Micro


Prevalence vs Incidence


prevalence: how many people have it at ANY giventime (often said as % of population).
incidence: number of people who have been affected over a long period of time (ex: per year). Normal stats out of 100,000. We would see inour class something like 50/52. Incidence istypically higher than prevalence.


mortality vs. morbidity vs. comorbidity


Mortality: % of people it killsMorbidity: how many people are afflicted over time --> similar to incidence but we don�t put them per 100,000. Comorbidity: what other diseases do they have that might impact the disease that you�re studying.(ex: pt has lupus, shogrins (salivary glands don�t produce saliva), immunosuppressed, diabetic, etc.))


endemic, epidemic and pandemic diseases


Endemic: diseases occurs at an expected rate in a geographic area. Always present & frequently have low mortality rates(ex: ghiardia endemic in Colorado springs/water sources)Epidemic: more cases than expected; can have 1% prevalence, but still epidemic proportions if youdidn�t expect any�Pandemic: epidemic that�s spread to all of the continents. Used to be rare, but now we travel so much, so almost everything goes pandemic.


virulence, pathogenicity, infectiousness


virulence: how many people diepathogenic: how many people are exposed & how many get the symptoms. Pathogenic: everyone exposed gets the disease. Number exposedvs symptoms. Causes a CLINICAL disease.infectiousness: how many actually catch the disease. You get the bug butyou may not get the disease.


5 stages of an infectious disease


- Exposed to illness 1st1) Incubation period (no signs or symptoms) --> asymptomatic2) Prodromal period (mild signs or symptoms) --> period of impending doom (generally the most infectious between prodromal and illness periods)3) Period of illness (most severe signs and symptoms)4) Period of decline (signs and symptoms) --> microbes decline5) Period of convalescence


Describe primary, secondary and tertiary prevention.


* can interfere BEFORE EXPOSURE via PRIMARY PREVENTION: just don�t expose people to microbes (wash hands, stay home if sick, wear a mask, etc.)* somewhere between incubation and prodromal period can do SECONDARY PREVENTION: screen and treat so you don�t get symptoms* TERTIARY PREVENTION: between illness and decline period --> treat symptoms


Host, agent, environment, and vector


host (mostly human); good host: must have the right environment, must have right receptors (forviruses)--> tissue-trophic, immunosuppressed or notagent (the bact, virus)environment (is there a reservoir?)vector (transmits disease; must be able to carry organism from a source/reservoir to a host; frequently an insect (ex: mosquito for West Nile, tick in Lime Disease); vectors rarely show signs of the symptoms)


State how herd immunity can protect susceptible individuals.


Herd immunity: if you can get all those around you to get immunized, then you don�t have to b/c who would you get the disease from? If population is protected, then YOU are protected. Takes between 70 & 95% protection, depending on the bug. Protection includes those who have disease and then recovered.


The acronym �BEINGS� describes the major categories of risk factors for disease. List these risk factors and understand each.


B: biological (age, weight, immune system hardwired to you) or behavorial (where did you travel, nutrition?)E: Environmental factors: where are you? Likely to pick up something there? What are you exposed to?I: Immunological factors: how is your immune system? Weakened? Suppressed?N: NutritionG: genetic: some are more susceptible to diseases, some are resistantS: Services, Social, and Spiritual: Service: can�t access services, you�re more susceptible. Social: more chance for exposure?Spiritual: patients who have belief system may fare better w infectious disease�


What's being stained in Gram Staining?


Staining the cell wall! Gram +: thick peptidoglycan layer, iodine crystallizes, alcohol wash (blows away bonus layer on +), decolorizes it counterstained w saphrinin. Staining a cell wall and Purple = +, Pink = -Gram +: thick peptidoglycan and NO bonus lipidbilayer on outside; lipoteichoic acid also presentGram - : thin peptidoglycan layer and bonus lipid bilayer; endotoxin also (LPS� lipopolysacchride). Our bodies react to LPS in call wall Gram -, so get fevers, etc.


Describe the role of the bacterial glycocalyx.


