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Microbiology

Follow a specimen from collection through organism detection, identification, susceptibility testing, reporting, and referral.

Steps

  1. Collecting, transporting and prioritizing specimens15 min
    3 skills
    • Choose a collection device compatible with the requested microbiology test
    • Choose room temperature or refrigeration for a specimen and its requested test
    • Prioritize a limited or irreplaceable microbiology specimen

    At the bench Select specimen preparation, media, and incubation for a culture

  2. Direct stains, media and incubation16 min
    3 skills
    • Read a direct Gram stain and compare it with the culture growth
    • Select primary media for the specimen source and suspected organism group
    • Choose ambient air, CO₂, or anaerobic incubation for each culture plate

    At the bench Read an organism stain and communicate a significant preliminary finding · Select specimen preparation, media, and incubation for a culture

  3. Blood cultures16 min
    3 skills
    • Check each blood-culture set's fill volume and collection site
    • Choose the first laboratory actions after a blood-culture bottle signals positive
    • Tell a blood-culture contaminant from a pathogen by organism and number of positive sets

    At the bench Read an organism stain and communicate a significant preliminary finding

  4. Gram-positive isolates from blood16 min
    3 skills
    • Tell S. aureus from S. lugdunensis and other staphylococci in blood
    • Tell streptococci from enterococci and their vancomycin-resistant look-alikes in blood
    • Recognize a catalase-positive blood rod that needs a Listeria workup
  5. Gram-negative, fastidious and vector-borne blood isolates18 min
    4 skills
    • Confirm a gram-negative diplococcus to species before reporting it
    • Distinguish nonfermenting gram-negative rods from enteric fermenters
    • Recognize a HACEK or Haemophilus blood isolate that needs special identification
    • Read vector-borne infection serology against the week of illness and paired titers
  6. CSF and sterile body fluids16 min
    3 skills
    • Process CSF for culture at once and keep it at room temperature
    • Read a CSF molecular panel against its target list and continue the culture
    • Split a sterile body fluid between culture bottles, a Gram stain, and plates

    At the bench Select specimen preparation, media, and incubation for a culture

  7. Respiratory cultures16 min
    4 skills
    • Screen a sputum Gram stain for squamous cells before routine bacterial culture
    • Match a lower respiratory colony count to the threshold for its collection method
    • Select tests for Legionella, Mycoplasma, and other agents routine culture misses
    • Decide when a negative rapid strep antigen needs culture or NAAT backup

    At the bench Select specimen preparation, media, and incubation for a culture

  8. Stool cultures and C. difficile17 min
    4 skills
    • Choose stool media and toxin or NAAT tests for the suspected enteric pathogen
    • Identify Enterobacterales species from TSI and other biochemical reactions
    • Tell Vibrio, Aeromonas, and Campylobacter from enteric fermenters in stool culture
    • Tell C. difficile carriage from toxin production using NAAT and toxin results

    At the bench Select specimen preparation, media, and incubation for a culture

  9. Wounds, tissue and anaerobes15 min
    2 skills
    • Select a wound specimen that represents the infected tissue
    • Recognize bite wounds and deep abscesses that need anaerobic culture

    At the bench Select specimen preparation, media, and incubation for a culture

  10. Genital specimens and group B streptococcus16 min
    3 skills
    • Identify bacterial vaginosis by Nugent score, Amsel criteria, or a validated NAAT
    • Decide when gonococcal culture is needed in addition to NAAT
    • Process an antepartum group B streptococcus screen through enrichment broth
  11. Urine cultures15 min
    3 skills
    • Choose the correct sampling site for a catheter urine culture
    • Calculate CFU/mL from a colony count and the calibrated loop volume
    • Match a urine colony-count cutoff to the collection method and the organisms grown
  12. MALDI-TOF, molecular detection and strain typing15 min
    4 skills
    • Recall how MALDI-TOF matches a protein spectrum to identify an organism
    • Select a suitable isolated colony for MALDI-TOF identification
    • Tell NAAT target detection from active infection, carriage, or leftover DNA
    • Tell isolates of one strain from isolates that only share a species, using strain typing

    At the bench Reconcile organism identification with specimen source and observed growth

  13. Setting up susceptibility tests16 min
    4 skills
    • Recognize agar depth, cation, or thymidine errors in an AST setup
    • Distinguish broth dilution from agar and gradient-diffusion AST formats
    • Read the inhibition-zone diameter for a valid disk-diffusion test
    • Check that AST control strains are in range before releasing patient results

    At the bench Review susceptibility results for method validity and expected resistance

  14. Reading MICs and breakpoints16 min
    4 skills
    • Read the minimum inhibitory concentration from a valid dilution series
    • Assign a susceptibility category to an MIC with the organism-drug breakpoint
    • Distinguish growth inhibition from the bactericidal endpoint
    • Flag a susceptible result for a drug the species is intrinsically resistant to
  15. Drug targets, beta-lactamases and the antibiogram17 min
    4 skills
    • Match a major antimicrobial class to its cellular target
    • Select eligible isolates for a cumulative antibiogram
    • Distinguish ESBL, AmpC, and carbapenemase resistance patterns
    • Distinguish resistant-organism surveillance from diagnostic susceptibility testing

