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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., Hubbard, Alasdair ORCID: https://orcid.org/0000-0001-6668-9179, 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., Anjum, Muna F., Walker, A. Sarah and Stoesser, Nicole (2021) 'Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae'. Science Advances, Vol 7, Issue 15, eabe3868.

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Abstract

Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes1,2, where genes move intra- and inter-species via horizontal gene transfer3. These species can cause clinical infections4,5 as well as persist environmentally6,7. Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates8,9, the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828 Enterobacteriaceae, including 553 Escherichia spp. and 275 non-Escherichia species with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing on E. coli, we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.

Item Type: Article
Subjects: QW Microbiology and Immunology > Bacteria > QW 138 Enterobacteriaceae
WA Public Health > Sanitation. Environmental Control > General Sanitation and Environmental Control > WA 670 General works
WA Public Health > Water > WA 675 Water. Water supply. Sources
Faculty: Department: Biological Sciences > Department of Tropical Disease Biology
Digital Object Identifer (DOI): https://doi.org/10.1101/2020.07.23.215756
Depositing User: Cathy Waldron
Date Deposited: 10 May 2021 08:27
Last Modified: 10 May 2021 08:27
URI: https://archive.lstmed.ac.uk/id/eprint/17696

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