Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

Thomas Vognbjerg Sydenham, József Sóki, Henrik Hasman, Mikala Wang, Ulrik Stenz Justesen, ESGAI (ESCMID Study Group on Anaerobic Infections)

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http://cge.cbs.dtu.dk/services/ResFinder/) and a custom BLAST database. Combinations of cfxA, cepA, cfiA, nimA, nimD, nimE, nimJ, tetQ, ermB, ermF, bexB, linAn2 and mefEn2 genes were identified in the six isolates. blaOXA-347, an open reading frame predicted to be a β-lactamase (Cheng et al., 2012), was identified in one strain. Full length IS elements were identified directly upstream of four genes, but in most cases contigs terminated 100-150 bases upstream of the gene in question. Even though partial IS elements were identified in these short sequences, certain identification could not be ascertained. Full antiobiograms for B. fragilis from genetic data will most likely require complete or nearly complete genomes. Current approaches to this are laborious and/or costly. Emerging technologies such as nanopore based single DNA strand sensing could perhaps provide a solution in the future.

OriginalsprogEngelsk
TidsskriftAnaerobe
Vol/bind31
Sider (fra-til)59-64
ISSN1075-9964
DOI
StatusUdgivet - 2015

Fingeraftryk

MDR Genes
Firearms
Insertional Mutagenesis
Open Reading Frames
Databases
DNA

Citer dette

Sydenham, Thomas Vognbjerg ; Sóki, József ; Hasman, Henrik ; Wang, Mikala ; Justesen, Ulrik Stenz ; ESGAI (ESCMID Study Group on Anaerobic Infections). / Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing. I: Anaerobe. 2015 ; Bind 31. s. 59-64.
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title = "Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing",
abstract = "Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http://cge.cbs.dtu.dk/services/ResFinder/) and a custom BLAST database. Combinations of cfxA, cepA, cfiA, nimA, nimD, nimE, nimJ, tetQ, ermB, ermF, bexB, linAn2 and mefEn2 genes were identified in the six isolates. blaOXA-347, an open reading frame predicted to be a β-lactamase (Cheng et al., 2012), was identified in one strain. Full length IS elements were identified directly upstream of four genes, but in most cases contigs terminated 100-150 bases upstream of the gene in question. Even though partial IS elements were identified in these short sequences, certain identification could not be ascertained. Full antiobiograms for B. fragilis from genetic data will most likely require complete or nearly complete genomes. Current approaches to this are laborious and/or costly. Emerging technologies such as nanopore based single DNA strand sensing could perhaps provide a solution in the future.",
keywords = "Bacteroides Infections, Bacteroides fragilis, DNA Transposable Elements, DNA, Bacterial, Drug Resistance, Bacterial, Genes, Bacterial, Genome, Bacterial, Humans, Molecular Sequence Data, Sequence Analysis, DNA",
author = "Sydenham, {Thomas Vognbjerg} and J{\'o}zsef S{\'o}ki and Henrik Hasman and Mikala Wang and Justesen, {Ulrik Stenz} and {ESGAI (ESCMID Study Group on Anaerobic Infections)}",
note = "Copyright {\circledC} 2014 Elsevier Ltd. All rights reserved.",
year = "2015",
doi = "10.1016/j.anaerobe.2014.10.009",
language = "English",
volume = "31",
pages = "59--64",
journal = "Anaerobe",
issn = "1075-9964",
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Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing. / Sydenham, Thomas Vognbjerg; Sóki, József; Hasman, Henrik; Wang, Mikala; Justesen, Ulrik Stenz; ESGAI (ESCMID Study Group on Anaerobic Infections).

I: Anaerobe, Bind 31, 2015, s. 59-64.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

AU - Sydenham, Thomas Vognbjerg

AU - Sóki, József

AU - Hasman, Henrik

AU - Wang, Mikala

AU - Justesen, Ulrik Stenz

AU - ESGAI (ESCMID Study Group on Anaerobic Infections)

N1 - Copyright © 2014 Elsevier Ltd. All rights reserved.

PY - 2015

Y1 - 2015

N2 - Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http://cge.cbs.dtu.dk/services/ResFinder/) and a custom BLAST database. Combinations of cfxA, cepA, cfiA, nimA, nimD, nimE, nimJ, tetQ, ermB, ermF, bexB, linAn2 and mefEn2 genes were identified in the six isolates. blaOXA-347, an open reading frame predicted to be a β-lactamase (Cheng et al., 2012), was identified in one strain. Full length IS elements were identified directly upstream of four genes, but in most cases contigs terminated 100-150 bases upstream of the gene in question. Even though partial IS elements were identified in these short sequences, certain identification could not be ascertained. Full antiobiograms for B. fragilis from genetic data will most likely require complete or nearly complete genomes. Current approaches to this are laborious and/or costly. Emerging technologies such as nanopore based single DNA strand sensing could perhaps provide a solution in the future.

AB - Bacteroides fragilis constitutes the most frequent anaerobic bacterium causing bacteremia in humans. The genetic background for antimicrobial resistance in B. fragilis is diverse with some genes requiring insertion sequence (IS) elements inserted upstream for increased expression. To evaluate whole genome shotgun sequencing as a method for predicting antimicrobial resistance properties, one meropenem resistant and five multidrug-resistant blood culture isolates were sequenced and antimicrobial resistance genes and IS elements identified using ResFinder 2.1 (http://cge.cbs.dtu.dk/services/ResFinder/) and a custom BLAST database. Combinations of cfxA, cepA, cfiA, nimA, nimD, nimE, nimJ, tetQ, ermB, ermF, bexB, linAn2 and mefEn2 genes were identified in the six isolates. blaOXA-347, an open reading frame predicted to be a β-lactamase (Cheng et al., 2012), was identified in one strain. Full length IS elements were identified directly upstream of four genes, but in most cases contigs terminated 100-150 bases upstream of the gene in question. Even though partial IS elements were identified in these short sequences, certain identification could not be ascertained. Full antiobiograms for B. fragilis from genetic data will most likely require complete or nearly complete genomes. Current approaches to this are laborious and/or costly. Emerging technologies such as nanopore based single DNA strand sensing could perhaps provide a solution in the future.

KW - Bacteroides Infections

KW - Bacteroides fragilis

KW - DNA Transposable Elements

KW - DNA, Bacterial

KW - Drug Resistance, Bacterial

KW - Genes, Bacterial

KW - Genome, Bacterial

KW - Humans

KW - Molecular Sequence Data

KW - Sequence Analysis, DNA

U2 - 10.1016/j.anaerobe.2014.10.009

DO - 10.1016/j.anaerobe.2014.10.009

M3 - Journal article

VL - 31

SP - 59

EP - 64

JO - Anaerobe

JF - Anaerobe

SN - 1075-9964

ER -