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Microbiology

Specimen handling, bacterial identification by site, susceptibility testing, mycobacteria, fungi, parasites, and viruses.

Lessons
19
Sections
14
Sources checked
Aug 29 – Sep 11, 2026

Preanalytic Procedures

  1. Specimen Collection, Transport, and Primary Processing in MicrobiologyStart here

    A culture recovers the organisms present at the site only when collection, transport, rejection, biosafety, direct smears, media, inoculation, and incubation are handled correctly.

Blood and Bone Marrow

  1. Blood Cultures and Gram-Positive Blood Isolates

    Blood-culture volume, collection pattern, bottle monitoring, and isolate identification help distinguish gram-positive bloodstream infection from contamination.

  2. Gram-Negative, Fastidious, and Vector-Borne Agents of Bloodstream Infection

    Gram-negative and fastidious blood isolates require organism-specific identification, and several vector-borne agents of bloodstream infection are diagnosed by serology, blood smear, or molecular testing.

Sterile Body Fluids and the Eye

  1. Cerebrospinal Fluid and Sterile Body Fluid Cultures

    Cerebrospinal fluid and other normally sterile body fluids require immediate processing, concentration before smear and culture, rapid antigen and molecular testing, and careful separation of true pathogens from skin contaminants.

Respiratory Tract

  1. Lower and Upper Respiratory Tract Bacteriology

    Respiratory cultures require judging specimen adequacy, separating indigenous flora from pathogens, applying quantitative thresholds to bronchoscopy specimens, and using selective media or molecular assays for organisms routine culture cannot recover.

Enteric Bacteriology

  1. Enteric Bacteriology: Stool Workup, Enterobacterales, and Curved Oxidase-Positive Organisms

    Stool collection and rejection rules, selective media, and targeted testing are used to detect Salmonella, Shigella, STEC, Campylobacter, Vibrio, and Clostridioides difficile. Biochemical, MALDI-TOF, and molecular methods identify the Enterobacterales and related curved rods.

Wound and Genital Tract

  1. Wound, Tissue, and Genital Tract Bacteriology

    Wound and genital workup starts with a specimen collected from the lesion, followed by Gram stain, culture, or NAAT chosen for the organisms expected at that site.

Urinary Tract and Identification

  1. Urinary Tract Bacteriology and Identification MethodsUpdated

    Quantitative urine culture converts a calibrated-loop colony count into CFU/mL, then phenotypic, MALDI-TOF, and molecular methods identify the isolate that grew.

Antimicrobial Susceptibility Testing

  1. Antimicrobial Susceptibility Testing and Resistance MechanismsUpdated

    AST methods, breakpoints, and resistance-detection tests convert an isolate's growth response into a reportable category that matches the organism, drug, method, and current CLSI or FDA breakpoint in use.

Select Agents and Sentinel Laboratories

  1. Sentinel Recognition and Referral of Select Agents

    Sentinel laboratories rule out Bacillus anthracis, Brucella, Francisella tularensis, and Yersinia pestis with a short set of conventional bench tests, then contain, notify, and refer any isolate they cannot exclude.

Mycobacteriology

  1. Mycobacteriology: Acid-Fast Staining, Culture, and Identification

    Acid-fast smears, NALC-NaOH decontamination, broth and solid culture, and NAAT, MALDI-TOF, and sequencing methods recover and identify Mycobacterium tuberculosis complex and nontuberculous mycobacteria.

  2. Mycobacterial Susceptibility, Latent Infection Testing, Biosafety, and Nocardia

    Mycobacterial and Nocardia susceptibility testing follows CLSI M24 and M24S with WHO resistance terminology. Latent-infection tests are described with their performance limits, along with mycobacteriology biosafety and Nocardia identification.

Virology

  1. Viral Diagnosis: Respiratory, Herpesvirus, Congenital, and CNS Syndromes

    Respiratory, herpesvirus, congenital, and CNS viral results are interpreted using the specimen site, collection timing, assay design, and host response.

  2. Viral Diagnosis: Mucocutaneous, Enteric, Systemic, Immunocompromised, and Travel-Related Infections

    Choosing among viral NAAT, antigen testing, serology, tissue examination, and public-health confirmation starts from the specimen site, illness day, immune status, epidemiology, and vaccination history.

Parasitology

  1. Parasitology: Specimens, Blood and Tissue Protozoa

    Specimen selection, blood-film examination, parasite quantitation, and confirmatory testing support the diagnosis of malaria, babesiosis, hemoflagellates, toxoplasmosis, and free-living amebic disease.

  2. Parasitology: Intestinal Protozoa, Helminths, and Immunocompromised-Host Infections

    Specimen selection, microscopy, antigen tests, and NAAT support identification of intestinal protozoa, helminths, and parasitic infections that become severe during immunosuppression.

Mycology

  1. Mycology Laboratory Methods, Yeasts, and Dimorphic Pathogens

    Fungal direct examination, culture, MALDI-TOF and molecular methods identify Candida, Cryptococcus, Malassezia, and the thermally dimorphic pathogens. Suspected dimorphic cultures are sealed, handled only in a biosafety cabinet, and referred.

  2. Mycology: Dermatophytes, Molds, Pneumocystis, and Molecular Detection

    Laboratory diagnosis of dermatophytes, invasive molds, Pneumocystis, microsporidia, and Prototheca depends on specimen quality, direct examination, culture, biomarkers, and validated molecular identification interpreted together.

Postanalytic Procedures

  1. Microbiology Postanalytic Reporting: Critical Values, Documentation, and Public Health

    Microbiology reporting includes staged results, critical-result alerts, corrected reports, susceptibility interpretation, infection-prevention communication, and jurisdiction-specific public-health reporting.