Publication

Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis

Peker, N., Rossen, J. W. A., Deurenberg, R. H., Langereis, P. C., Raangs, E. G. C., Kluytmans, J. A., Friedrich, A., Veenemans, J. & Sinha, B., 11-Jan-2018, In : Microorganisms. 6, 1, 8 p., 6.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Peker, N., Rossen, J. W. A., Deurenberg, R. H., Langereis, P. C., Raangs, E. G. C., Kluytmans, J. A., ... Sinha, B. (2018). Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. Microorganisms, 6(1), [6]. https://doi.org/10.3390/microorganisms6010006

Author

Peker, Nilay ; Rossen, John W. A. ; Deurenberg, Ruud H. ; Langereis, Paula C. ; Raangs, Erwin G. C. ; Kluytmans, Jan A. ; Friedrich, AlexanderW. ; Veenemans, Jacobien ; Sinha, Bhanu. / Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. In: Microorganisms. 2018 ; Vol. 6, No. 1.

Harvard

Peker, N, Rossen, JWA, Deurenberg, RH, Langereis, PC, Raangs, EGC, Kluytmans, JA, Friedrich, A, Veenemans, J & Sinha, B 2018, 'Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis', Microorganisms, vol. 6, no. 1, 6. https://doi.org/10.3390/microorganisms6010006

Standard

Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. / Peker, Nilay; Rossen, John W. A.; Deurenberg, Ruud H.; Langereis, Paula C.; Raangs, Erwin G. C.; Kluytmans, Jan A.; Friedrich, AlexanderW.; Veenemans, Jacobien; Sinha, Bhanu.

In: Microorganisms, Vol. 6, No. 1, 6, 11.01.2018.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Peker N, Rossen JWA, Deurenberg RH, Langereis PC, Raangs EGC, Kluytmans JA et al. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis. Microorganisms. 2018 Jan 11;6(1). 6. https://doi.org/10.3390/microorganisms6010006


BibTeX

@article{e26815fe1d134e7189ca461d3a7ec40b,
title = "Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis",
abstract = "Outbreak management of extended spectrum beta-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1{\%}) samples were positive in either test. Sensitivity for CTX-M detection was 96.3{\%} for the phenotypic method and 85.2{\%} for the NGS method, and the specificity was 100{\%} for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100{\%} for both methods, and a negative predictive value (NPV) of 99.2{\%} and 96.8{\%} for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.",
keywords = "amplicon-based next-generation sequencing, E. coli, beta-lactamases, ESBL, CTX-M, outbreak surveillance, molecular diagnostics, SPECTRUM BETA-LACTAMASES, KLEBSIELLA-PNEUMONIAE, RESISTANCE, GENES, ENTEROBACTERIACEAE, EPIDEMIOLOGY, PREVALENCE",
author = "Nilay Peker and Rossen, {John W. A.} and Deurenberg, {Ruud H.} and Langereis, {Paula C.} and Raangs, {Erwin G. C.} and Kluytmans, {Jan A.} and AlexanderW. Friedrich and Jacobien Veenemans and Bhanu Sinha",
year = "2018",
month = "1",
day = "11",
doi = "10.3390/microorganisms6010006",
language = "English",
volume = "6",
journal = "Microorganisms",
issn = "2076-2607",
publisher = "MDPI AG",
number = "1",

}

RIS

TY - JOUR

T1 - Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis

AU - Peker, Nilay

AU - Rossen, John W. A.

AU - Deurenberg, Ruud H.

AU - Langereis, Paula C.

AU - Raangs, Erwin G. C.

AU - Kluytmans, Jan A.

AU - Friedrich, AlexanderW.

AU - Veenemans, Jacobien

AU - Sinha, Bhanu

PY - 2018/1/11

Y1 - 2018/1/11

N2 - Outbreak management of extended spectrum beta-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.

AB - Outbreak management of extended spectrum beta-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks.

KW - amplicon-based next-generation sequencing

KW - E. coli

KW - beta-lactamases

KW - ESBL

KW - CTX-M

KW - outbreak surveillance

KW - molecular diagnostics

KW - SPECTRUM BETA-LACTAMASES

KW - KLEBSIELLA-PNEUMONIAE

KW - RESISTANCE

KW - GENES

KW - ENTEROBACTERIACEAE

KW - EPIDEMIOLOGY

KW - PREVALENCE

UR - http://www.mdpi.com/2076-2607/6/1/6

U2 - 10.3390/microorganisms6010006

DO - 10.3390/microorganisms6010006

M3 - Article

VL - 6

JO - Microorganisms

JF - Microorganisms

SN - 2076-2607

IS - 1

M1 - 6

ER -

ID: 53102916