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

Nilay Peker; John W A Rossen; Ruud H Deurenberg; Paula C Langereis; Erwin G C Raangs; Jan A Kluytmans; Alexander W Friedrich; Jacobien Veenemans; Bhanu Sinha

doi:10.3390/microorganisms6010006

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. doi: 10.3390/microorganisms6010006.

Authors

Nilay Peker¹, John W A Rossen², Ruud H Deurenberg³, Paula C Langereis⁴, Erwin G C Raangs⁵, Jan A Kluytmans⁶, Alexander W Friedrich⁷, Jacobien Veenemans⁸, Bhanu Sinha⁹

Affiliations

¹ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. n.peker@umcg.nl.
² Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. j.w.a.rossen@rug.nl.
³ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. ruuddeurenberg@home.nl.
⁴ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. p.c.langereis@gmail.com.
⁵ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. g.c.raangs@umcg.nl.
⁶ Laboratory for Microbiology and Infection Control, Amphia Hospital, 4818 CK Breda, The Netherlands. jankluytmans@gmail.com.
⁷ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. alex.friedrich@umcg.nl.
⁸ Laboratory for Microbiology and Infection Control, Amphia Hospital, 4818 CK Breda, The Netherlands. jacobien.veenemans@gmail.com.
⁹ Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands. b.sinha@umcg.nl.

Abstract

Outbreak management of extended spectrum β-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: CTX-M; E. coli; ESBL; amplicon-based next-generation sequencing; beta-lactamases; molecular diagnostics; outbreak surveillance.