Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Bacterial Identification Flowcharts
This set of flowcharts is designed to familiarize you with the names and characteristics of
many bacterial genera with clinical significance. They are based, in part, on the biochemical
tests and culture media outlined in the Laboratory Diagnosis and Bacterial Identification
lecture. Here’s a good approach (but certainly not the only approach) to start learning these
organisms:
cocci
Gram-
positive
rods
Gram stain cocci
Gram-
negative
rods
Stain poorly Obligate
Intracellular
Spirochetes
Mycoplasmas
(mollicutes)
Acid-fast
(Mycobactera)
1
Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Gram-
positive
cocci
+ -
CATALASE
Staphylococci Streptococci/ Enterococci
• Facultative anaerobes • Anaerobes
Coagulase (+) Coagulase (-)
Staphylococcus • CoNS
-hemolytic -hemolytic non-hemolytic (γ)
aureus • Normal flora on
• Normal flora on skin, nares, vagina
skin, in nares • Most non-
• Colonies often hemolytic Enterococcus
yellow S. epidermidis
• Beta-hemolytic •Novobiocin • Some aerotolerant
• Salt tolerant susceptible • Lancefield group D
• Produces acid from S. saprophyticus • Black colonies on
mannitol •Novobiocin bile-esculin agar
resistant • Normal GI flora
Some
Streptococcus Streptococcus
pneumoniae Viridans • Clear colonies
streptococci or no growth
• Aerotolerant on bile-esculin
• Optochin • Some are
aerotolerant agar
susceptible
• Bile-soluble • Optochin
resistant Streptococcus Streptococcus
• Diplococci pyogenes
• Bile resistant agalactiae
• No Lancefield
antigen result • Normal oral • Aerotolerant • Aerotolerant
• Can be part of flora • Bacitracin • Bacitracin
normal • S. mitis susceptible resistant
pharyngeal important • PYR (+) • PYR (-)
flora example • Lancefield • Lancefield
• Various group A group B
Lancefield • Can be part of
groups normal
pharyngeal
flora
2
Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Gram-positive
bacilli
Endospore-forming Non endospore-forming
Spores not always produced in vivo
Aerobes Anaerobes
Aerobe Anaerobe
Bacillus Clostridium
• Found in soil • Found in soil,
and water water, GI tract
• Catalase (+) • Catalase (-)
Corynebacterium Listeria Nocardia
• Part of normal skin, • Will grow at low • Filamentous,
vaginal, pharyngeal temperatures (as branching
flora low as 2C) • Found in soil &
• Toxigenic strains • Facultative water
cause disease intracellular • Partially acid-fast
• Can be “club- • Distinctive
shaped” or can take tumbling motility
appearance of in broth
“Chinese letters”
• Brown/black
colonies on tellurite
agar Propionibacterium Lactobacillus Actinomyces
• On Loeffler agar,
colonies white, • Chains or • Part of normal • Filamentous,
cells have polar clumps, short flora (mouth, branching
“metachromatic rods vagina, GI) • Catalase (-)
granules” with • Common on • Rare pathogen • Part of normal oral,
special stains skin, vagina, (endocarditis, GI flora
oropharynx septicemia) • Cervicofacial
• Acne, • Strict or infections most
opportunistic aerotolerant common
infections • Catalase (-) • Knot up into yellow
flecks visible in pus
(“sulfur” granules)
3
Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Gram-negative
cocci
Neisseria sp. •Oxidase (+), catalase (+)
•Diplococci •Some species normal in throat
•Often associated with PMNs in direct smear •N. gonorrhoeae (UG, eye) oxidizes glucose
•Aerobes but like 5% CO2 •N. meningitidis (blood, CNS) oxidizes glucose
•Non-motile and maltose
•Need Chocolate (CAP) or Thayer-Martin agar
for N. gonorrhoeae
Gram-negative bacilli Straight rods
Coccobacilli/ pleomorphs Curved and Spiral rods
(most non-motile) (motile)
Aerobes (non-fermenters) Facultative Anaerobes Aerobes
Acinetobacter sp. Haemophilus Campylobacter sp.