Glycocalyx: capsule & slime layer: increase virulence (slippery so WBCs can�t engulf it, make�s them sticky to your insides, masks them from immune system)


What are fimbriae and pili?


Fimbriae: sticky bristlesPili: long tube; can be used for adhesion, but primary function: genetic transfer! Bact that can make pili have an F-plasmid --> �fertility�; allows bact to transfer genetic material between each other (ex drug resistance transferred this way)


Are spores produced by Gram positive or Gram negative bacteria? What is the purpose of a spore? What is inside a spore?


Bact. endospores are for survival ONLY, NOT for reproduction! Gram + rods: Ex: Bacillus and Clostridium � makes them super hardy!! Inside super tough container is calcium and dipicolinic acid; makes it resistant to about anything, even disinfection. Allows it to survive through all of disinfection efforts.


Sketch a typical bacterial growth curve. Identify lag,
log, stationary and death phases. Where do you calculate generation time?


Test bacteria in LOG PHASE of growth � review growth curve of bact. in CLOSED systemLAG phase- bact adjusting to new environment.Logrithmic growth � measure effectivness ofanti-microbialsStationary Phase: Carrying capacity --> growth levels out. Number dying = number dividingDeath phase: dying L don�t test anti-microbialshere


What is the purpose of an operon? What is the
difference between inducible and repressible operons? Using the lac operon as an example, state the function of the promoter, sigma factor, operator,
inducer, repressor.


Bact take genes and clump together by function --> can flip on and off a unit of genes by function. Grouping of genes by function = OPERONS.2 flavors: inducible (off, but can be turned on) or repressible (normally on, but can turn off)ex: LAC operon �discovered in E. Coli ability to break down lactose. INDUCIBLE: normally off but can be turned on when lactose in culture
Level 1 control of operon: If lactose is present, repressor binds to lactose instead of to operator (repressor comes off of operator), thus allowing gene transcription for lactose breakdown via polymerase advance down codeLevel 2 control of operon: cAMP/CAP system. �Cyclic AMP� -> cAMP goes up in cell when there�s no glucose. cAMP binds to CAP protein -> complex �CAM/CAP� binds to promotor and increases polymerase binding for increased transcription and translationLevel 3 control of operon: Sigma factors (accessorymolecules). true for almost all bact genes. Increases with sigma factors -> allow (required!) forRNA polymerase binding. Different genes use different sigma factors in order to allow RNA polymerase to bind to promotor. If sigma factor isn�t being made by cell, it decreases ability to transcribe desired genes.


Describe each of these three mechanisms of gene
transfer: conjugation, transformation and transduction.


Rough: without capsule Smooth: with capsule If you injected heat-killed bact w capsules with live bact without capsules, live ones take up capsules from non-capsulated dead ones and use those genes - TRANSFORMATION: bact can take up nakedDNA from environment and incorporate it. (ex: get a capsule to increase virulence). Don�t even have to be same species. Can even pass it on to offspring.- CONJUGATION: swapping genes; uses pili. Swapping plasmids for antibiotic resistance. Doesn�t always transfer a whole plasmid! Notice: �fertility factor�, as noted in book. Some of these are special, unique genes called �transposons�- Transposons: JUMPING GENES. Start on a plasmids and integrate into main chromosome -> all offspring then have it. Humans can�t do that -> bact regeneration time is about 30 minutes. Can also inactivate vital gene or remove control that should be on certain genes. (Plasmids are self-replicating, so may or may not be distributed equally among offspring. Transposons is a section of plasmid that can jump; a stretch of DNA; has signals/handles on either end that allow enzymes to clip them.)
Slime layer:transientCapsules: makes bact slippery and phagocytes can�t pick them up. If lose capsule, often lose virulence. - TRANSDUCTION: �carrying of DNA�; more general term for transfer of DNA from one place toanother. Special type of transduction: viral! Bacteria can get infected by viruses -> �phages� (bact virus). Doesn�t happen in humans b/c DNA housed in nucleus; bact don�t have nucleus so when bact infected w phage, bact chops up own (viral?) DNA w restriction enzymes, DNA gets packagedin viral coat -> then goes on to infect other cells with these little vesicles. Restriction enzymes are like bact immune system.


