Chapter 3.8 : Fecal and Other Gastrointestinal Cultures and Toxin Assays

Table 3.8.1-1

Commonly used primary plating and broth media for isolation of Salmonella and Shigella a

a Either bile salts, deoxycholate, or Selenite is present in each medium to inhibit gram-positive microbiota. Abbreviations: D, differential; E, enriched; S, selective. Ferric ammonium citrate reacts with hydrogen sulfide (H2S) from organism to produce black color of colony.

Table 3.8.1-2

Special highly selective media for specific pathogen requests

a Incubate at 37°C in O2 unless otherwise stated.

b Since as many as 20% of asymptomatic hospitalized patients may be colonized with C. difficile, tests for the presence of toxin in stool are more specific for diagnosis of C. difficile-associated diarrhea. Isolation of the organism should only be done for epidemiological studies, with confirmation that the isolated strain is a toxin producer. CCFA (containing cycloserine, cefoxitin, fructose, egg yolk, and neutral red) can also be used for isolation. Do not use a medium with neutral red to demonstrate colonial fluorescence ( 3 ).

c Prepare TCBS fresh for use from powder or by melting previously prepared or purchased “deeps.” If made from powder, boil but do not autoclave prior to use.

Table 3.8.1-3a

QC of specialized media for detection of fecal pathogens

a Abbreviations are as follows. A, for testing nutritive properties. Inoculate each medium with 10 µl of a 1:100 dilution of standardized cell suspension (0.5 McFarland). If isolated colonies are not obtained, use a 10-fold-lighter inoculum. B, for testing selective properties. Inoculate each medium with 10 µl of a 1:10 dilution of standardized cell suspension (0.5 McFarland). Although ATCC strains are listed, any organism that will yield the identical result is acceptable. For medium abbreviations, refer to Table 3.8.1-2 .

Table 3.8.1-3b

QC of specialized media for detection of fecal pathogens

a Abbreviations are as follows. A, for testing nutritive properties. Inoculate each medium with 10 µl of a 1:100 dilution of standardized cell suspension (0.5 McFarland). If isolated colonies are not obtained, use a 10-fold-lighter inoculum. B, for testing selective properties. Inoculate each medium with 10 µl of a 1:10 dilution of standardized cell suspension (0.5 McFarland). Although ATCC strains are listed, any organism that will yield the identical result is acceptable. For medium abbreviations, refer to Table 3.8.1-2 .

Table 3.8.1-4

Microscopic and gross observations of fecal specimens associated with various infections a

a Data are only a guideline, and in any infection, observations are variable. For example, only 50% of C. difficile-associated cases of diarrhea demonstrate the presence of PMNs.

Table 3.8.1-5

Biochemical differentiation of selected members of the Salmonella group a

a Symbols: −, =9% of strains positive; V, 10 to 89% of strains positive; +, ≥90% of strains positive.

Table 3.8.1-6

Summary of detection media and identification methods for fecal pathogens a

a For Campylobacter species, see procedure 3.8.2. NA, not applicable.

Table 3.8.2–1a

Taxonomic position, known sources, and common disease associations of Campylobacter, Arcobacter, Helicobacter, and related species a

a able adapted from reference 16 .

b All organisms listed belong to rRNA superfamily VI. Organisms in boldface type are associated wih human sources. Validly published or most commonly used nomenclature of the taxa described are given priority, with superseded (in quotation marks) or less common nomenclature given in parentheses. Names that have not been validly published are given in single quotation marks. Abbreviations: CNW, catalase negative—weak; NNC, nitrate-negative Campylobacter; NARTC, NA-resistant thermophilic Campylobacter; CLO, Campylobacter-like organism; IDO, intracellular Desulfovibrio organism.

c Likely phylogenetic position of taxon in rRNA superfamily VI based on 16S rRNA sequence comparisons or DNA-DNA hybridization data.

d Biovar descriptions conform with recent suggestions by On ( 16 ).

e Original phylogenetic position in rRNA superfamily VI emended with reference to available 16S rRNA sequence comparisons. Brackets indicate that the taxon is generically misnamed.

f The proposed name of ‘H. heilmannii’ did not distinguish between the two phylogenetically distinct taxa referred to as ‘G. hominis 1’ and ‘G. hominis 2.’

g Taxonomic position based upon marked morphological similarity to ‘Gastrospirillum’ spp.

h Most current taxonomy indicates C. hyoilei to be indistinguishable from C. coli( 23 ).

i Helicobacter canadensis is a newly described agent of human gastroenteritis and is closely related to H. pullorum( 6 ).

