Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

Ea Zankari, Henrik Hasman, Rolf Sommer Kaas, Anne Mette Seyfarth, Yvonne Agersø, Ole Lund, Mette Voldby Larsen, Frank Møller Aarestrup

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Objectives: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.
Methods: Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to
identify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.
Results: A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.
Conclusions: High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.
Original languageEnglish
JournalJournal of Antimicrobial Chemotherapy
Volume68
Issue number4
Pages (from-to)771-777
ISSN0305-7453
DOIs
Publication statusPublished - 2013

Keywords

  • Resistance genes
  • MLST
  • Genomic
  • Salmonella
  • Escherichia coli
  • Enterococcus

Cite this

@article{15613af0dc8b403c8be4796f688a36eb,
title = "Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing",
abstract = "Objectives: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.Methods: Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used toidentify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.Results: A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.Conclusions: High concordance (99.74{\%}) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.",
keywords = "Resistance genes, MLST, Genomic, Salmonella, Escherichia coli, Enterococcus",
author = "Ea Zankari and Henrik Hasman and Kaas, {Rolf Sommer} and Seyfarth, {Anne Mette} and Yvonne Agers{\o} and Ole Lund and Larsen, {Mette Voldby} and Aarestrup, {Frank M{\o}ller}",
year = "2013",
doi = "10.1093/jac/dks496",
language = "English",
volume = "68",
pages = "771--777",
journal = "Journal of Antimicrobial Chemotherapy",
issn = "0305-7453",
publisher = "Oxford University Press",
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}

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. / Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller.

In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 4, 2013, p. 771-777.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

AU - Zankari, Ea

AU - Hasman, Henrik

AU - Kaas, Rolf Sommer

AU - Seyfarth, Anne Mette

AU - Agersø, Yvonne

AU - Lund, Ole

AU - Larsen, Mette Voldby

AU - Aarestrup, Frank Møller

PY - 2013

Y1 - 2013

N2 - Objectives: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.Methods: Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used toidentify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.Results: A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.Conclusions: High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.

AB - Objectives: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures.Methods: Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used toidentify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types.Results: A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates.Conclusions: High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.

KW - Resistance genes

KW - MLST

KW - Genomic

KW - Salmonella

KW - Escherichia coli

KW - Enterococcus

U2 - 10.1093/jac/dks496

DO - 10.1093/jac/dks496

M3 - Journal article

C2 - 23233485

VL - 68

SP - 771

EP - 777

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

IS - 4

ER -