Clinical Microbiology

This ones a tough one :(

Primary disinfectant used in Lab

Vesphene → kills and washes

Homeostasis in general

Bringing stability back to internal while changes are happening externally (stimulus)

Disease definition

Homeostasis is exceeded (something much more is happening) → acute vs. chronic

The Subclinical stage of infection

infected however non-symptomatic

Symbiotic relationships relative to humans (3)

Mutual - 😉 vs. Parasitic - ☹ vs. Commensual - 😑

Types of Colonization (+examples) (5)

body surface selection → Normal flora vs. Transient - survive exposure but no multiplication vs. Nosocomial - hospitalization transient colonization → antibiotic resistance infection (MSRA) vs. Carriers - nonnormal flora → infect others (Strep) vs. Endogenous - opportunistic normal flora → infection (CoN)

Pattern steps of infection

exposure (noncontagious) → incubate → prodromal (vague symptoms) → acute (signs) → decline vs. convalescent (death)

Sources of infection (3)

Congenital - before/at birth vs. Endogenous - opportunistic normal flora vs. Exogenous - not normal flora → direct (immediate transfer)/indirect (intermediate)

Virulence factors

adaptation, capsule, replication, a pathogens toxins, adhesion, chemokines

Gram Stain - Bacteria exceptions that do not stain***

Mycoplasms - free living but no cell wall vs. Rickettsiaceae - vector → no culture vs. Chlamdyiales - no peptidoglycan → no culture growth (elementary - not active/reticulate - active)

Mycology vs. Parasitology vs. Virology

eukayotic budding → smooth(yeast)/hyphae(mold) vs. eukaryotic variety vs. noncellular, needs host genetic material

Taxonomy general Conventions & Exceptions

Genus species  (specific) or Genus species → coagulase-negative staphylococci, viridans group of streptococci, and Group ___ streptococci (by serology)

Types of Recombination (3)

Transduction - virus vs. Transform - foreign vs. Congugation - pilus between bacteria

Bacterial genetic material

Plasmid - self-replication/adaptation/transfer/replication, vs. Transposons - movement/functional and jumping inbetween sequence, vs. Integron (integration) - gene cassette (capturing), and Insertion sequence - movement gene

Bacterial Binary Fission

Elongation → DNA replication → cross wall → two bacterial cells

Proportiating Doubling time

proportional to nutrients and inversely proportional to size of colony

Types of Cultivations (2)

direct smear (same day) vs. plating ]→ stain

Growth Curve phases

Lag → Log (most utilized for cultures) → Stationary → Decline

Order for recording Culture growth from a plate

Amount (+#) → Hemolysis → Size → Colour → Texture

Amount of Growth on a plate (miro)

+1 vs. +2 vs. +3 vs. +4

Hemolysis of growth on a plate culture (miro)

Beta - basal membrane diffusion around growth (hold to light) vs. Alpha - green/darker diffusion vs. Gamma (none) - no diffusion vs. Alpha-prime - two zones beta → alpha vs. metabolic waste - light dot surrounded by diffusion ]→ TRANSMITTED LIGHT

Sizing of colony growth (plate)

pinpoint - ppt vs. small - sm vs. medium - med vs. large - lrg ]→ doubling time

Texture of a BAP colony growth

opaque - op *GP vs. translucent - trans vs. mucoid - runny vs. metallic - rusty/two-tones (E. coli)

Culture media classification compared to the media types (solid)

BAP - enriched/differential vs. CNA - enriched/selective vs. BRU - ANO2/enriched/differential vs. MAC - selective/differential vs. CHOC - enriched vs. MH - basal

enriched - X (at least), differential - there is a noticeable appearance change, enrichment - broth enhancement and inhibition

Stain Theory Primary Mechanisms

Chromophore - dye/colour vs. Auxochrome - bind/stain dye to cells

Types of Dyes

Anionic - acidic → stains background (target is not stained) vs. Cationic - basic (Bacteria is negatively charged) → Crystal violet/safranin vs. Neutral → Giemsa malaria

Gram Stain procedure steps

Chromophore - crystal violet → Auxochrome - iodine → Decolourize - acetone alcohol (gn - thin peptidoglycan layer) → Counter stain - safranin (gn → pink, gp → purple)

