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Chapter 37 : , and Other

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Abstract:

This chapter talks about the new species of that have been added to or transferred between existing genera. Most common gram-negative organisms isolated from respiratory tract, urinary tract, and bloodstream infections from intensive care unit patients in the United States were (15%), (9%), (6%), (4%), (4%), (3%), and (2%). The organisms are, in general, readily isolated from clinical material, and few of the clinically relevant strains covered present difficulties in isolation from sterile body sites. Isolation from nonsterile body or environmental sites may require specialized media such as CHROMagar Orientation and chromID CPS, which perform similarly for the detection of urinary tract pathogens covered in the chapter and can reliably replace MacConkey and blood agars. The chapter also discusses diarrheal pathogens that are easily isolated, and about biochemical tests most useful for separating members. Even when unusual enterobacteria covered in the chapter are included in commercial system databases, the number of strains available to use in challenge studies is very limited; therefore, the ability of these systems to accurately identify these organisms is really unknown. General antimicrobial susceptibility and specialized phenotypic testing procedures are also discussed in the chapter.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
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Tables

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TABLE 1

Nomenclature, isolation source, and significance of selected genera of the family

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
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TABLE 2

Other members of the family

References given in parentheses. Genomospecies listed cannot be biochemically separated from other species within their genus and/or only a single strain exists.

Rare human isolates of no, or questionable, significance.

Environmental isolates; fish, marine, animal, or bird isolates; insect isolates or pathogens; plant isolates or phytopathogens.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 3

Separation of members of the genus

Abbreviations and symbols: ODC, ornithine decarboxylase; +, ≥85%; V, 15 to 84%; –, <15%.

Fermentation reactions in commercial systems should be similar to reactions in conventional fermentation broths (1% carbohydrate in broth with indicator).

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 4

Differentiation of and members of the genus ,

See the text for and subsp. and identification.

Abbreviations and symbols: LDC, lysine decarboxylase; ADH, arginine dihydrolase; ODC, ornithine decarboxylase; VP, Voges-Proskauer; +, ≥90%; V, 11 to 89%; –, ≤10%.

See Table 3 , footnote b.

Separated from P. agglomerans by a negative malonate reaction and fermentation of d-sorbitol( ).

Separated from E. gergoviae by positive reactions in potassium cyanide broth and myo-inositol.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 5

Separation of some members of the genera and ,

biochemicals not available; only a single strain known.

Abbreviations and symbols: ODC, ornithine decarboxylase; VP, Voges-Proskauer; ONPG, -nitrophenyl-β-d-galactopyranoside; NA, not available; +, ≥90%; V, 11 to 89%; –, ≤10%.

See Table 3, footnote .

A negative adonitol reaction may be an indication that the strain is but this must be confirmed with gene sequencing ( ).

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 6

Biochemical characterization of members of the genus ,

subsp. is reportedly a spore-forming organism; is urea positive; only a single strain is known.

Abbreviations and symbols: LDC, lysinedecarboxylase; ODC, ornithine decarboxylase; Mal, malonate; l-Rham, l-rhamnose; d-Xyl, d-xylose; Suc, sucrose; Adon, adonitol; d-Sorb, d-sorbitol; Cello, cellobiose; +, ≥90%; V, 11 to 89%; –, ≤10%; NA, information not available.

See Table 3, footnote .

Growth at 37°C but biochemical characterization optimal at 30°C.

May fail to grow at 37°C.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
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TABLE 7

Separation of members of the genera and

Abbreviations and symbols: Ind, indole; HS, hydrogen sulfide; ODC, ornithine decarboxylase; +, ≥90%; V, 11 to 89%; –, ≤10%.

See Table 3, footnote .

genomospecies 4, 5, and 6 cannot be differentiated phenotypically.

Some members of some biogroups are HS positive.

Some members of some biogroups are ornithine decarboxylase negative.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 8

Separation of from selected and species (VP, ADH, and ODC variable or positive)

Abbreviations and symbols: VP, Voges-Proskauer; ADH, arginine dihydrolase; ODC, ornithine decarboxylase; +, ≥90%; V, 11 to 89%; –, ≤10%.

See Table 3, footnote .

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 9

Differentiation of Kluyvera from commonly seen indole-positive, VP-negative organismsa

Abbreviations and symbols: VP, Voges-Proskauer; LDC, lysine decarboxylase; KCN, potassium cyanide; +, ≥90%; V, 11 to 89%; –, ≤10%. and are also indole positive and VP negative and can be found in Tables 10and 12, respectively.

Includes ( and combined) ( ).

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 10

Separation of LDC-, ODC-, and ADH-negative unusual found in clinical specimens

Abbreviations and symbols: LDC, lysine decarboxylase; ODC, ornithine decarboxylase; ADH, arginine dihydrolase; KCN, potassium cyanide; VP, Voges-Proskauer; +, ≥90%; V, 11 to 89%; –, ≤10%. is also LDC, ODC, and ADH negative and can be found in Table 12.

See Table 3, footnote .

subsp. can be separated from subsp. by fermentation of maltose and glycerol.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
Table 11

Separation of from

Abbreviations and symbols: VP, Voges-Proskauer; +, ≥90%; V, 11 to 89%; –, ≤10%. Data from reference .

See Table 3, footnote .

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 12

Separation of that may be H2S positive

Abbreviations and symbols: LDC, lysine decarboxylase; ODC, ornithine decarboxylase; KCN, potassium cyanide; ONPG, -nitrophenol-β-d-galactopyranoside; +, ≥90%; V, 11 to 89%; –, ≤10%.

See Table 3, footnote .

is positive, is negative.

Found in clinical specimens but of questionable or no significance.

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37
Generic image for table
TABLE 13

Resistance mediators of the

Abbreviations: S, susceptible; R, resistant, BMD, broth microdilution; TEM, from patient's name Temoneira; SHV, sulfhydryl reagent variable; CTX-M, active on cefotaxime, isolated in Munich; CMY, active on cephamycins; MOX, active on moxalactam; FOX, active on cefoxitin; DHA, discovered at Dhahran; KPC, carbapenemase; GES, Guiana-extended spectrum; SME, enzyme; IMI, imipenem-hydrolyzing β-lactamase; NMC, not metalloenzyme carbapenemase; IMP, active on meropenem; VIM,Verona integron-encoded metallo-β-lactamase. Data are from references , and .

Class A and C mediators are serine β-lactamases, and class B mediators are metallo-β-lactamases (named for serine or zinc, respectively, present at the active site involved in hydrolysis of the beta-lactam ring).

Citation: Abbott S. 2011. , and Other , p 639-657. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch37

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