Table 3.8.2–1b

Taxonomic position, known sources, and common disease associations of Campylobacter, Arcobacter, Helicobacter, and related species a

a able adapted from reference 16 .

b All organisms listed belong to rRNA superfamily VI. Organisms in boldface type are associated wih human sources. Validly published or most commonly used nomenclature of the taxa described are given priority, with superseded (in quotation marks) or less common nomenclature given in parentheses. Names that have not been validly published are given in single quotation marks. Abbreviations: CNW, catalase negative—weak; NNC, nitrate-negative Campylobacter; NARTC, NA-resistant thermophilic Campylobacter; CLO, Campylobacter-like organism; IDO, intracellular Desulfovibrio organism.

c Likely phylogenetic position of taxon in rRNA superfamily VI based on 16S rRNA sequence comparisons or DNA-DNA hybridization data.

d Biovar descriptions conform with recent suggestions by On ( 16 ).

e Original phylogenetic position in rRNA superfamily VI emended with reference to available 16S rRNA sequence comparisons. Brackets indicate that the taxon is generically misnamed.

f The proposed name of ‘H. heilmannii’ did not distinguish between the two phylogenetically distinct taxa referred to as ‘G. hominis 1’ and ‘G. hominis 2.’

g Taxonomic position based upon marked morphological similarity to ‘Gastrospirillum’ spp.

h Most current taxonomy indicates C. hyoilei to be indistinguishable from C. coli( 23 ).

i Helicobacter canadensis is a newly described agent of human gastroenteritis and is closely related to H. pullorum( 6 ).

Table 3.8.2–1c

Taxonomic position, known sources, and common disease associations of Campylobacter, Arcobacter, Helicobacter, and related species a

a able adapted from reference 16 .

b All organisms listed belong to rRNA superfamily VI. Organisms in boldface type are associated wih human sources. Validly published or most commonly used nomenclature of the taxa described are given priority, with superseded (in quotation marks) or less common nomenclature given in parentheses. Names that have not been validly published are given in single quotation marks. Abbreviations: CNW, catalase negative—weak; NNC, nitrate-negative Campylobacter; NARTC, NA-resistant thermophilic Campylobacter; CLO, Campylobacter-like organism; IDO, intracellular Desulfovibrio organism.

c Likely phylogenetic position of taxon in rRNA superfamily VI based on 16S rRNA sequence comparisons or DNA-DNA hybridization data.

d Biovar descriptions conform with recent suggestions by On ( 16 ).

e Original phylogenetic position in rRNA superfamily VI emended with reference to available 16S rRNA sequence comparisons. Brackets indicate that the taxon is generically misnamed.

f The proposed name of ‘H. heilmannii’ did not distinguish between the two phylogenetically distinct taxa referred to as ‘G. hominis 1’ and ‘G. hominis 2.’

g Taxonomic position based upon marked morphological similarity to ‘Gastrospirillum’ spp.

h Most current taxonomy indicates C. hyoilei to be indistinguishable from C. coli( 23 ).

i Helicobacter canadensis is a newly described agent of human gastroenteritis and is closely related to H. pullorum( 6 ).

Table 3.8.2–2

Human disease associations of Campylobacter species by clinical syndrome

a GI, gastrointestinal.

Table 3.8.2–3

Commercial systems for generating microaerobic environments and the approximate atmospheric content

a This system produces negligible H2 and may not grow H2-requiring species.

Table 3.8.2–4

Phenotypic reactions of clinically important Campylobacter and Helicobacter species a

a +, positive reaction; 0, negative reaction; w, weakly positive; V, variable reaction, NA, not available. See procedure 3.8.4 for H. pylori identification.

b Urease-positive thermophilic campylobacters or C. lari-like strains may be found ( 12 ).

c Growth at 42°C; catalase negativity suggests A. butzleri.

d H. cinaedi/CLO1B can be separated by DNA homology tests. H. cinaedi/CLO1B, H. fennelliae, and H. pylori can be definitively identified by cellular fatty acid analysis ( 10 ).

e Rare C. fetus subsp. fetus strains are aerobic.

f These species are historically sensitive to NA; however, resistant strains are seen in as high as 35% of isolates due to acquired fluoroquinolone resistance, which may make this assay less useful in identification.

g H2S in TSI suggests C. coli.

h There are isolated reports of Helicobacter species that are urease producing other than H. pylori ( 24 ).

Untitled

Untitled

Untitled

Untitled