Genomic network analysis of environmental and livestock F-type plasmid populations

Matlock, William; Chau, Kevin K.; AbuOun, Manal; Stubberfield, Emma; Barker, Leanne; Kavanagh, James; Pickford, Hayleah; Gilson, Daniel; Smith, Richard P.; Gweon, H. Soon ORCID: https://orcid.org/0000-0002-6218-6301; Hoosdally, Sarah J.; Swann, Jeremy; Sebra, Robert; Bailey, Mark J.; Peto, Timothy E.A.; Crook, Derrick W.; Anjum, Muna F.; Read, Daniel S. ORCID: https://orcid.org/0000-0001-8546-5154; Walker, A. Sarah; Stoesser, Nicole; Shaw, Liam P.; REHAB consortium. 2021 Genomic network analysis of environmental and livestock F-type plasmid populations. ISME Journal, 15. 2322-2335. 10.1038/s41396-021-00926-w

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Official URL: http://dx.doi.org/10.1038/s41396-021-00926-w

Abstract/Summary

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1038/s41396-021-00926-w
UKCEH and CEH Sections/Science Areas:	Soils and Land Use (Science Area 2017-) Water Resources (Science Area 2017-) Directors, SCs UKCEH Fellows
ISSN:	1751-7362
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link. REHAB consortium includes additional UKCEH author: Mike J. Bowes.
Additional Keywords:	environmental microbiology, genomics
NORA Subject Terms:	Biology and Microbiology
Date made live:	25 Mar 2021 12:36 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/529950

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1038/s41396-021-00926-w

UKCEH and CEH Sections/Science Areas:

Soils and Land Use (Science Area 2017-)
Water Resources (Science Area 2017-)
Directors, SCs
UKCEH Fellows

ISSN:

1751-7362

Additional Information. Not used in RCUK Gateway to Research.:

Open Access paper - full text available via Official URL link. REHAB consortium includes additional UKCEH author: Mike J. Bowes.

Additional Keywords:

environmental microbiology, genomics