Basic identification of bacteria Flashcards
List genera of aerobic Gram-negative bacilli that are oxidase-negative.
(8)
OX- GNB:
- Acinetobacter (2xCB)
- Morganella
- Proteus
- Providencia
- Salmonella
- Shigella
- Stenotrophomonas (lab grown green, ox “yellow”)
- Yersinia
List genera of aerobic Gram-negative bacilli that are oxidase-positive.
(5)
OX+ GNB:
- Aeromonas
- Pasteurella (safety pin)
- Plesiomonas
- Pseudomonas
- Vibrio (vibroid)
What are two types of alpha-hemolytic streptococci,
and what biochemical can you use to differentiate them?
S.pneumo
- capsule -> optichin-R
Viridans Group streptococci (VGS) (S.mitis/S.mutans)
- no capsule = opt-S
What are two types of beta-hemolytic streptococci,
and what biochemicals can you use to differentiate them?
GAS (bacitracin-s, PYR+)
GBS (bacitrcin-R, PYR-, CAMP+)
What are two types of gamma-hemolytic streptococci,
and what biochemical can you use to differentiate them?
GDS (e.g. S.bovis)
Enterococcus (g. in 6.5% NaCl)
When is bacitracin used in the lab?
a.k.a. TaxoA
Differentiates GAS vs GBS
- GAS = bac-S
- GBS = bac-R
Catalase positive organisms
- Nocardia
- Pseudomonas
- Listeria
- Aspergillus
- Candida
- E. coli
- Staphylococci
- Serratia
What test can you use to detect DNase activity?
Toluidine Blue O
E.g. for Elizabethkingea meningoseptica
What test can you use to detect DNase activity?
Toluidine Blue O
E.g. for Elizabethkingea meningoseptica
Genera of lactose-fermenting gut microbiota
- Citrobacter
- Escherichia
- Enterobacter
- Klebsiella
When is optichin used in the lab?
a.k.a. TaxoP
Differentiates S.pneumo vs. VGS
- S.pneumo = opti-s
- VGS = opti-R
Bacteria that are oxidase-positive:
(Genera)
- Neisseria
- Pseudomonas
- Burkholderia
- Brucella
- Legionella
- Vibrio
- Campylobacter
- Helicobacter
What are the general traits of Pseudomonas spp.?
- Gram stain
- Motility
- Oxygen requirements
- Oxidase
- Catalase
- Indole
- Sugar fermentation & TSI reaction
- Nitrate reduction
- Citrate
- Lipase
- GS: GNB thin
- motile by polar flagellum (<=1)
- Facultative anaerobe
- OX +
- CAT +
- Indole -
- Non-lactose fermenter (TSI K/K)
- Nitrate reduction +
- Citrate +
- Lipase +
What are three biochemical tests you can use to distinguish S.pneumoniae from VGS?
- Optichin/TxP (S.pneumo = S)
- Bile solubility (S.pneumo = +)
- Inulin fermentation (S.pneumo = +)
Urease Positive Organisms
- Cryptococcus
- H. pylori
- Proteus
- Ureaplasma
- Nocardia
- Klebsiella
- S. epidermidis
- S. Saprophyticus
Bacillus
O2: O2 (obl/facan)
CAT+
Gram: GP bacilli. Oval endospores, central to subterminal.
ANTHRACIS:
- GV, Long chains.
- BAP colonies ground glass, beaten egg.
CEREUS:
- Pallisades (not long chains)
- BAP colonies ~green, larger than anthracis.
Corynebacterium
O2: O2 (obl/facan) CAT+ GS: GP bacilli Club/diphtheroid shape Form V’s, palisades, or Chinese letters
Erysipelothrix
O2: O2 (obl/facan) CAT- GS: Weak GP bacilli
Gardnerella
O2: FACAN CAT- GS: GV coccobacilli.
GI commensals (MGIF)
OX- L(N)F GNB Enterococcus ANA’s
GP branching filaments
AEROBIC: Nocardia (weakly acid-fast) ANO2: Actinomyces (not AF)
You see Gram-negative bacilli on your slide from a culture grown aerobically.
