ABPath Medical Microbiology cheat sheet

Biosafety levels: BSL-1 nonpathogenic; BSL-2 clinical/diagnostic work with human specimens; BSL-3 aerosol-transmitted agents (M. tuberculosis); BSL-4 no treatment or vaccine available.

Standard precautions apply to all blood and body fluids regardless of suspected infection status; they replace universal precautions and body-substance isolation.

OSHA Bloodborne Pathogens Standard requires an exposure control plan, hepatitis B vaccination offer, PPE, and post-exposure evaluation.

Chemical hazard communication requires Safety Data Sheets (SDS) for every hazardous reagent and a written hazard communication program.

Formaldehyde, glutaraldehyde, and xylene are common lab hazards; formaldehyde is a carcinogen and requires monitoring and ventilation.

Sentinel laboratory refers to a clinical lab that recognizes and refers possible biothreat agents (e.g., Bacillus anthracis, Francisella tularensis) to an LRN reference lab.

Reportable disease lists are set by state/jurisdiction; notifiable conditions must be reported to public health authorities, often within specified timeframes.

Spill response: absorb, disinfect with appropriate agent (e.g., 1:10 bleach for bloodborne pathogens), and dispose per biohazardous waste rules.

QC frequency: external quality assessment (proficiency testing) at least twice per year per regulated analyte; internal QC per manufacturer/lab policy.

Levey-Jennings chart plots QC values over time; Westgard rules (1-3s, 2-2s, R-4s, 4-1s, 10x) flag random vs systematic error.

1-3s rule (one value >3 SD) is a warning/rejection rule; 2-2s (two consecutive >2 SD same side) indicates systematic error.

Sterility assurance for autoclaves uses biological indicators (Geobacillus stearothermophilus spores) and chemical/mechanical monitors.

Hand hygiene is the single most effective infection prevention measure; alcohol-based rubs preferred unless hands visibly soiled.

CLSI and M100 provide standard methods for antimicrobial susceptibility testing and interpretation (breakpoints).

Media QC requires testing with ATCC reference strains to verify growth support, selectivity, and biochemical reactions.

Healthcare-associated infection surveillance uses standardized definitions (e.g., NHSN) to calculate infection rates per device-days.

Binomial nomenclature: genus capitalized, species lowercase, both italicized (e.g., Escherichia coli); abbreviated genus after first use (E. coli).

Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species; family names end in -aceae (bacteria) or -idae (protozoa).

Bergey's Manual classifies bacteria by phenotypic and phylogenetic characteristics; 16S rRNA sequencing is the standard for bacterial phylogeny.

Prokaryotes lack a nucleus and membrane-bound organelles; eukaryotes (fungi, protozoa, helminths) have a nucleus.

Viruses are classified by genome type (DNA/RNA, ss/ds), replication strategy (Baltimore classification), and morphology.

Fungi: yeasts (single cell, budding), molds (hyphae, mycelium), dimorphic fungi (mold at 25°C, yeast at 37°C).

Virulence factors distinguish pathogens: capsules, toxins, adhesins, invasins, and immune-evasion mechanisms.

Strain typing methods include serotyping, MLST, and whole-genome sequencing for outbreak investigation.

Collect before antimicrobial therapy when possible; timing and site selection affect yield and interpretation.

Blood cultures: collect 2-3 sets (each set = aerobic + anaerobic bottle) from separate sites; adequate volume (20-30 mL total in adults) improves sensitivity.

Sputum is acceptable if it shows >25 PMNs and <10 squamous epithelial cells per low-power field (Bartlett criteria); otherwise reject for culture.

CSF: do not refrigerate for bacterial culture if fastidious organisms (e.g., Neisseria meningitidis, Haemophilus influenzae) are suspected; process immediately.

Urine culture: clean-catch midstream; colony count interpretation (≥10^5 CFU/mL historically significant, lower counts may be significant in symptomatic patients).

Anaerobic specimens: collect with anaerobic transport systems; avoid swabs; tissue or aspirates preferred; reject for anaerobes if not properly transported.

Stool for bacterial culture: transport in Cary-Blair; do not refrigerate if suspecting Shigella or Campylobacter (fastidious).

Rejection criteria include unlabeled/mislabeled specimens, inappropriate container, delayed transport, and improper preservation.

Adherence via pili/fimbriae and adhesins is required for colonization (e.g., E. coli P-fimbriae in pyelonephritis).

Toxins: exotoxins (secreted, often A-B type; e.g., diphtheria, cholera, botulinum) vs endotoxin (LPS, Gram-negative, triggers TLR4 and cytokine storm).

Capsules resist phagocytosis (e.g., Streptococcus pneumoniae, Klebsiella pneumoniae, Cryptococcus neoformans).

