STEPTRACKERMICROBIOLOGY | LAB CLUES | RAPID-FIRE REVIEW

Lab Clue → Organism

Stains, culture media, colony traits, microscopy and biochemical tests that point to a single organism — with links back to the full pages.

FOCUS ON
Learn lab clues in three groups: stains (Gram, acid-fast, silver, India ink, Giemsa, PAS), special media (chocolate, Thayer-Martin, Löwenstein-Jensen, BCYE, Bordet-Gengou/Regan-Lowe, TCBS, Sabouraud, Eaton, Tellurite, MacConkey, EMB) and bedside or biochemical tests (catalase, coagulase, optochin, bacitracin, CAMP, urease, oxidase, germ tube, Tzanck, KOH, India ink, cold agglutinins, heterophile). Sorting flowchart for gram-positive cocci is on 1.06.
LAB CLUE
ORGANISM
NOTE
PAGE
Gram ⁺ cocci in clusters, catalase ⁺, coagulase ⁺
S aureus
Protein A, golden colonies
2.01
Lancet-shaped diplococci, α-hemolytic, optochin-sensitive, bile-soluble
S pneumoniae
Quellung reaction (capsule)
2.02
β-hemolytic, bacitracin-resistant, CAMP ⁺, hippurate ⁺
S agalactiae (GBS)
Neonatal sepsis
2.03
Grows in bile and 6.5% NaCl, PYR ⁺
Enterococcus
Also GAS is PYR ⁺
2.03
Tumbling motility, cold growth, β-hemolytic gram ⁺ rod
Listeria
Actin rockets
2.05
Metachromatic granules, Tellurite or Loeffler medium
C diphtheriae
Elek test for toxin
2.05
Medusa-head colonies, box-car rods, D-glutamate capsule
B anthracis
Painless black eschar
2.05
Double zone of hemolysis, boxcar anaerobe, gas
C perfringens
Lecithinase (α-toxin)
2.04
Branching, weakly acid-fast aerobe
Nocardia
vs Actinomyces (anaerobe, sulfur granules)
2.06
Acid-fast rods, Löwenstein-Jensen, cord factor
M tuberculosis
Slow growth
3.01
No cell wall, fried-egg colonies on Eaton agar, cold agglutinins
M pneumoniae
Cholesterol in membrane
3.03
Gram ⁻ diplococci, Thayer-Martin, maltose ⁺
N meningitidis
Gonococcus: glucose only
4.01
Chocolate agar, needs factors V and X
H influenzae
Satellites around S aureus
4.02
Bordet-Gengou / Regan-Lowe agar
B pertussis
PCR now preferred
4.02
Silver stain, BCYE agar (iron + cysteine)
Legionella
Urine antigen
4.03
Oxidase ⁺, non-lactose fermenter, blue-green pigment, grape odor
Pseudomonas
Pyocyanin
4.03
Pink on MacConkey, green sheen on EMB
E coli
Lactose fermenter
4.04
Mucoid lactose-fermenting colonies
Klebsiella
Capsule
4.04
Swarming motility, urease ⁺
Proteus
Struvite stones
4.04
H₂S ⁺ non-lactose fermenter, motile
Salmonella
Shigella: H₂S −, nonmotile
4.05
Comma shape, grows at 42 °C
Campylobacter
Vibrio grows on alkaline TCBS
4.05
Urease ⁺ curved rod in gastric biopsy
H pylori
Breath test
4.06
Dark-field: thin motile spirals
T pallidum
Too thin for Gram stain
4.08
Clue cells, ⁺ whiff test
Gardnerella (BV)
pH > 4.5
4.09
Owl's-eye nuclear inclusions
CMV
Heterophile-negative mono
6.02
Multinucleated giant cells on Tzanck
HSV, VZV
PCR preferred
6.01
Negri bodies
Rabies
Purkinje cells, hippocampus
7.04
India ink halo, mucicarmine ⁺ capsule
Cryptococcus
CSF antigen
8.02
Germ tube at 37 °C, pseudohyphae
Candida albicans
—
8.02
Silver stain of BAL: cup-shaped cysts
Pneumocystis
↑ LDH, β-D-glucan
8.02
Banana gametocytes · Maltese cross
P falciparum · Babesia
Thin smear
9.03

Mechanism — why selective media work

Nutrient needsChocolate (V, X), BCYE (iron, cysteine), LJ (egg)
InhibitorsThayer-Martin (vanco, colistin, nystatin), MacConkey (bile salts, crystal violet)
IndicatorsLactose → pink (MacConkey), H₂S → black

Stains at a glance

STAIN
SHOWS
EXAMPLES
Ziehl-Neelsen
Acid-fast
Mycobacteria, Nocardia (weak), Cryptosporidium
Silver
Fungi, Legionella, Pneumocystis, H pylori
Bartonella
India ink
Capsule
Cryptococcus
Giemsa
Blood/intracellular
Plasmodium, Borrelia, Chlamydia, Rickettsia
PAS
Glycogen, mucopolysaccharide
Tropheryma whipplei

How it's tested

COMMON CONFUSIONCatalase separates staph from strep; coagulase separates S aureus from the coagulase-negative staph; optochin and bacitracin then sort the streptococci.
THE TRAPOrganisms that don't Gram stain well (mycobacteria, Mycoplasma, Chlamydia, Rickettsia, Treponema, Legionella) need a different stain or test, so a "negative Gram stain" doesn't rule them out.
YOUR APPROACHMorphology → Gram reaction → one decisive test or medium → organism → confirm with the clinical picture.

If you see… think…

Satellite colonies around S aureus → H influenzae (V factor)
Thayer-Martin medium → Neisseria
Löwenstein-Jensen → M tuberculosis
Eaton agar → Mycoplasma
TCBS agar → Vibrio
Sabouraud agar → fungi
PAS-positive macrophages in small bowel → Whipple disease
Weakly acid-fast branching rods → Nocardia
Quellung reaction → capsule swelling (pneumococcus)
Elek test → diphtheria toxin