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.

中文翻译：

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大肠杆菌和克雷伯菌属的基因组监测。在医院的水槽排水口和患者中。

大肠杆菌 和克雷伯菌属。是导致多种临床疾病的重要人类病原体。在医疗机构中，水槽和其他废水场所已被证明是具有抗药性的大肠杆菌和克雷伯菌的储水池，尤其是在患者中爆发抗药性菌株的情况下。无需专门关注耐药标记或临床暴发，我们证明了许多医院的水槽排水道被大量且持久地定居于大肠杆菌，肺炎克雷伯菌和产氧克雷伯菌的不同种群中 ，包括抗微生物菌株和易感菌株。使用439个分离株的全基因组测序，我们显示环境细菌种群主要由病房和水槽组成，只有少数谱系（例如E. coli ST635）广泛分布，这表明不同的流行生态可能会有所不同。输入和选择压力不同的结果。对46个同期患者分离株进行全基因组测序，鉴定出一株（2％； 95％CI 0.05–11％）大肠杆菌 与尿液感染相关的分离株与先前的水槽分离株具有高度相似性，表明在同一时间范围内，水槽可能占病房患者中由这些微生物引起的感染的多达10％。使用来自20个汇点时间的宏基因组学，我们显示汇也包含许多临床相关的抗菌素耐药基因，包括bla CTX-M，bla SHV和mcr，并且可能充当这些基因的交换和扩增的利基。我们的研究加强了水槽在医院患者肠杆菌感染和抗菌素耐药性中的潜在作用，这可能需要进行干预。本文包含Microreact托管的数据。