What genera could they be?
Coliforms:
- Escherichia
- Klebsiella (encapsulated)
- Enterobacter
- Serratia
- Citrobacter
- Shigella
- Salmonella
- & other Enterobacterales
Non-fermenters:
- Pseudomonas
- Acinetobacter
Pasteurella
HACEK organisms:
- Haemophilus (can be coccobacilli)
- Aggregatibacter
- Cardiobacter
- Eikenella
- Kingella
Bacillus*
*Bacillus & related genera can easily over-decolourize on Gram stains.
You see Gram-negative cocci on your slide from a culture grown aerobically.
What genera could they be?
- Neisseria (coffee-bean shape)
- Moraxella (coffee-bean shape)
- Haemophilus/HACEK (coccobacilli)
You see Gram-positive bacilli on your slide from a culture grown aerobically.
What genera could they be?
- Corynebacterium
- Bacillus
- Listeria
- Erysipelothrix
You see Gram-positive cocci on your slide from a culture grown aerobically.
What genera could they be?
- Staphylococcus
- Streptococcus
- Enterococcus
- “Nutritionally variant streptococci” (Granulicatella, Abiotrophia)
You see Gram-negative bacilli on your slide from a culture grown ANaerobically.
What genera could they be?
- Bacteroides
- Fusobacterium
- Prevotella
- Prophyromonas
- Leptotrichia
You see Gram-negative cocci on your slide from a culture grown ANaerobically.
What genera could they be?
- Veillonella*
* Veillonella is phylogenetically Gram-positive, within the Negativicute**s group, so stains Gram-negative.
You see Gram-positive bacilli on your slide from a culture grown ANaerobically.
What genera could they be?
- Clostridium
- Actinomyces
- Cutibacterium & Propionibacterium
- Eggerthella
- Eubacterium
You see Gram-positive cocci on your slide from a culture grown ANaerobically.
What genera could they be?
- Peptostreptococcus
- Parvimonas
- Finegoldia
- Staphylococcus saccharolyticus
You see Gram-negative bacilli on your slide. They appear curved.
What genera could they be?
- Vibrio (comma-shaped)
- Campylobacter (gull-winged)
- Helicobacter
- Anaerobiospirillum
- Arcobacter
You see Gram-negative bacilli on your slide. They appear fusiform.
What genera could they be?
- Fusobacterium
- Leptotrichia
- Capnocytophaga
You see Gram-negative coccobacilli on your slide.
What genera could they be?
- Haemophilus*
- Acinetobacter*
- Aggregatibacter*
- Moraxella*
- Pasteurella*
- Bacteroides*
- Brucella* (RG3!)
- Francisella* (RG3!)
You see Gram-variable bacilli on your slide.
What genera could they be?
- Bacillus (Paenibacillus, Lysinibacillus)
- Clostridium
- Gardnerella
- Leptotrichia
What bacterial are obligate intracellular bacteria?
(genera)
- Chlamydia/Chlamydophila
- Coxiella
- Rickettsia
- Orientia
- Ehrlichia
- Anaplasma
What bacterial are spirochetes?
(genera)
- Borrelia/Borreliella
- Leptospira
- Treponema
You see TINY Gram-negative bacilli on your slide.
What genera could they be?
- Brucella (RG3!)
- Francisella (RG3!)
How can we determine the serotype of an H.influenzae isolate?
Latex agglutination
(unless non-mucoid strain, a.k.a. non-typeable)
How can we determine the serotype of an H.influenzae isolate?
Latex agglutination
(unless non-mucoid strain, a.k.a. non-typeable)
Lactobacillus
O2: FACAN. (Grows better ANO2) CAT- GS: GP bacilli Colonies: Look like VGS (but different GS) ID with growth on LBS
Listeria
O2: FACAN CAT- GS: GPB (can be coccobacilli). Single or short chains. - GS of CSF or old cultures look GV coccoid, very similar to S.pneumo!
