh risks  ACIP doctors and scientists review data before adding new vaccines to schedule  Vaccine safety continues to be monitored even after global use and approval  Vaccines are tested, and tested together  Even if healthy, you get vaccines to prevent illness AND for herd immunity to protect our neighbors and loved ones and to try to prevent breakthrough strains  Aluminum salts are safe, tested, and there’s more aluminum in breastmilk and formula than all of the vaccines  There is no dangerous mercury in vaccines, thimerosol is ethylmercury (safe mercury) but also removed from vaccines as a show of good faith  More formadelhyde in a pear  No aborted fetal tissue (processed out OR grown in chicken eggs, not fetal cell lines)  Vaccines do NOT cause autism