Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Shaw, Liam P.; Chau, Kevin K.; Kavanagh, James; AbuOun, Manal; Stubberfield, Emma; Gweon, H. Soon; Barker, Leanne; Rodger, Gillian; Bowes, Mike J. ORCID:; Hubbard, Alasdair T.M.; Pickford, Hayleah; Swann, Jeremy; Gilson, Daniel; Smith, Richard P.; Hoosdally, Sarah J.; Sebra, Robert; Brett, Howard; Peto, Tim E.A.; Bailey, Mark J.; Crook, Derrick W.; Read, Daniel S. ORCID:; Anjum, Muna F.; Walker, A. Sarah; Stoesser, Nicole. 2021 Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Science Advances, 7 (15), eabe3868. 11, pp.

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Escherichia coli and other Enterobacteriaceae are diverse species with “open” pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.

Item Type: Publication - Article
Digital Object Identifier (DOI):
UKCEH and CEH Sections/Science Areas: Soils and Land Use (Science Area 2017-)
Directors, SCs
UKCEH Fellows
Water Resources (Science Area 2017-)
ISSN: 2375-2548
Additional Information. Not used in RCUK Gateway to Research.: Open Access paper - full text available via Official URL link.
NORA Subject Terms: Biology and Microbiology
Date made live: 10 May 2021 13:58 +0 (UTC)

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