Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

N. Stoesser; E. M. Batty; D. W. Eyre; M. Morgan; D. H. Wyllie; C. Del Ojo Elias; J. R. Johnson; A. S. Walker; T. E.A. Peto; D. W. Crook

doi:10.1093/jac/dkt180

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

N. Stoesser, E. M. Batty, D. W. Eyre, M. Morgan, D. H. Wyllie, C. Del Ojo Elias, J. R. Johnson, A. S. Walker, T. E.A. Peto, D. W. Crook

Medicine - Veteran's Administration Medical Center

Research output: Contribution to journal › Article › peer-review

232 Scopus citations

Abstract

Objectives:Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.Methods: Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted fromgenomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of>100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses. Results:A wide variety of antimicrobial resistance genes were identified, including bla_CTX-M, bla_LEN, bla_OKP, bla_OXA, bla_SHV, bla_TEM, aac(3′)-Ia, aac-(3′)-IId, aac-(3′)-IIe, aac(6′)-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6′)-Id, aph(3′)-Ia, qnrB and qnrS, aswell as resistance-associatedmutations in chromosomal gyrA and parCgenes. The sensitivityofgenome- basedresistancepredictionacrossallantibiotics forbothspecieswas0.96(95%CI: 0.94-0.98)and the specificity was 0.97 (95%CI: 0.95-0.98). Very major and major error rates were 1.2%and 2.1%, respectively.Conclusions: Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.

Original language	English (US)
Article number	dkt180
Pages (from-to)	2234-2244
Number of pages	11
Journal	Journal of Antimicrobial Chemotherapy
Volume	68
Issue number	10
DOIs	https://doi.org/10.1093/jac/dkt180
State	Published - Oct 2013

Bibliographical note

Funding Information:
This work was supported by the Wellcome Trust (doctoral fellowship award to N. S.). It was also supported by the National Institute for Health Research (NIHR) under its Oxford Biomedical Research Centre Infection Theme and the UKCRC Modernising Medical Microbiology Consortium, the latter funded under the UKCRC Translational Infection Research Initiative supported by the Medical Research Council, the Biotechnology and Biological Sciences Research Council and the National Institute for Health Research on behalf of the Department of Health [Grant G0800778] and the Wellcome Trust [Grant 087646/Z/08/Z]. D. W. C. and T. E. A. P. are NIHR Senior Investigators. D. W. E. is an NIHR Doctoral Research Fellow. This material is also based partly upon work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs, grant # 1 I01 CX000192 01 (J. R. J.).

Keywords

Antibiotic
Gram-negative
Phenotype

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/jac/dkt180

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Stoesser, N., Batty, E. M., Eyre, D. W., Morgan, M., Wyllie, D. H., Del Ojo Elias, C., Johnson, J. R., Walker, A. S., Peto, T. E. A., & Crook, D. W. (2013). Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. Journal of Antimicrobial Chemotherapy, 68(10), 2234-2244. Article dkt180. https://doi.org/10.1093/jac/dkt180

Stoesser, N, Batty, EM, Eyre, DW, Morgan, M, Wyllie, DH, Del Ojo Elias, C, Johnson, JR, Walker, AS, Peto, TEA & Crook, DW 2013, 'Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data', Journal of Antimicrobial Chemotherapy, vol. 68, no. 10, dkt180, pp. 2234-2244. https://doi.org/10.1093/jac/dkt180

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abstract = "Objectives:Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.Methods: Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted fromgenomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of>100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses. Results:A wide variety of antimicrobial resistance genes were identified, including blaCTX-M, blaLEN, blaOKP, blaOXA, blaSHV, blaTEM, aac(3′)-Ia, aac-(3′)-IId, aac-(3′)-IIe, aac(6′)-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6′)-Id, aph(3′)-Ia, qnrB and qnrS, aswell as resistance-associatedmutations in chromosomal gyrA and parCgenes. The sensitivityofgenome- basedresistancepredictionacrossallantibiotics forbothspecieswas0.96(95%CI: 0.94-0.98)and the specificity was 0.97 (95%CI: 0.95-0.98). Very major and major error rates were 1.2%and 2.1%, respectively.Conclusions: Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.",

keywords = "Antibiotic, Gram-negative, Phenotype",

author = "N. Stoesser and Batty, {E. M.} and Eyre, {D. W.} and M. Morgan and Wyllie, {D. H.} and {Del Ojo Elias}, C. and Johnson, {J. R.} and Walker, {A. S.} and Peto, {T. E.A.} and Crook, {D. W.}",

