Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak
Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak
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DOI：
10.1099/mgen.0.000236
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发表时间：
2019-01-01
影响因子：
3.9
通讯作者：
Hayashi, Tetsuya
中科院分区：
文献类型：
--
作者：
Gotoh, Yasuhiro;Taniguchi, Takako;Hayashi, Tetsuya
胃螺杆菌是一种新出现的病原体，可引起菌血症和蜂窝织炎。已经描述了这种微生物的医院传播，但尚未进行详细的分子流行病学分析。在这里，我们描述了对日本一家医院发生的疑似院内嗜血杆菌暴发的多步骤全基因组系统发育分析的结果。医院感染控制小组（ICT）将此次疫情确认为灰线虫菌血症突然增加。 ICT根据16S rRNA序列数据和流行病学信息对本次疫情进行了界定，但无法确定感染源和感染途径。因此，我们使用全基因组测序（WGS）重新研究了这个案例。我们首先使用公开的基因组序列进行了物种范围的分析，以了解这个待研究物种的基因组多样性水平。然后使用每个簇中代表性菌株的基因组序列作为参考，对所识别的簇进行单独分析。这些分析提供了每个簇的高水平系统发育分辨率，确定了一组可信的爆发分离株，并将它们与其他密切相关但不同的克隆区分开来，这些克隆在同一时期在当地传播并入侵医院。通过考虑流行病学数据，推断出可能的菌株传播链，这凸显了无症状携带者或环境污染的作用。还认识到在疫情中出现了对氟喹诺酮类药物耐药性增强的亚克隆。我们的结果证明了使用密切相关的基因组作为参考来最大限度地发挥 WGS 能力的影响。
Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia. ICT defined this outbreak case based on 16S rRNA sequence data and epidemiological information, but were unable to determine the source and route of the infections. We therefore re-investigated this case using whole-genome sequencing (WGS). We first performed a species-wide analysis using publicly available genome sequences to understand the level of genomic diversity of this under-studied species. The clusters identified were then separately analysed using the genome sequence of a representative strain in each cluster as a reference. These analyses provided a high-level phylogenetic resolution of each cluster, identified a confident set of outbreak isolates, and discriminated them from other closely related but distinct clones, which were locally circulating and invaded the hospital during the same period. By considering the epidemiological data, possible strain transmission chains were inferred, which highlighted the role of asymptomatic carriers or environmental contamination. The emergence of a subclone with increased resistance to fluoroquinolones in the outbreak was also recognized. Our results demonstrate the impact of the use of a closely related genome as a reference to maximize the power of WGS.