    At the bench Review susceptibility results for method validity and expected resistance

  16. Methicillin resistance in staphylococci15 min
    3 skills
    • Detect methicillin resistance in staphylococci with a cefoxitin screen
    • Recall the altered penicillin-binding protein encoded by mecA
    • Name what a negative mecA, nitrocefin, or other targeted test cannot detect
  17. Vancomycin, enterococci and pneumococci17 min
    4 skills
    • Select a validated vancomycin MIC method for S. aureus
    • Investigate unexpected reduced vancomycin susceptibility in S. aureus
    • Read enterococcal high-level gentamicin and streptomycin screens for synergy
    • Choose meningitis or nonmeningitis breakpoints for a pneumococcal MIC

    At the bench Review susceptibility results for method validity and expected resistance

  18. The sentinel laboratory and select agents16 min
    3 skills
    • Stop routine identification and contain a suspected select agent
    • Run sentinel rule-out tests for B. anthracis, Brucella, and F. tularensis
    • Report and refer an isolate that cannot be ruled out as a select agent

    At the bench Reconcile organism identification with specimen source and observed growth

  19. Acid-fast stains and mycobacterial culture16 min
    3 skills
    • Grade an acid-fast smear on the correct scale and report it without a species
    • Match mycobacterial decontamination to the specimen and its contamination rate
    • Distinguish M. tuberculosis complex from nontuberculous mycobacteria

    At the bench Read an organism stain and communicate a significant preliminary finding

  20. Mycobacterial susceptibility and Nocardia17 min
    4 skills
    • Pair a TB rifampin-resistance NAAT with growth-based testing for the other drugs
    • Keep a rapid-grower clarithromycin result pending until the day-14 read
    • Tell Nocardia from other branching rods with a modified acid-fast stain
    • Extend culture incubation when Nocardia is suspected

    At the bench Review susceptibility results for method validity and expected resistance · Select specimen preparation, media, and incubation for a culture

  21. Viral specimens, antigens and congenital infection16 min
    4 skills
    • Choose a viral test and specimen for the syndrome and the day of illness
    • Decide when a negative rapid influenza antigen needs a molecular test
    • Read a negative CSF viral NAAT against the day of illness and its target list
    • Distinguish direct evidence of congenital infection from transferred maternal antibody
  22. Viral loads and travel-related viruses15 min
    3 skills
    • Calculate a serial viral-load change in log₁₀ and compare it with assay variability
    • Distinguish a result detected below quantification from a negative viral result
    • Choose NAAT, NS1 antigen, or serology for a returning traveler by day of illness
  23. Malaria and Babesia on blood films18 min
    3 skills
    • Distinguish the roles of thick and thin blood films for parasite examination
    • Recognize malaria species features that need confirmatory identification
    • Tell Babesia from malaria and blood-film artifacts

    At the bench Read an organism stain and communicate a significant preliminary finding

  24. Parasitemia and tissue parasites15 min
    3 skills
    • Calculate asexual parasitemia from infected and total red cells
    • Calculate parasite density using the measured leukocyte count
    • Select a specimen and method for a suspected tissue protozoal infection
  25. Stool parasite methods, amebae and coccidia16 min
    3 skills
    • Choose stool parasite methods that match the collection and preservative
    • Distinguish pathogenic intestinal amebae from morphologic look-alikes
    • Select a targeted stain or NAAT when intestinal coccidia are suspected
  26. Nematodes, cestodes and trematodes16 min
    3 skills
    • Differentiate intestinal nematodes using the observed egg or larval stage
    • Identify Taenia species from segments, scolex, or molecular testing
    • Match each trematode egg to the specimen it appears in, such as urine or stool
  27. Yeasts, Cryptococcus and dimorphic fungi17 min
    4 skills
    • Read a KOH or calcofluor white preparation and state what a negative can miss
    • Confirm a presumptive yeast identification, such as possible C. auris, before release
    • Check a negative cryptococcal antigen against India ink, culture, and prozone
    • Recognize a mold that may be a dimorphic pathogen and move it into a safety cabinet

    At the bench Read an organism stain and communicate a significant preliminary finding · Reconcile organism identification with specimen source and observed growth

  28. Dermatophytes, molds, fungal biomarkers and Pneumocystis17 min
    4 skills
    • Confirm a dermatophyte from skin, hair, or nail by colony and microscopic features
    • Distinguish broad pauciseptate from narrow septate hyphal patterns
    • Read galactomannan and beta-D-glucan results against the fungi they miss
    • Report a quantitative Pneumocystis PCR without overcalling pneumonia or colonization
  29. Reporting, corrections and public health15 min
    2 skills
    • Distinguish preliminary, final, addendum, and corrected microbiology reports
    • Meet jurisdiction-specific public-health reporting duties for a result