Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK
- University of Oxford, United Kingdom
- Animal and Plant Health Agency, United Kingdom
- Oxford University Hospitals NHS Trust, United Kingdom
- Centre for Ecology and Hydrology, United Kingdom
Abstract
Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is highly relevant to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008-2020 from sites <60km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared 'backbones', with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid 'backbones' were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.
Data availability
Accessions for existing BSI and REHAB reads and assemblies can be found in Lipworth et al., 2021 (BioProject PRJNA604975) and Shaw et al., 2021 (BioProject PRJNA605147) respectively. Analysis scripts can be found in the GitHub repository https://github.com/wtmatlock/oxfordshire-overlap.
Article and author information
Author details
Funding
Medical Research Foundation (MRF-145-0004-TPG-AVISO)
- William Matlock
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Marc J Bonten, University Medical Center Utrecht, Netherlands
Version history
- Preprint posted: May 6, 2022 (view preprint)
- Received: December 1, 2022
- Accepted: March 22, 2023
- Accepted Manuscript published: March 24, 2023 (version 1)
- Version of Record published: December 7, 2023 (version 2)
Copyright
© 2023, Matlock et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK
eLife 12:e85302.
https://doi.org/10.7554/eLife.85302
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