The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies
Abstract Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-45761-7 |
| _version_ | 1797209232710303744 |
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| author | Samuel Lipworth William Matlock Liam Shaw Karina-Doris Vihta Gillian Rodger Kevin Chau Leanne Barker Sophie George James Kavanagh Timothy Davies Alison Vaughan Monique Andersson Katie Jeffery Sarah Oakley Marcus Morgan Susan Hopkins Timothy Peto Derrick Crook A. Sarah Walker Nicole Stoesser |
| author_facet | Samuel Lipworth William Matlock Liam Shaw Karina-Doris Vihta Gillian Rodger Kevin Chau Leanne Barker Sophie George James Kavanagh Timothy Davies Alison Vaughan Monique Andersson Katie Jeffery Sarah Oakley Marcus Morgan Susan Hopkins Timothy Peto Derrick Crook A. Sarah Walker Nicole Stoesser |
| author_sort | Samuel Lipworth |
| collection | DOAJ |
| description | Abstract Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes. |
| first_indexed | 2024-03-07T14:51:56Z |
| format | Article |
| id | doaj.art-c56d4a213dff4d18a116a92ca0f30949 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T09:51:26Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-c56d4a213dff4d18a116a92ca0f309492024-04-14T11:22:07ZengNature PortfolioNature Communications2041-17232024-02-0115111110.1038/s41467-024-45761-7The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assembliesSamuel Lipworth0William Matlock1Liam Shaw2Karina-Doris Vihta3Gillian Rodger4Kevin Chau5Leanne Barker6Sophie George7James Kavanagh8Timothy Davies9Alison Vaughan10Monique Andersson11Katie Jeffery12Sarah Oakley13Marcus Morgan14Susan Hopkins15Timothy Peto16Derrick Crook17A. Sarah Walker18Nicole Stoesser19Nuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordDepartment of Zoology, University of OxfordDepartment of Engineering Science, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordOxford University Hospitals NHS Foundation TrustOxford University Hospitals NHS Foundation TrustOxford University Hospitals NHS Foundation TrustOxford University Hospitals NHS Foundation TrustNational Infection Service, United Kingdom Health Security AgencyNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordAbstract Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative ‘backbone’ of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.https://doi.org/10.1038/s41467-024-45761-7 |
| spellingShingle | Samuel Lipworth William Matlock Liam Shaw Karina-Doris Vihta Gillian Rodger Kevin Chau Leanne Barker Sophie George James Kavanagh Timothy Davies Alison Vaughan Monique Andersson Katie Jeffery Sarah Oakley Marcus Morgan Susan Hopkins Timothy Peto Derrick Crook A. Sarah Walker Nicole Stoesser The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies Nature Communications |
| title | The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies |
| title_full | The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies |
| title_fullStr | The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies |
| title_full_unstemmed | The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies |
| title_short | The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies |
| title_sort | plasmidome associated with gram negative bloodstream infections a large scale observational study using complete plasmid assemblies |
| url | https://doi.org/10.1038/s41467-024-45761-7 |
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