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Selected Topics in Anaerobic Bacteriology

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  • Author: Deirdre L. Church1
  • Editors: Randall T. Hayden2, Donna M. Wolk3, Karen C. Carroll4, Yi-Wei Tang5
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4; 2: St. Jude Children’s Research Hospital, Memphis, TN; 3: Geisinger Clinic, Danville, PA; 4: Johns Hopkins University Hospital, Baltimore, MD; 5: Memorial Sloan-Kettering Institute, New York, NY
    • Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
  • Received 05 June 2015 Accepted 27 August 2015 Published 12 August 2016
  • Deirdre L. Church, [email protected], [email protected]
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  • Abstract:

    Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent infection, and may become feasible for other conditions in the future.

  • Citation: Church D. 2016. Selected Topics in Anaerobic Bacteriology. Microbiol Spectrum 4(4):DMIH2-0015-2015. doi:10.1128/microbiolspec.DMIH2-0015-2015.

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/content/journal/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015
2016-08-12
2019-10-15

Abstract:

Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent infection, and may become feasible for other conditions in the future.

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Selected Topics in Anaerobic Bacteriology
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Citation: Church D. 2016. Selected topics in anaerobic bacteriology. microbiolspec 4(4): doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.fig1
FIGURE 1

Anaerobic collection devices. BBL Port-A-Cul Transport System (BD Diagnostics); BD Eswab (BD Diagnostics); BBL Anaerobic Vacutainer Specimen Collector (BD Diagnostics); AnaeroGro – Prereduced anaerobic-culture medium (Hardy Diagnostics); Anaerobic Tissue Transport Surgery Pack (Anaerobic Systems); Starplex Anaerobic Transport Medium (Fisher Scientific); Copan Liquid Amies Elution Swab (Eswab) (Copan Diagnostics Inc.); Anaerobic Transport Medium – PRAS (Anaerobic Systems).

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FIGURE 1

Anaerobic collection devices. BBL Port-A-Cul Transport System (BD Diagnostics); BD Eswab (BD Diagnostics); BBL Anaerobic Vacutainer Specimen Collector (BD Diagnostics); AnaeroGro – Prereduced anaerobic-culture medium (Hardy Diagnostics); Anaerobic Tissue Transport Surgery Pack (Anaerobic Systems); Starplex Anaerobic Transport Medium (Fisher Scientific); Copan Liquid Amies Elution Swab (Eswab) (Copan Diagnostics Inc.); Anaerobic Transport Medium – PRAS (Anaerobic Systems).

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FIGURE 2

Anaerobic culture-incubation systems. BBL GasPak Plus and Anaerobic Jar (BD Diagnostics); Anoxomat Mark II System and jars (Advanced Instruments, Inc.); Different types of anaerobic chambers, including systems that require the use of gloves to access the chamber (top and middle images are from Plas-Labs and Bactron [ShelLabs]), and gloveless systems (bottom image) (Coy).

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FIGURE 2

Anaerobic culture-incubation systems. BBL GasPak Plus and Anaerobic Jar (BD Diagnostics); Anoxomat Mark II System and jars (Advanced Instruments, Inc.); Different types of anaerobic chambers, including systems that require the use of gloves to access the chamber (top and middle images are from Plas-Labs and Bactron [ShelLabs]), and gloveless systems (bottom image) (Coy).

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FIGURE 3

Antibiotic-susceptibility disk testing – Gram-positive anaerobic bacteria.

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FIGURE 3

Antibiotic-susceptibility disk testing – Gram-positive anaerobic bacteria.

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
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FIGURE 4

Antibiotic-susceptibility disk testing – Gram-negative anaerobic bacteria.

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FIGURE 4

Antibiotic-susceptibility disk testing – Gram-negative anaerobic bacteria.

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FIGURE 5

Clostridial-necrotizing skin and soft-tissue infection. .

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FIGURE 5

Clostridial-necrotizing skin and soft-tissue infection. .

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
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FIGURE 6

Yellow pseudomembranes of colitis. .

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FIGURE 6

Yellow pseudomembranes of colitis. .

