Micro

• prevalence: how many people have it at ANY given
• time (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 in
• our class something like 50/52. Incidence is
• typically higher than prevalence.

• Mortality: % of people it kills
• Morbidity: 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: 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 you
• didn’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: how many people die
• pathogenic: how many people are exposed & how many get the symptoms. Pathogenic: everyone exposed gets the disease. Number exposed
• vs symptoms. Causes a CLINICAL disease.
• infectiousness: how many actually catch the disease. You get the bug but
• you may not get the disease.

• - Exposed to illness 1st
• 1) Incubation period (no signs or symptoms) --> asymptomatic
• 2) 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 decline
• 5) Period of convalescence

• * 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 (mostly human); good host: must have the right environment, must have right receptors (for
• viruses)--> tissue-trophic, immunosuppressed or not
• agent (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)

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.

• 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: Nutrition
• G: genetic: some are more susceptible to diseases, some are resistant
• S: 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…

• 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 lipid
• bilayer on outside; lipoteichoic acid also present
• Gram - : thin peptidoglycan layer and bonus lipid bilayer; endotoxin also (LPSà lipopolysacchride). Our bodies react to LPS in call wall Gram -, so get fevers, etc.

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)

• Fimbriae: sticky bristles
• Pili: 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)

• Bact. endospores are for survival ONLY, NOT for reproduction!
• Gram + rods: Ex: Bacillus and Clostridium à 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.

• Test bacteria in LOG PHASE of growth à review growth curve of bact. in CLOSED system
• LAG phase- bact adjusting to new environment.
• Logrithmic growth à measure effectivness of
• anti-microbials
• Stationary Phase: Carrying capacity --> growth levels out. Number dying = number dividing
• Death phase: dying L don’t test anti-microbials
• here

• 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 code
• Level 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 translation
• Level 3 control of operon: Sigma factors (accessory
• molecules). true for almost all bact genes. Increases with sigma factors -> allow (required!) for
• RNA 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.

• 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 naked
• DNA 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:transient
• Capsules: 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 to
• another. 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 packaged
• in viral coat -> then goes on to infect other cells with these little vesicles. Restriction enzymes are like bact immune system.

• 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 unaffected
• Mutualistic: 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 in
• mouth. Ex: 1 bact produces antibiotic (unaffected) secretes it and another species is harmed. This is where most antibiotics have
• come 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!!

• Parasitic relationship: host is damaged in some way
• Pathogen: parasite that can and does damage the host and cause disease
• Infection: process where pathogen or parasite is causing disease
• exogenous source: caused by microbe from outside own body
• endogenous source: caused by normal flora; already on/in body OR a latent infxn (ex Shingles à 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 the
• right 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 bugs
• that should never be on/in human body. Ex-mycobacterium tuburculosis.

• Eye: tears FLUSH -> lysozyme, Staphlococci
• (from skin around eye)
• Respiratory tract: mucous, cilia, (prevents adherence à ciliary escalator moves mucous), enzymes (IgA),
• macrophages. Deeper into resp tract, the fewer normal flora you should be seeing
• Mouth: lined with epithelial cells, IgA, bact in mouth are opportunistic à 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

• Virulence: ability to cause disease
• LD50: 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) à not endemic here for TB so don’t use it in US but do in India

• Bact become more virulent (swap genes, rapidly mutate, etc)
• - adherence: fimbria (bristles), pili, glycocalyx (capsule), adhesins (specific molecules that bind
• to 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: biofilms
• form on teeth à “quorum sensing”: coordinate activities so WHOLE colony makes same
• move, like making same toxins at same time

• 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 your
• cells. Ex- hemolysins (break down
• RBCs) -> 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).

• -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 à not used internally! And not injected, peroxide, etc)
• - Disinfectants: killing most but not all microbes.
• Not given to patients, with one exception à 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 all
• viruses. 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 à they’ve been through radiation), filtered (solutions) à warning: some viruses are so small, they pass through filters
• - Sanitization: decontaminate something to make it safe to use
• Physical means: heat, radiation, filtration
• Chemical: antiseptics, disinfectants, sterilants
• Topical methods: antiseptics, soap, mouthwash, etc.
• In vivo methods: “used in live patient” -> antibiotics

• Chlorhexidine: disrupts bact cell membrane; absorbs into gum tissue & on teeth -> residual activity
• Flouride: inhibits an enzyme in glycolosis (inhibits enolase). Only good for application; not good for ingestion
• Diluted 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 molecules
• Scope: quat ammonium-> target lipids. Inactivated by organics.

• sterilization: test strips have bacillus clostridium (high level) à 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,
• phenolics
• Low level indicator: most viruses, get rid of most germs

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

• Heat (dry and moist): dry heat (use this for things that corrode) -> takes WAY longer to bake things
• Ethylene oxide: gas; cold sterilizing
• 2% gluteraldehyde: liquid

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

• resolving power: ability to see 2 separate points as separate.
• Oil immersion: makes light go straight up instead of dispersing
• brighfield: resolving power à 2 microns
• darkfield: 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. Using
• antibodies conjugated w fluorescence to stain.
• electron microscopy: TEM (electron beam aimed at specimen and went through it; can see less/more
• dense 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!

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

• PCR: copy machine for DNA; can copy specific stretches of DNA for microbe and find if microbe is
• there 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)

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

• 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 a
• certain point; diagnosed using Ab-fluorescence
• ELISA: assay that looks for antigen (look at Fig 17.5 in book for HIV test -> put viral protein into
• wells -> 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 Western
• Blot)
• Western Blot: looking for protein. Run on a gel
• several proteins from the HIV virus (envelope, polymerase, GAG, etc) -> can transfer to piece of
• paper. 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).

Innoculate, Incubate, Isolate, Inspect, ID

• 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 on
• tonsils
• Quick immunological test: Suspected bladder infxn: they’re looking for nitrites. Normally, shouldn’t have nitrites, onlynitrates -> bact break down nitrates to nitrites.

• Idiopathic: we don’t know the cause
• Iatrogenic: disease that came from a healthcare procedure or healthcare setting (vs: nosicomial:
• from hospital!)

• bacteremia: bact in blood
• fungemia: fungi in the blood
• septicemia: either fungi or bact. in the blood