Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients
Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients
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DOI：
10.1099/mgen.0.000391
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发表时间：
2020-07-01
影响因子：
3.9
通讯作者：
Stoesser, Nicole
中科院分区：
文献类型：
--
作者：
Constantinides, Bede;Chau, Kevin K.;Stoesser, Nicole
大肠埃希菌和克雷伯菌属。是引起广泛临床疾病的重要人类病原体。在医疗机构中，水槽和其他废水处理场所已被证明是耐抗生素E。大肠杆菌和克雷伯氏菌属，特别是在患者中爆发耐药菌株的情况下。我们没有专门关注耐药标志物或临床爆发，我们证明了许多医院的水槽排水沟中大量和持续地定植有不同的E。大肠杆菌、肺炎克雷伯氏菌和产酸克雷伯氏菌，包括抗微生物剂抗性和敏感菌株。通过对439个分离株的全基因组测序，我们发现环境细菌种群主要由病房和水槽组成，只有少数谱系，如E。coliST 635，广泛分布，表明不同的流行生态，这可能是不同的输入和选择压力的结果。对46个同期患者分离株的全基因组测序鉴定出一个（2%; 95%CI 0.05-11%）E.大肠杆菌尿液感染相关的分离株与先前的水槽分离株高度相似，表明水槽可能导致在同一时间段内病房患者中由这些生物体引起的高达10%的感染。使用来自20个汇时间点的宏基因组学，我们发现汇也含有许多临床相关的抗菌药物耐药基因，包括bla（CTX-M），bla（SHV）和mcr，并可能作为这些基因交换和扩增的小生境。我们的研究加强了水槽在医院患者中导致肠道菌感染和抗菌素耐药性的潜在作用，这可能是适合干预的。本文包含由Microreact托管的数据。
Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2%; 95 % CI 0.05-11%) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10% of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including bla(CTX-M), bla(SHV) and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.