What organisms can grow on B.cepacia selective agar?
- B.cepacia complex
- Ralstonia spp.
What organisms can grow on B.cepacia selective agar?
- B.cepacia complex
- Ralstonia spp.
What’s in Chocolate agar that allows it to support Haemophilus influenzae growth?
- NAD (Factor V)
- Hemin (Factor X)
What genus is Lowenstein-Jensen agar used to culture?
Mycobacterium spp., including M.tuberculosis
What organisms grow on MacConkey agar?
Enteric Gram-negative organisms.
Fermentation of lactose in the medium turns colonies pink.
What organisms grow on Sabouraud agar?
Fungi
What is in Thayer-Martin agar that allows it to select for Neisseria gonorrhoeae and N. meningitidis?
- Vancomycin
- Trimethoprim
- Colistin
- Nystatin
How can we determine the serogroup of an N.meningitidis isolate?
PCR assay with two targets:
- ctrA = N.meningitidis capsular transport gene (confirms spp. ID & encapsulated).
- said = serogroup-specific poly-sialyltransferase gene.
NB: Serotyping done @NML for surveillance.
How can we determine the serogroup of an N.meningitidis isolate?
PCR assay with two targets:
- ctrA = N.meningitidis capsular transport gene (confirms spp. ID & encapsulated).
- said = serogroup-specific poly-sialyltransferase gene.
NB: Serotyping done @NML for surveillance.
Nocardia
O2: STRICT aerobe CAT+ GS: GP bacilli, weakGPB - Long, thin, delicate,branching chains/filaments. - Filaments can break apart from culture
Obligate intracellular bacteria
- Chlamydia
- Coxiella
- Ehrlichia
- Rickettsia
Oral cavity commensals (MOF)
CoNS Dips NP Neisseria VGS ANA GPC + Lactobacillus
How do we determine S.pneumoniae serotypes?
Done by Quellung reaction
How do we determine S.pneumoniae serotypes?
Done by Quellung reaction
Skin commensals (MSF)
CoNS Dips NP Neisseria VGS ANA GPC + Propioni
What is the Trichrome stain used for?
To detect intestinal protozoa/spx
What is the Trichrome stain used for?
To detect intestinal protozoa/spx
Which bacteria stain acid-fast:
(genera)
- Mycobacterium spp.
- Actinomycetes (e.g. Nocardia, Rhodococcus).
- Legionella micdadei
What organisms would you want to use a Fite stain to see?
-
Mycobacterium leprae
- Often decolourizes with ZN/Kinyoun stains
NB: Nocardia will also stain Fite+, so non-specific.
What organisms would only stain weakly with Gram stain, so a Giemsa stain would be preferred?
(genera)
- Borrelia/Borreliella
- Ehrlichia
- Anaplasma
- Rickettsia
- Helicobacter
What organisms would you want to use a GMS stain to see?
(GMS = Gomori methenamine silver)
Fungi
- Used broadly as a fungal screen in histology
- Including Pneumocystis jiroveci
(Histoplasma granuloma shown with question)
What organisms would you want to use an India ink stain to see?
Cryptococcus spp.
What organisms would you want to use a Mucicarmine stain to see?
- Cryptococcus spp.
What organisms would you want to use PAS (Period acid-Schiff) stain to see?
Tropheryma whipplei in tissue
(PAS+ macrophages in the lamina propria are pathognomonic for Whipple’s disease)
What organisms would you want to use a Warthin-Starry stain to see?
- Spirochetes:
- Treponema (e.g. syphilis)
- Borrelia/Borreliella
- Leptospira
- Helicobacter pylori
- Bartonella henselae (bacillary angiomatosis)
What organisms would you want to use a Ziehl-Neelsen stain to see?
- Acid fast bacteria:
- Mycobacterium spp.
- Actinomycetes (e.g. Nocardia, Tsukamurella, Gordonia)
- Legionella micdadei
- Coccidian parasites, e.g. Cryptosporidium
Strictly aerobic GN bacilli
Pseudomonas
