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, AlexanderW. Friedrich, Jacobien Veenemans, Bhanu Sinha

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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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.

Original languageEnglish
Article number6
Number of pages8
Issue number1
Publication statusPublished - 11-Jan-2018


  • amplicon-based next-generation sequencing
  • E. coli
  • beta-lactamases
  • ESBL
  • CTX-M
  • outbreak surveillance
  • molecular diagnostics

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