Gram stain decolourization

gp - thick murein layers vs. gn - thin sandwich → permeability is less selective → dehydration and defatting ]- shrinks pores and strips lipid layer → removing gn CV/I

Gram Positive → Pink

Old/fragile, gram variability, overcolourization

Steps in preparing a colony smear → gram

label → saline → colony → emulsify → fix (methanol) → gram stain theory

Cocci vs. Bacilli vs. Pleomorphism

circular → (not marked in colony smears) chain/pair/cluster/tetras/sarcinae vs. rod shaped → VLK, palicades ]→ gpb sm reg/irreg (clubs), (gpb irreg) boxcar, gull-wing vs. mixture

Wet mount technique

Unfixed stain ]→ saline emulsify → cover slip → lower SSC slightly → no 100x

India Ink (negative) vs. Lactophenol cotton blue vs. endospore

Acidic dye → stain background/clear cell vs. fungal → phenol/disinfect/kill → lactic preservation → blue vs. heat stain → wash → safranin → green spores/pink cell

Direct fluorescence Ab vs. acridine orange vs. calcofluor white vs. Truant’s

Ab-Ag complex vs. non-gram/low #s vs. fungal chitin vs. acid-fastness

Acid-fast stains overview (3)

long-chain fatty acids - mycolic → mycobacteria reatin stain after decolourization]→ Truant’s - fluorescent stain → decolour (alcohol/HCl) → potassium permanganate (oxidizing agent) → green-yellow acid fast vs. ZN - heat vs. kinyoun - phenol ]- carbol fuchsin → decolour (EtOH/acid-alcohol/HCl) → malachite green or methylene blue → red acid-fast

Metabolism Types

Catabolism - degradation → subunits/energy vs. Anabolism - uses catabolism products → cell growth

Strategies of respiration (terminal electron acceptor → energy (3)

Aerobic - O2 vs. Anarobic - inorganic vs. Fermentation - organic only → mixed acids → strong acids vs. butanediol → neutral

Terminology for nutrient requirement

nonfastidious - min/basal vs. semi-fastidious -blood vs. fastidious - chocolate (nonambient air)

Temperature needs terminology

thermophile - above 45 vs. mesophile - 25-45 vs. psychophile - 20

Routine Incubation - Ambient air vs. Anaerobic (ANO2)

35-37 degrees, 21% O2, 78% N2, 0.03% CO2 vs. 0% O2, 80%N2, 20% CO2

Aerobes vs. Anaerobes (conditions)

Obligate aerobes - ambient air, vs. Facultative anaerobes - both, vs. obligate anaerobes → aerotolerant - prefers CO2 but can grow in O2 vs. moderate - <= 3% O2, strict - < 0.5% O2

Capnophile - 5-10% CO2 (facultative anaerobes) vs. Microaerophile - 5-10% O2

Oxygen reduction potential (Eh) indicators and voltages

indicators when reduced → no oxygen → colourless (colour=O2) and O2 → +0.2V vs. CO2 → -0.2V vs. ANO2 → -0.35V

Transport culture vs. Normal culture

viability/preservation vs. grow/observe

Liquid media phase viewable growth

<= 1.0×10^6 CFU/ml turbidity

Normal Properties of agar (temperatures)

red algae → sterilized at 121C, gel at 40C, and melt at 85C (additions at 50C)

Preparation of Agar

powder → dH2O → 20min sterile → heat-labile additions → quality check (ATOC)

BHIB vs. THIO

enriched, fildes (X + V) → sterile sites vs. 0.075% agar → pink O2 zone (aerobic)

Extent of Identification is based on…

Clinical significance (normal vs. pathogen), location - sterile pathogen sources distinguishes and identifiers

Length of identification

Spot test/MALDI - fast vs. tubes/API - slow/incubation

Complexity of an organisms proportionality to the number of testings being done

common → more tests vs. unique → less tests

Overview of gram stain morphology

BH vs. AH vs. NH (gn - no opacity) → MAC - gnb non-fastidious vs. CNA - gp → no strict obligate anaerobe (more than 5min in O2) → gp (purple stain) vs. gn (pink stain) → cocci - tetrads (direct smear → pair/chains) vs. bacilli

