PDF(Pubmed)
Abstract：
We identified 23 cases of Mycobacterium immunogenum respiratory acquisition linked to a colonized plumbing system at a new hospital addition. We conducted a genomic and epidemiologic investigation to assess for clonal acquisition of M. immunogenum from hospital water sources and improve understanding of genetic distances between M. immunogenum isolates. We performed whole-genome sequencing on 28 M. immunogenum isolates obtained from August 2013 to July 2021 from patients and water sources on four intensive care and intermediate units at an academic hospital. Study hospital isolates were recovered from 23 patients who experienced de novo respiratory isolation of M. immunogenum and from biofilms obtained from five tap water outlets. We also analyzed 10 M. immunogenum genomes from previously sequenced clinical (n = 7) and environmental (n = 3) external control isolates. The 38-isolate cohort clustered into three clades with pairwise single-nucleotide polymorphism (SNP) distances ranging from 0 to 106,697 SNPs. We identified two clusters of study hospital isolates in Clade 1 and one cluster in Clade 2 for which clinical and environmental isolates differed by fewer than 10 SNPs and had less than 0.5% accessory genome variation. A less restrictive combined threshold of 40 SNPs and 5% accessory genes reliably captured additional isolates that met clinical criteria for hospital acquisition, but 12 (4%) of 310 epidemiologically unrelated isolate pairs also met this threshold. Core and accessory genome analyses confirmed respiratory acquisition of multiple clones of M. immunogenum from hospital water sources to patients. When combined with epidemiologic investigation, genomic thresholds accurately distinguished hospital acquisition.
摘要：
我们在新的医院中发现了23例与定植的管道系统相关的免疫原性分枝杆菌呼吸道获取。我们进行了基因组和流行病学调查，以评估从医院水源中克隆获得的免疫原分枝杆菌，并增进对免疫原分枝杆菌分离株之间遗传距离的了解。我们对2013年8月至2021年7月在一家学术医院的4个重症监护病房和中间病房从患者和水源获得的28个免疫原分枝杆菌分离株进行了全基因组测序。研究医院分离株是从23例经历了免疫原分枝杆菌从头呼吸分离的患者和从五个自来水出口获得的生物膜中回收的。我们还分析了来自先前测序的临床(n=7)和环境(n=3)外部对照分离株的10μM免疫源基因组。38个分离的队列聚集成三个进化枝，成对的单核苷酸多态性（SNP）距离范围为0至106,697个SNP。我们确定了Clade1中的两个研究医院分离株集群和Clade2中的一个集群，其中临床和环境分离株的差异少于10个SNP，并且辅助基因组变异少于0.5％。40个SNP和5％辅助基因的限制性较低的组合阈值可靠地捕获了符合医院采集临床标准的其他分离株，但在310对流行病学无关的分离株中,有12对(4%)也达到了这一阈值.核心和辅助基因组分析证实了从医院水源到患者的多个免疫原分枝杆菌克隆的呼吸道获取。结合流行病学调查，基因组阈值准确区分医院采集。
