Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

Abstract

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. DATA SummARyRaw sequencing data are available under NCBI SRA accessions PRJNA604910 and PRJNA604975 (cultured isolates), and ENA project PRJEB36775 (metagenomes). A supporting data repository containing metadata, phylogenies, Jupyter notebooks and Pavian reports is archived at Figshare (doi:10.6084/m9.figshare.12337283). Microreact projects are available for E. coli, K. oxytoca and K. pneumoniae cultures. The authors confirm all supporting data, code and protocols have been provided within the article or the supporting data repository.

Limited Phylogenetic Overlap Between Fluoroquinolone-Resistant Escherichia coli Isolated on Dairy Farms and those Causing Bacteriuria in Humans Living in the Same Geographical Region

“…A core genome SNP distance of 30 or fewer is commonly seen in phylogenetic analyses of Enterobacteriales isolates that are confirmed to be part of an acute outbreak of foodborne illness 37 and hospital studies frequently set a cut-off of <100 SNPs to define an outbreak. 38 Finding FQ-R human/cattle isolates pairs differing by 71 (ST744) or 63 (ST162) SNPs is therefore suggestive of a situation where human and cattle isolates in this region do intermingle. However, this observation should be considered in the context of our finding that the closest isolates from two different farms were only three and seven SNPs apart for ST162 and ST744, respectively ( Figure 3 ).…”

Migration of <em>Escherichia coli</em> and <em>Klebsiella pneumoniae</em> Carbapenemase (KPC)-Producing <em>Enterobacter cloacae</em> through Wastewater Pipework and Establishment in Hospital Sink Waste Traps in a Laboratory Model System

“…Recent work looking into the ecology of E. coli and Klebsiella spp. populations in hospital waste traps has shown that different wards and even different sinks harbour distinct ecosystems, with few shared lineages [10]. It seems therefore unlikely that identical strains were found in different waste traps by chance.…”

Migration of Escherichia coli and Klebsiella pneumoniae Carbapenemase (KPC)-Producing Enterobacter cloacae through Wastewater Pipework and Establishment in Hospital Sink Waste Traps in a Laboratory Model System

“…Hospital reservoirs for Carbapenemase-producing Enterobacterales (CPE) include colonized patients and wastewater, with contaminated sinks being the most commonly re-Microorganisms 2021, 9, 1868 2 of 7 ported environmental reservoir [6]. In fact, shower and sink drains can harbour identical or highly similar strains to patients and are considered a potential source of transmission [7][8][9]. Although bacteria resistant to antibiotics are most often investigated, many sensitive Enterobacterales, including E. coli, can also be recovered from sink waste traps [8].…”