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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
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 suggest...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Association for the Advancement of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034854/ https://www.ncbi.nlm.nih.gov/pubmed/33837077 http://dx.doi.org/10.1126/sciadv.abe3868 |
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author | Shaw, Liam P. Chau, Kevin K. Kavanagh, James AbuOun, Manal Stubberfield, Emma Gweon, H. Soon Barker, Leanne Rodger, Gillian Bowes, Mike J. 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. Anjum, Muna F. Walker, A. Sarah Stoesser, Nicole |
author_facet | Shaw, Liam P. Chau, Kevin K. Kavanagh, James AbuOun, Manal Stubberfield, Emma Gweon, H. Soon Barker, Leanne Rodger, Gillian Bowes, Mike J. 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. Anjum, Muna F. Walker, A. Sarah Stoesser, Nicole |
author_sort | Shaw, Liam P. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8034854 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80348542021-04-21 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 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. Anjum, Muna F. Walker, A. Sarah Stoesser, Nicole Sci Adv Research Articles 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. American Association for the Advancement of Science 2021-04-09 /pmc/articles/PMC8034854/ /pubmed/33837077 http://dx.doi.org/10.1126/sciadv.abe3868 Text en Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Shaw, Liam P. Chau, Kevin K. Kavanagh, James AbuOun, Manal Stubberfield, Emma Gweon, H. Soon Barker, Leanne Rodger, Gillian Bowes, Mike J. 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. Anjum, Muna F. Walker, A. Sarah Stoesser, Nicole Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title | Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title_full | Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title_fullStr | Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title_full_unstemmed | Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title_short | Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae |
title_sort | niche and local geography shape the pangenome of wastewater- and livestock-associated enterobacteriaceae |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8034854/ https://www.ncbi.nlm.nih.gov/pubmed/33837077 http://dx.doi.org/10.1126/sciadv.abe3868 |
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