Define the following microbe-host relationships: commensalism, symbiosis, mutualism, ammensalism and latency.


Lots of bact in body in symbiotic relationship (stable relationship between 2 populations). Have loads of commensals on skin: one benefits and the other is unaffectedMutualistic: symbiotic relationship where both are benefiting. E coli in mouth make Vitamin K for you. Competitive exclusion: fill a niche so something worse can�t.Ammensalism: one is injured and other is unaffected. Doesn�t describe bact in your body and you; usually between two different types of bugs inmouth. Ex: 1 bact produces antibiotic (unaffected) secretes it and another species is harmed. This is where most antibiotics havecome from�Latency: infection that�s dormant within the host. Ex: Mycobact. TBi is latent infection. Ex2: latent phase in HIV. Ex3: chickenpox lays dormant in ganglia & can get Shingles later on; reactivation of this bact. infection. can still be infectious with latent disease!!


Define the following classifications of microbe host interactions: parasite, strict and opportunistic pathogen, infection, endogenous disease, exogenous disease, colonization, normal flora and disease.


Parasitic relationship: host is damaged in some wayPathogen: parasite that can and does damage the host and cause diseaseInfection: process where pathogen or parasite is causing diseaseexogenous source: caused by microbe from outside own bodyendogenous source: caused by normal flora; already on/in body OR a latent infxn (ex Shingles � virus that person already has from chickenpox as child)If you�re immunosuppressed, your own flora can become a problem- Opportunistic Pathogen: will cause disease in theright time and place (ex- flora in body; E coli in gut can be bad in an abdominal surgery.- Strict Pathogen: NOT flora EVER. A few bugsthat should never be on/in human body. Ex-mycobacterium tuburculosis.


Describe the flora of the eye as well as the defenses found there.
Describe the flora and defenses in the respiratory tract.
List the defenses and the flora found in the GI tract.


Eye: tears FLUSH -> lysozyme, Staphlococci(from skin around eye) Respiratory tract: mucous, cilia, (prevents adherence � ciliary escalator moves mucous), enzymes (IgA),macrophages. Deeper into resp tract, the fewer normal flora you should be seeingMouth: lined with epithelial cells, IgA, bact in mouth are opportunistic � can and will go systemic GI tract: lots of bact here. 1 gram = 1x10^11 bact. in it in feces. Lots of anaerobes. Asymptomatic carriers of salmonella. Acids in stomach protect us. Notice: OTC acid-blockers enable bact thrive in stomach b/c no longer killing bacteria. Secretory IgA protects this tract. LOADS of flora here also! In dentistry: can seriously disrupt GI tract w antibiotics. Ex: clindimyacin -> bad diarrhea b/c normal flora disrupted Skin: waterproof, keratinized, slightly acidic, has normal flora


Define virulence, LD50 and attenuation.


Virulence: ability to cause diseaseLD50: measure of virulence. Tells how many bact.cells are needed to kill half the animals in a study. Low LD50 or High LD50. More virulent: low LD50 (lower the LD50, the more virulent the bacteria).Attenuation: make an organism less virulent. Do this with vaccines: they�re live, but they�re less virulent (get infection but not likely to get �sick� from it). Ex: BCG (attenuated vaccine for TB) � not endemic here for TB so don�t use it in US but do in India


Describe several virulence factors as they relate to adherence, invasion and colonization.