Intracellular survival: Mycobacterium tuberculosis prevents phagosome-lysosome fusion; Listeria escapes into cytoplasm via actin-based motility.

Immune evasion: antigenic variation (influenza hemagglutinin, Borrelia VlsE), IgA protease (Neisseria, Haemophilus), and biofilm formation (Staphylococcus, Pseudomonas).

Superantigens (TSST-1, streptococcal pyrogenic exotoxin) cross-link MHC II and TCR, causing massive cytokine release.

Invasins and tissue-destroying enzymes: hyaluronidase, streptokinase, coagulase (Staphylococcus aureus), and collagenase.

Biofilms on catheters and prosthetic devices increase resistance to antibiotics and host defenses.

Cell wall synthesis inhibitors: beta-lactams (penicillins, cephalosporins, carbapenems, monobactams) and glycopeptides (vancomycin).

Protein synthesis inhibitors: aminoglycosides (30S), tetracyclines (30S), macrolides/clindamycin/chloramphenicol (50S), oxazolidinones (50S).

Nucleic acid inhibitors: fluoroquinolones (DNA gyrase/topoisomerase IV), rifampin (RNA polymerase), metronidazole (DNA damage).

Folate pathway inhibitors: sulfonamides (dihydropteroate synthase) and trimethoprim (dihydrofolate reductase); combination is synergistic.

Beta-lactam resistance mechanisms: beta-lactamase production, altered PBPs (MRSA, penicillin-resistant pneumococcus), and efflux.

Disk diffusion (Kirby-Bauer) uses CLSI zone diameter breakpoints; broth microdilution yields MIC; E-test provides gradient MIC.

MRSA detection: cefoxitin disk or oxacillin MIC; mecA/mecC PCR or PBP2a latex agglutination confirm.

ESBL and carbapenemase detection: phenotypic synergy tests and molecular methods (e.g., carbapenemase gene PCR).

Blood agar: nonselective, differential for hemolysis (alpha, beta, gamma); supports most pathogens.

MacConkey agar: selective for Gram-negative bacilli (bile salts, crystal violet) and differential for lactose fermentation (pink colonies = lactose fermenter).

Chocolate agar: heated blood releases factors V and X; supports fastidious organisms (Haemophilus, Neisseria).

Gram stain: crystal violet, iodine (mordant), alcohol decolorizer, safranin counterstain; Gram-positive purple, Gram-negative pink.

Acid-fast stain (Ziehl-Neelsen or Kinyoun): mycolic acid retains carbolfuchsin; acid-fast organisms appear red on blue background.

Fungal stains: calcofluor white (fluorescence), lactophenol cotton blue (mold morphology), and India ink (Cryptococcus capsule).

Selective media: mannitol salt agar (Staphylococcus), colistin-nalidixic acid (CNA) for Gram-positives, and thiosulfate-citrate-bile salts-sucrose (TCBS) for Vibrio.

Special stains: Giemsa (blood parasites), trichrome (protozoa), and silver stain (Pneumocystis, fungi).

Culture remains the reference standard for most bacteria; incubation conditions (temperature, atmosphere) must match organism requirements.

MALDI-TOF MS identifies organisms by protein mass fingerprint; rapid and cost-effective for bacteria and yeasts.

Nucleic acid amplification tests (NAATs) detect pathogen DNA/RNA; PCR, real-time PCR, and TMA are common platforms.

Sequencing (Sanger, NGS) enables identification, resistance detection, and outbreak typing.

Serology detects host antibody or antigen (e.g., HIV antibody/antigen combo, hepatitis serology); window period affects sensitivity.

Antigen tests (e.g., rapid strep, influenza) are fast but less sensitive than NAATs.

Parasite diagnosis: microscopy of concentrated stool (O&P), antigen tests (Giardia, Cryptosporidium), and serology for tissue parasites.

Viral culture and shell vial assays detect cytopathic effect; viral load assays quantify nucleic acid for monitoring.

Critical value reporting: positive blood cultures, CSF Gram stains, and acid-fast smears require immediate notification to the care team.

Antimicrobial stewardship: de-escalate to narrowest effective agent based on culture and susceptibility results.

Interpret susceptibility in context: MIC alone does not predict outcome; consider site of infection, drug penetration, and dosing.

Contamination vs true bacteremia: coagulase-negative staphylococci in a single bottle often represent skin contamination; multiple bottles suggest true infection.

Therapeutic drug monitoring (e.g., vancomycin, aminoglycosides) uses trough/peak levels to balance efficacy and toxicity.

Report turnaround time and method limitations to clinicians; explain false-positive/negative risks for NAATs and serology.

Consult on appropriate specimen selection and timing to maximize diagnostic yield and avoid unnecessary testing.

Notify public health for reportable organisms and assist with contact tracing and outbreak investigation.