note = "Funding Information: This work was supported by the Wellcome Trust (doctoral fellowship award to N. S.). It was also supported by the National Institute for Health Research (NIHR) under its Oxford Biomedical Research Centre Infection Theme and the UKCRC Modernising Medical Microbiology Consortium, the latter funded under the UKCRC Translational Infection Research Initiative supported by the Medical Research Council, the Biotechnology and Biological Sciences Research Council and the National Institute for Health Research on behalf of the Department of Health [Grant G0800778] and the Wellcome Trust [Grant 087646/Z/08/Z]. D. W. C. and T. E. A. P. are NIHR Senior Investigators. D. W. E. is an NIHR Doctoral Research Fellow. This material is also based partly upon work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs, grant # 1 I01 CX000192 01 (J. R. J.).",

year = "2013",

month = oct,

doi = "10.1093/jac/dkt180",

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TY - JOUR

T1 - Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

AU - Stoesser, N.

AU - Batty, E. M.

AU - Eyre, D. W.

AU - Morgan, M.

AU - Wyllie, D. H.

AU - Del Ojo Elias, C.

AU - Johnson, J. R.

AU - Walker, A. S.

AU - Peto, T. E.A.

AU - Crook, D. W.

N1 - Funding Information: This work was supported by the Wellcome Trust (doctoral fellowship award to N. S.). It was also supported by the National Institute for Health Research (NIHR) under its Oxford Biomedical Research Centre Infection Theme and the UKCRC Modernising Medical Microbiology Consortium, the latter funded under the UKCRC Translational Infection Research Initiative supported by the Medical Research Council, the Biotechnology and Biological Sciences Research Council and the National Institute for Health Research on behalf of the Department of Health [Grant G0800778] and the Wellcome Trust [Grant 087646/Z/08/Z]. D. W. C. and T. E. A. P. are NIHR Senior Investigators. D. W. E. is an NIHR Doctoral Research Fellow. This material is also based partly upon work supported by the Office of Research and Development, Medical Research Service, Department of Veterans Affairs, grant # 1 I01 CX000192 01 (J. R. J.).

PY - 2013/10

Y1 - 2013/10

N2 - Objectives:Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.Methods: Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted fromgenomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of>100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses. Results:A wide variety of antimicrobial resistance genes were identified, including blaCTX-M, blaLEN, blaOKP, blaOXA, blaSHV, blaTEM, aac(3′)-Ia, aac-(3′)-IId, aac-(3′)-IIe, aac(6′)-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6′)-Id, aph(3′)-Ia, qnrB and qnrS, aswell as resistance-associatedmutations in chromosomal gyrA and parCgenes. The sensitivityofgenome- basedresistancepredictionacrossallantibiotics forbothspecieswas0.96(95%CI: 0.94-0.98)and the specificity was 0.97 (95%CI: 0.95-0.98). Very major and major error rates were 1.2%and 2.1%, respectively.Conclusions: Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.

AB - Objectives:Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms and predicting phenotype, and strain type, for both clinical and epidemiological purposes. This retrospective study aimed to determine the efficacy of whole genome-based antimicrobial resistance prediction in clinical isolates of Escherichia coli and Klebsiella pneumoniae.Methods: Seventy-four E. coli and 69 K. pneumoniae bacteraemia isolates from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes were predicted fromgenomic sequences using BLASTn-based comparisons of de novo-assembled contigs with a study database of>100 known resistance-associated loci, including plasmid-associated and chromosomal genes. Predictions were made for seven commonly used antimicrobials: amoxicillin, co-amoxiclav, ceftriaxone, ceftazidime, ciprofloxacin, gentamicin and meropenem. Comparisons were made with phenotypic results obtained in duplicate by broth dilution (BD Phoenix). Discrepancies, either between duplicate BD Phoenix results or between genotype and phenotype, were resolved with gradient diffusion analyses. Results:A wide variety of antimicrobial resistance genes were identified, including blaCTX-M, blaLEN, blaOKP, blaOXA, blaSHV, blaTEM, aac(3′)-Ia, aac-(3′)-IId, aac-(3′)-IIe, aac(6′)-Ib-cr, aadA1a, aadA4, aadA5, aadA16, aph(6′)-Id, aph(3′)-Ia, qnrB and qnrS, aswell as resistance-associatedmutations in chromosomal gyrA and parCgenes. The sensitivityofgenome- basedresistancepredictionacrossallantibiotics forbothspecieswas0.96(95%CI: 0.94-0.98)and the specificity was 0.97 (95%CI: 0.95-0.98). Very major and major error rates were 1.2%and 2.1%, respectively.Conclusions: Our method was as sensitive and specific as routinely deployed phenotypic methods. Validation against larger datasets and formal assessments of cost and turnaround time in a routine laboratory setting are warranted.

KW - Antibiotic

KW - Gram-negative

KW - Phenotype

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Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

Abstract

Bibliographical note

Keywords

UN SDGs

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