Bact become more virulent (swap genes, rapidly mutate, etc)- adherence: fimbria (bristles), pili, glycocalyx (capsule), adhesins (specific molecules that bindto host receptors)- invasion: increase virulence factors by making lots of enzymes (hylauronidase, fibrolisin, collagenase, etc.) -> breaks down your tissue, more likely to invade, more virulent- colonization: biofilm forms. In mouth: biofilmsform on teeth � �quorum sensing�: coordinate activities so WHOLE colony makes samemove, like making same toxins at same time


Define exotoxin, endotoxin and enterotoxin. Give several examples of exotoxins


exotoxin: secreted toxins. Bact doesn�t have to be there to make you sick. Bact have no stomachs->want to break something down, they make exoenzymes to be secreted and start to break down in environemtn and then transport pieces in. Some enzymes are exotoxins -> they damage yourcells. Ex- hemolysins (break downRBCs) -> you will try to make a blood clot; if bact can evade clot, they invade body. Ex2- A-B toxins. A subunit is translation inhibitor in human cells -> alters translation. Potent in GI tract. Ex3-Superantigens: something that activates 20% of T-cells at the same time, non-specifically -> non-specific immune cell activation!- endotoxin: part of bact itself that isn�t secreted, but that body responds to. Part of bact. cell. Often part of cell wall. Ex- LPS (Gram (-) cell walls -> causes fever result in us).


Differentiate between, based on appropriate use, antiseptics, disinfectants and sterilants.


-Sepsis: infection- Antiseptic: works on infection; used on outside of body, working against infection. Ex: soap, triclosan, alcohol, iodine (in mouth: mouthwash � has antiseptic agents � not used internally! And not injected, peroxide, etc) - Disinfectants: killing most but not all microbes. Not given to patients, with one exception � proper when use alcohol on skin. Does not kill spores. (bact makes spores only for survival (bacillus and clostridium), NOT for reproduction) Will not kill allviruses. NOT for instruments!! OK for countertops, chair, etc.- Sterilants: kill ALL microbes, EVEN spores (bacterial). Use autoclave, gas (ethylene oxide), buy things that�ve been erradiated (gloves have �gamma� symbol � they�ve been through radiation), filtered (solutions) � warning: some viruses are so small, they pass through filters- Sanitization: decontaminate something to make it safe to use Physical means: heat, radiation, filtrationChemical: antiseptics, disinfectants, sterilantsTopical methods: antiseptics, soap, mouthwash, etc.In vivo methods: �used in live patient� -> antibiotics


Give examples of antiseptic agents used in oral health and their mechanism of action.


Chlorhexidine: disrupts bact cell membrane; absorbs into gum tissue & on teeth -> residual activityFlouride: inhibits an enzyme in glycolosis (inhibits enolase). Only good for application; not good for ingestionDiluted hydrogen peroxide: (H2O2) -> oxidizing agent. Very damaging to skin, especially at high concentrations. Kills bact. b/c bact can�t handle oxidative stress.Mouthwash: Listerine has phenolics (denatures enzymes& proteins) -> remains active in presence of other organic moleculesScope: quat ammonium-> target lipids. Inactivated by organics.


Define sterilization and contrast with disinfection. Identify the indicator organism for disinfection and sterilization.


sterilization: test strips have bacillus clostridium (high level) � check for spores from bacteria during process. Gluderaldehyde, bleach, etc.Intermediate level: mycobacterium TB � has waxy cell wall, so harder to kill than most bact., alcohols,phenolicsLow level indicator: most viruses, get rid of most germs


List several properties of disinfectants.


want it to be germicidal, fast-acting, sustained, stable chemically, etc


Know the specific mode of action and use for the following: heat, ethylene oxide, 2% gluteraldehyde


Heat (dry and moist): dry heat (use this for things that corrode) -> takes WAY longer to bake thingsEthylene oxide: gas; cold sterilizing2% gluteraldehyde: liquid


What time, temperature and pressure is needed for an autoclave?


- 121 deg C, 15-20 min, 15 PSI


Explain the principles underlying brightfield,
darkfield, phase contrast, fluorescent and electron microscopy. Give examples of the use of each.


resolving power: ability to see 2 separate points as separate. Oil immersion: makes light go straight up instead of dispersingbrighfield: resolving power � 2 micronsdarkfield: use condenser that scatters the light -> org is illuminated against a dark background. Increases resolving power: 0.02 microns. Disadvantage: can�t see any internal structures. Used for thin organisms (ex Treponema- spirochete; causative agent of syphilis) phase contrast: use a special objective that has rings etched on it -> causes light to bounce slightly out of phase. Denser things bounce light differently, so can see internal structures. Use on live specimens b/c you don�t stain them. Can see cilia, flagella, etc. fluorescent: can stain live specimens. Usingantibodies conjugated w fluorescence to stain. electron microscopy: TEM (electron beam aimed at specimen and went through it; can see less/moredense areas) & SEM (gives 3-D images b/c aim beam of electrons at what you�re looking at). Only time you can see a virus!


