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

Matlock, W. ORCID: https://orcid.org/0000-0001-5608-0423, Chau, K. K., AbuOun, M., Stubberfield, E., Barker, L., Kavanagh, J., Pickford, H., Gilson, D., Smith, R. P., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Hoosdally, S. J., Swann, J., Sebra, R., Bailey, M. J., Peto, T. E. A., Crook, D. W., Anjum, M. F., Read, D. S., Walker, A. S., Stoesser, N. and Shaw, L. P. (2021) Genomic network analysis of environmental and livestock F-type plasmid populations. The ISME Journal, 15. pp. 2322-2335. ISSN 1751-7370 doi: 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 likely reflects their suitability for rapid niche adaptation.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/96140
Identification Number/DOI	10.1038/s41396-021-00926-w
Refereed	Yes
Divisions	Life Sciences > School of Biological Sciences > Biomedical Sciences Life Sciences > School of Biological Sciences > Ecology and Evolutionary Biology
Publisher	Nature Publishing Group
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