Peker Nilay, Rossen John W A, Deurenberg Ruud H, Langereis Paula C, Raangs Erwin G C, Kluytmans Jan A, Friedrich Alexander W, Veenemans Jacobien, Sinha Bhanu
Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
Laboratory for Microbiology and Infection Control, Amphia Hospital, 4818 CK Breda, The Netherlands.
Microorganisms. 2018 Jan 11;6(1):6. doi: 10.3390/microorganisms6010006.
Outbreak management of extended spectrum -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 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.
产超广谱β-内酰胺酶（ESBL）病原体的暴发管理需要快速准确的诊断。然而，传统筛查方法速度慢且 labor-intensive。绝大多数被筛查的样本为阴性，且检测与暴发无关的耐药微生物常常使暴发管理复杂化。在一次由CTX-M-15引起的暴发中，通过横断面调查在一家荷兰养老院收集了149份粪便样本和直肠拭子。样本采用常规诊断方法进行处理。回顾性地，通过基于扩增子的新一代测序（NGS）方法和培养，在不进行预先富集培养的情况下，直接从拭子培养基中加速检测产ESBL细菌和耐药基因。两种检测方法中共有27份（18.1%）样本呈阳性。表型方法检测CTX-M的敏感性为96.3%，NGS方法为85.2%，两种方法的特异性均为100%，经微阵列确认。这使得两种方法的阳性预测值（PPV）均为100%，表型方法和NGS方法的阴性预测值（NPV）分别为99.2%和96.8%。表型方法和NGS方法的出结果时间分别为4天和14小时。总之，不进行富集的敏感性显示出基于扩增子的NGS在暴发期间进一步用于筛查有良好前景。