What factors influence success of a culture?


1) Depends on biology of organism (aerobes/anaerobes, temp preferences, etc)2) Site of infection3) Is patient mounting immune response to bact? (ex: infective endocarditis � difficult to diagnoseb/c can draw blood and it appears sterile; bact have settled down on heart valve and not shedding biofilm)4) Media (right growth conditions?)


Describe how researchers identify and differentiate between different strains of bacteria (include PCR, RFLP, DNA hybridization and in situ hybridization).


PCR: copy machine for DNA; can copy specific stretches of DNA for microbe and find if microbe isthere or not. Started w thermophiles from Yellowstone.RFLP: Restriction Fragment Length Polymorphism. Cut DNA -> gel -> �fingerprint�. (ex: bact in wounds from Iraq -> now showing up in civilian hospitals too)DNA hybridization: allows you to look for certain DNA in a sample.In situ hybridization: using DNA probes to look for DNA in tissue samples (ex: virus in a solid tumor)


What is the theory behind serological diagnosis? HINT: what are you detecting?


-> looking for an Ab-> staining for monoclonal Abs mouse + antigen -> collect Ab in serum -> want tocollect B-cells from mouse, but they die in culture� SOOO you mouse + antigen -> collect B-cells -> FUSE them w tumor cell -> SCREEN 1000s of thefused cells -> looking for Ab production and immortality


Be familiar with manufacture and use of monoclonal antibodies. Give examples of antibody use including FLOW cytometry, ELISA, Western blot, RIA.


flow cytometry: cell sorting. Congugate flourscence to Ab -> flow cyto will sort based on what color they�re staining. (ex: HIV patients w clinically measured AIDs when CD8+ T-cell count drops to acertain point; diagnosed using Ab-fluorescenceELISA: assay that looks for antigen (look at Fig 17.5 in book for HIV test -> put viral protein intowells -> does patient have antibodies to the HIV virus? -> add patient�s serum -> if patient has Abs, they will bind. Come back with anti-human IgAb that�s fluorescently labeled. Cross-reactivity -> if patient has a cross-reactive Ab that�s binding this test � to be certain this isn�t the case if you test positive ELISA, complete a WesternBlot)Western Blot: looking for protein. Run on a gelseveral proteins from the HIV virus (envelope, polymerase, GAG, etc) -> can transfer to piece ofpaper. Lab takes paper and they add patient Abs. If you light up 3 bands, then that means you have Ab to ALL 3 HIV proteins -> now confirms that you�re HIV + RIA: radiation + Ab. Blood test for allergies: RAST (stopped using these b/c they�re radio and harms employees).


What are the 5 I's to pathogen identification?


Innoculate, Incubate, Isolate, Inspect, ID


What's a pathognomonic symptom in diagnosis?


Pathignomonic symptoms: indicates a given disease. Ex: Koplic spot (have measles!). Ex2: tetanus -> bact secretes neurotoxin that causes total body tetani (rigidity); have face into horrible grimace, characteristic of clostridium tetani. Ex3: Diptheria -> has pseudomembrane ontonsilsQuick immunological test: Suspected bladder infxn: they�re looking for nitrites. Normally, shouldn�t have nitrites, onlynitrates -> bact break down nitrates to nitrites.


Define idiopathic and iatrogenic diseases


Idiopathic: we don�t know the causeIatrogenic: disease that came from a healthcare procedure or healthcare setting (vs: nosicomial:from hospital!)


Define bacteremia, fungemia and septicemia.


bacteremia: bact in bloodfungemia: fungi in the bloodsepticemia: either fungi or bact. in the blood