Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis
| Autor: | Paula C Langereis, Ruud H. Deurenberg, Jacobien Veenemans, Jan Kluytmans, Erwin C. Raangs, John W. A. Rossen, Nilay Peker, Bhanu Sinha, Alexander W. Friedrich |
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| Přispěvatelé: | Microbes in Health and Disease (MHD), Critical care, Anesthesiology, Peri-operative and Emergency medicine (CAPE) |
| Jazyk: | angličtina |
| Předmět: |
0301 basic medicine
Microbiology (medical) Diagnostic methods GENES Klebsiella pneumoniae 030106 microbiology Biology medicine.disease_cause Microbiology Article DNA sequencing beta-lactamases molecular diagnostics 03 medical and health sciences ENTEROBACTERIACEAE Virology amplicon-based next-generation sequencing E. coli ESBL CTX-M outbreak surveillance medicine EPIDEMIOLOGY lcsh:QH301-705.5 Escherichia coli Outbreak Amplicon Molecular diagnostics biology.organism_classification Predictive value 3. Good health PREVALENCE 030104 developmental biology lcsh:Biology (General) SPECTRUM BETA-LACTAMASES KLEBSIELLA-PNEUMONIAE RESISTANCE |
| Zdroj: | Microorganisms Microorganisms, Vol 6, Iss 1, p 6 (2018) Microorganisms; Volume 6; Issue 1; Pages: 6 Microorganisms, 6(1):6. MDPI AG |
| ISSN: | 2076-2607 |
| DOI: | 10.3390/microorganisms6010006 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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