Bacteriology
Core concepts
Begin with preanalytic decisions, because many exam items hinge on them: specimen site and source (expectorated vs. induced sputum vs. bronchoalveolar lavage), collection timing, and whether an anaerobic transport system is required. Know what each primary medium selects for: sheep blood agar (hemolysis patterns, nonselective), chocolate agar (fastidious Haemophilus and Neisseria), MacConkey (lactose fermentation by gram-negative bacilli), Columbia colistin-nalidixic acid (gram-positive selection), phenylethyl alcohol, thioglycollate broth, and selective plates such as CIN, TCBS, and Campylobacter media.
Then master identification algorithms. For gram-positive cocci, catalase separates staphylococci from streptococci; coagulase separates Staphylococcus aureus from coagulase-negative staphylococci; novobiocin resistance flags S. saprophyticus. For streptococci, bacitracin and PYR identify S. pyogenes, hippurate and CAMP identify S. agalactiae, and bile esculin with 6.5% NaCl identifies enterococci. For gram-negative bacilli, use oxidase, lactose fermentation, TSI for H2S and glucose, indole, citrate, urease, and motility. Mycobacteria need acid-fast staining, with niacin and NAP inhibition for slow growers.
Traps
- Reading hemolysis on colonies grown in the wrong atmosphere, or after refrigeration.
- Calling enterococci group D streptococci; both are bile esculin positive, so add salt tolerance and PYR.
- Reporting mixed flora from a specimen showing squamous epithelial cells, indicating oral contamination.
- Treating an oxidase-positive fermenter as a routine Enterobacterales isolate.
Rule of thumb
A lactose-positive, oxidase-negative, indole-positive gram-negative rod from urine or stool is reported as Escherichia coli. An unexpected oxidase-positive result on a fermenting rod should prompt a repeat and a check for a nonfermenter such as Pseudomonas.