•Cocci or rods •Often seen as a rod, can grow •“Gull wing” appearance
• May resemble Neisseria as long filaments •Oxidase (+)
•Oxidase (-), catalase (+) •Requires factor X (heme) and •Microaerophilic
•Normal oropharyngeal flora factor V (NAD) •Grow at 42C
•Soil/plants •Chocolate agar (CAP) •Motile
•Easy to grow on blood agar •Oxidase (+/-) Helicobacter sp.
Moraxella sp. Pasteurella •Oxidase (+)
•Often diplococcus •Can display bi-polar staining •Urease (+)
• Resembles Neisseria •Blood or chocolate •Microaerophilic
•Oxidase (+), catalase (+) •Oxidase (+) •Motile
•Normal respiratory flora
•Grows well on blood agar Anaerobes
Francisella sp. Facultative Anaerobe
•Very small, faint staining Bacteroides
•BCYE or chocolate agars + cys •Pleomorphic Vibrio sp.
•3 day incubation •Stain poorly •Comma-shaped rods
•Oxidase (-) •Easy to grow •Oxidase (+)
•Diagnose via serology •Normal GI, oral flora •Alkalophile
Brucella sp. •A few species motile •Motile
•Small, intracellular Prevotella •Likes/may need salt
•Enriched blood agar, 3 day + •Very small
•Oxidase (+) •Slow growing, fastidious
•Serology (presumptive) •Normal oral flora (bites)
Bordetella sp. •Black colonies on BAP
•Bordet-Gengou, Regan-Lowe Porphyromonas
agar, 4-12 d incubation •Very small
•PCR often used •Slow growing, fastidious
•Oxidase variable, motility •Normal (?) oral flora
variable (species-dependent) •Black colonies on BAP 4
Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Gram-negative bacilli
Straight rods
Facultative Anaerobes Aerobes (non-fermenters)
Oxidase (-) Oxidase (+)
Enterobacteriaceae Pseudomonas sp.
• Ferment glucose •Beige on MacConkey
• Normal GI flora •Resists cetrimide
• Many species of medical •Produces pyocyanin
importance •Multi-drug resistant
• Serratia can be lac(+/-), •Can grow anaerobically with
often produces red alternate electron acceptors
pigment Legionella sp.
•Thin, short or long
•Gram stain poorly
•Dieterle silver stain
•Direct fluorescent antibody
test (DFA)
•BCYE agar + cysteine, iron
•3-5 day incubation
Anaerobe
Lactose- Lactose non-
Fusobacterium
fermenting (CEEK) fermenting (ShYPS)
•Thin and pointy
Citrobacter
•Motile
•Urease and H2S (+/-) Non-H2S -
H2S -producing
Enterobacter producing
•Motile Shigella Proteus
•Urease (+/-) •Non-motile •Swarming motility
Escherichia •Urease (-) •Urease (+)
•Motile Yersinia Salmonella
•Often encapsulated •Bipolar staining •Motile
•Urease and H2S (-) •Slower growing •Urease (-)
Klebsiella than others, can
•Often highly mucoid grow <4˚C
•Non-motile •Coagulase (+/-)
•Urease (+) •Urease (+/-)
•H2S (-) •Motility (+/-) 5
Fundamentals 2 Bacterial Identification Flowcharts Drummelsmith
Organisms that do not Gram-
stain
Obligate
Spirochetes Mycobacteria Mycoplasma
Intracellular
• Long, flexible • Cannot replicate outside • Small rods, no outer • Extracellular
spirals of host cells membrane • Very small
• Endoflagella • Requires cell culture • Cell wall contains waxy • Lack a cell wall
• Gram-negative • Usually no peptidoglycan mycolic acids • Pleomorphic
cell envelope (no -lactam target!) • Acid-fast staining • Require
• Diagnose by FTA- Chlamydia/Chlamydophila • Resistant to drying, sterols
ABS, serology • Cannot make ATP chemical agents, • Sensitive to
Treponema • Vacuolar growth germicides, Gram stain environment
Borrelia (inclusion body) • Aerobes • Extremely
Leptospira • Protein cell wall • Slow growing fastidious
• 2 forms • Tiny “fried-egg”
Rickettsia colonies on
• Cytoplasmic or nuclear agar
replication
Orientia
• Cytoplasmic or nuclear
replication
Ehrlichia
• Vacuolar replication
(morula)
• 2 forms
Anaplasma
• Vacuolar replication
(morula)
• 2 forms
Coxiella
• Vacuolar replication
• 2 forms
