Journal article
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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Publisher copy:
- 10.1099/mgen.0.000391
Authors
- Publisher:
- Microbiology Society
- Journal:
- Microbial Genomics More from this journal
- Volume:
- 6
- Issue:
- 7
- Article number:
- e000391
- Publication date:
- 2020-06-18
- Acceptance date:
- 2020-05-24
- DOI:
- EISSN:
-
2057-5858
- Language:
-
English
- Keywords:
- Pubs id:
-
1106849
- Local pid:
-
pubs:1106849
- Deposit date:
-
2020-05-26
Terms of use
- Copyright holder:
- Constantinides et al.
- Copyright date:
- 2020
- Rights statement:
- © 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
- Licence:
- CC Attribution (CC BY)
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