Next-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli
Next-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli
复制标题
DOI：
10.1128/jcm.00313-14
复制
发表时间：
2014-07-01
影响因子：
9.4
通讯作者：
Kluytmans, J. A. J. W.
中科院分区：
文献类型：
--
作者：
Veenemans, J.;Overdevest, I. T.;Kluytmans, J. A. J. W.
下一代测序（NGS）有可能在一次检测中提供分型结果并检测耐药基因，从而指导及时的治疗决策，并允许快速跟踪耐药克隆的传播。我们评估了一种新的NGS检测方法（医院获得性感染生物检测系统; Pathogenica）在荷兰一家疗养院爆发序列型131（ST 131）大肠杆菌感染期间的性能。对56株产超广谱β-内酰胺酶（ESBL）的大肠埃希菌进行检测。在2次流行率调查（2013年3月和5月）中收集的大肠杆菌分离株。分型结果进行了比较，扩增片段长度多态性（AFLP），从而我们直观地评估了协议的生物检测系统发育树与AFLP定义的集群。微阵列被认为是检测耐药基因的金标准。AFLP确定了一个大的集群31个难以区分的分离株相邻部门，表明克隆传播。BioDetection系统发育树显示，该暴发群的所有分离株都有很强的亲缘关系，而进一步的系统发育树排列也与AFLP所定义的其他群基本一致。BioDetection检测试剂在除1株分离株外的所有分离株中检出了ESBL基因（灵敏度为98%），但无法区分ESBL和非ESBL TEM和SHV β-内酰胺酶或按组指定CTX-M基因。医院获得性感染（HAI）生物检测系统对大肠杆菌分型的性能。coli分离株的扩增结果与AFLP结果吻合较好。它的性能与来自不同地点的较大的集合，并为其他物种的分型，没有评估，需要进一步研究。
Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.