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Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

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  • Santiago Redondo-Salvo

    (Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22)

  • Raúl Fernández-López

    (Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22)

  • Raúl Ruiz

    (Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22)

  • Luis Vielva

    (Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria)

  • María de Toro

    (CIBIR, Centro de Investigación Biomédica de La Rioja)

  • Eduardo P. C. Rocha

    (Microbial Evolutionary Genomics, Institut Pasteur, CNRS)

  • M. Pilar Garcillán-Barcia

    (Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22)

  • Fernando de la Cruz

    (Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22)

Abstract

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I–VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.

Suggested Citation

  • Santiago Redondo-Salvo & Raúl Fernández-López & Raúl Ruiz & Luis Vielva & María de Toro & Eduardo P. C. Rocha & M. Pilar Garcillán-Barcia & Fernando de la Cruz, 2020. "Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17278-2
    DOI: 10.1038/s41467-020-17278-2
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    Cited by:

    1. Hanpeng Liao & Chen Liu & Shungui Zhou & Chunqin Liu & David J. Eldridge & Chaofan Ai & Steven W. Wilhelm & Brajesh K. Singh & Xiaolong Liang & Mark Radosevich & Qiu-e Yang & Xiang Tang & Zhong Wei & , 2024. "Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. 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 , 2024. "The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Yiqing Wang & Tal Dagan, 2024. "The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Mislav Acman & Ruobing Wang & Lucy Dorp & Liam P. Shaw & Qi Wang & Nina Luhmann & Yuyao Yin & Shijun Sun & Hongbin Chen & Hui Wang & Francois Balloux, 2022. "Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Angelina Beavogui & Auriane Lacroix & Nicolas Wiart & Julie Poulain & Tom O. Delmont & Lucas Paoli & Patrick Wincker & Pedro H. Oliveira, 2024. "The defensome of complex bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Peter J. Diebold & Matthew W. Rhee & Qiaojuan Shi & Nguyen Vinh Trung & Fayaz Umrani & Sheraz Ahmed & Vandana Kulkarni & Prasad Deshpande & Mallika Alexander & Ngo Hoa & Nicholas A. Christakis & Najee, 2023. "Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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