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FIGURE 7

Three-step testing algorithm for laboratory diagnosis of infection. Adapted from reference ( 263 ) and reprinted with permission.

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FIGURE 7

Three-step testing algorithm for laboratory diagnosis of infection. Adapted from reference ( 263 ) and reprinted with permission.

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FIGURE 8

C. DIFF QUIK CHEK Complete Assay. Illustration shows both GDH- and toxin-positive samples on the left, and a GDH-positive but toxin-negative sample on the right; see product monograph (TechLab, Blacksburg, VA, USA. See http://www.techlab.com/diagnostics/c-difficile/c-diff-quik-chek-complete-30525c-30550c-t30525c-t20550c/)

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FIGURE 8

C. DIFF QUIK CHEK Complete Assay. Illustration shows both GDH- and toxin-positive samples on the left, and a GDH-positive but toxin-negative sample on the right; see product monograph (TechLab, Blacksburg, VA, USA. See http://www.techlab.com/diagnostics/c-difficile/c-diff-quik-chek-complete-30525c-30550c-t30525c-t20550c/)

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Tables

Selected Topics in Anaerobic Bacteriology
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015-1,webId=/content/author/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015-1,properties={foaf_givenname=Deirdre L., foaf_name=Deirdre L. Church, foaf_surname=Church, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015-aff1]]}]]
Citation: Church D. 2016. Selected topics in anaerobic bacteriology. microbiolspec 4(4): doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T1
TABLE 1

Diversity of anaerobes in the human body

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TABLE 1

Diversity of anaerobes in the human body

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T2
TABLE 2

Acceptable and unacceptable types of specimens for anaerobic culture

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TABLE 2

Acceptable and unacceptable types of specimens for anaerobic culture

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T3
TABLE 3

Description of commonly used anaerobic-culture media

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TABLE 3

Description of commonly used anaerobic-culture media

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T4
TABLE 4

Rapid identification of anaerobic Gram-negative bacilli

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TABLE 4

Rapid identification of anaerobic Gram-negative bacilli

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T5
TABLE 5

Rapid identification of spp.

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TABLE 5

Rapid identification of spp.

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T6
TABLE 6

Rapid identification of beta-hemolytic and/or swarming spp.

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TABLE 6

Rapid identification of beta-hemolytic and/or swarming spp.

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T7
TABLE 7

Rapid identification of spp. that on Gram stain appear Gram-negative

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TABLE 7

Rapid identification of spp. that on Gram stain appear Gram-negative

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T8
TABLE 8

Rapid identification of aerotolerant spp.

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TABLE 8

Rapid identification of aerotolerant spp.

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T9
TABLE 9

Rapid identification of nonspore-forming anaerobic Gram-positive bacilli

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TABLE 9

Rapid identification of nonspore-forming anaerobic Gram-positive bacilli

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T10
TABLE 10

Rapid identification of anaerobic cocci

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TABLE 10

Rapid identification of anaerobic cocci

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T11
TABLE 11

Laboratory guidelines for work-up of anaerobes isolated from nonsterile-specimen cultures

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TABLE 11

Laboratory guidelines for work-up of anaerobes isolated from nonsterile-specimen cultures

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T12
TABLE 12

Clinical indications for susceptibility testing of anaerobic bacteria

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TABLE 12

Clinical indications for susceptibility testing of anaerobic bacteria

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T13
TABLE 13

CLSI -suggested grouping of antimicrobial agents to be considered for routine testing and reporting on anaerobic organisms

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TABLE 13

CLSI -suggested grouping of antimicrobial agents to be considered for routine testing and reporting on anaerobic organisms

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T14
TABLE 14

Population-based risk for anaerobic bacteremia associated with underlying conditions

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TABLE 14

Population-based risk for anaerobic bacteremia associated with underlying conditions

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015
/content/microbiolspec/10.1128/microbiolspec.DMIH2-0015-2015.T15
TABLE 15

Guidelines for the use of diagnostic tests for detection of infection

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TABLE 15

Guidelines for the use of diagnostic tests for detection of infection

Source: microbiolspec August 2016 vol. 4 no. 4 doi:10.1128/microbiolspec.DMIH2-0015-2015

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