Microbiology

Steps

1. 1Collecting, transporting and prioritizing specimens15 min · 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
2. 2Direct stains, media and incubation16 min · 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
3. 3Blood cultures16 min · 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
4. 4Gram-positive isolates from blood16 min · 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. 5Gram-negative, fastidious and vector-borne blood isolates18 min · 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. 6CSF and sterile body fluids16 min · 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
7. 7Respiratory cultures16 min · 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
8. 8Stool cultures and C. difficile17 min · 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
9. 9Wounds, tissue and anaerobes15 min · Select a wound specimen that represents the infected tissue · Recognize bite wounds and deep abscesses that need anaerobic culture
10. 10Genital specimens and group B streptococcus16 min · 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. 11Urine cultures15 min · 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. 12MALDI-TOF, molecular detection and strain typing15 min · 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
13. 13Setting up susceptibility tests16 min · 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
14. 14Reading MICs and breakpoints16 min · 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. 15Drug targets, beta-lactamases and the antibiogram17 min · 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
16. 16Methicillin resistance in staphylococci15 min · 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. 17Vancomycin, enterococci and pneumococci17 min · 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
18. 18The sentinel laboratory and select agents16 min · 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
19. 19Acid-fast stains and mycobacterial culture16 min · 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
20. 20Mycobacterial susceptibility and Nocardia17 min · 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
21. 21Viral specimens, antigens and congenital infection16 min · 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. 22Viral loads and travel-related viruses15 min · 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. 23Malaria and Babesia on blood films16 min · 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
24. 24Parasitemia and tissue parasites15 min · 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. 25Stool parasite methods, amebae and coccidia16 min · 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. 26Nematodes, cestodes and trematodes16 min · 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. 27Yeasts, Cryptococcus and dimorphic fungi17 min · 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
28. 28Dermatophytes, molds, fungal biomarkers and Pneumocystis17 min · 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. 29Reporting, corrections and public health15 min · Distinguish preliminary, final, addendum, and corrected microbiology reports · Meet jurisdiction-specific public-health reporting duties for a result

What you'll be able to do