Differential Media Potential ingredients (for what) (11)

Water, Agar (reflects use), Carbon (identification - glucose/lactose/Sorbitol), Nitrogen (peptones), Sulfur (H2S → ferrous sulfide → TSI blackening), NaCl (Salt tolerance - enterococci in 6.5%), Neutralizing agents (detox and buffer), Reducing agents (anaerobic conditions), Growth factors, Selective agents (bile/dyes/antimicrobials), Indicators (pH/Eh)

pH Indicator rules

Acidic = Yellow, Basic = Colour from name, Exceptions: Methyl red and Neutral red (reverse)

Types of Differential Tests (2)

Spot test - product of pre-formed enzymes, vs. Incubation Tube test - need enzymes to be formed/accumulate (Tolerance/Simple substrate/Enzyme)

Catalase test (false negatives/positives)

Spot test, break down hydrogen peroxide (3%), wooden stick → petri dish lid, Many rapid bubbles, False+ - metal loop/no RBCs from media vs. False- - old/delay

Oxidase test (false negatives/positives)

Spot test, cytochrome oxidase (aerobic) + electron rich dye TMPD (donor) → redox indicator - electron accepted, (no dyed/reducing agent media) wooden stick → filter paper, colourless (redox) → blue (oxidized) - producing ]- 10 secs (NOT FROM MAC), False+ - within 10s/metal loop vs. False- - old/fermentation

Spot Indole Test (false negatives/positives)

tryptophanase → indole + ρ-dimethylaminocinnamaldehyde → colour, BAP (tryptophan) → moist filter paper - cinnamaldehyde, well isolated colony → teal within 30s, False+ - mixed vs. False- - old/acidic

Differential test Inoculation order

Liquid → slant (aerobic) → stab (anaerobic) → purity plate

Purity plate

viability/correct/pure - MAC growth → MACpp vs. BAP/CNA growth → BAPpp 

6.5% NaCl test (false negatives/positives)

Liquid Tolerance tube test, heart infusion broth → liquid swish, Turbidity/pellet → gpc/Enterococcus, False+ - overinoculate vs. False- - 

Bile Esculin Agar Test

Selective (bile)/Differential (Esculin) Tolerance tube test, Slant → Esculin hydrolysis + ferric ammonium citrate, BOTH growth on slant and half blackening of the tube → gpc

MRVP Test and Theory

Liquid Fermentation tube test, mixed acid (MR) vs. butanediol (VP) ]- most perform one, highly buffered glucose broth → two separate test MR (48hr → methyl red) vs. VP - acetonin, atm O2 + KOH (VP2) + acetonin → pink → α-naphthol amplifies colour (VP1) → red → gnb - Entereobacterales, Limits: heavy inoculation/VP1 (aerate) before VP2 (aerate) 9:3 → RT 10min, no colour → 35C 20min

Adontinol Test

Liquid single-enzyme fermentation tube test, ferment alcohol sugar, Phenol Red, turbid and yellow → positive (always turbid) → Entereobacterales

Decarboxylase test

Liquid Multiple-enzyme tube test, glucose fermentation → acidic → deoxycarboxylase (NOT deanimases) → alkalis, Base and Lysine or Ornithine ]- bromocresol purple and cresol red and overlaid oil, Base: yellow/no colour change (non-fermenters) and turbid → OK → no amino acids to decarboxylate → no alkaline pH vs. other amino acids: purple and turbid → positive → anaerobic non-fastidious gnb, Limits: overinoculation/overincubation → bleaching → positive, OIL OVERLAY 

Phenylalanine Deanimase Agar test

Single-enzyme Slant tube test, deaminating phenylalanine, detection by 10% ferric chloride, Positive: growth on slant → green (1-5mins) → Entereobacterales

Citrate test (false positives/negatives)

Simple substrate slant tube test (green), Sodium citrate (C) and ammonium phosphate (N) → conversion → alkaline, bromothymol blue, Positive: growth OR blue colour → use simple sources → Entereobacterales, False+ - overinoculation vs. False- - check for growth even when green

Urease test