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Nature communications
07 17, 2020;11 (1): 3602.

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

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
Author Information
  1. Santiago Redondo-Salvo: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain. ORCID
  2. Raúl Fernández-López: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain. ORCID
  3. Raúl Ruiz: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain. ORCID
  4. Luis Vielva: Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain. ORCID
  5. María de Toro: CIBIR, Centro de Investigación Biomédica de La Rioja, Logroño, Spain.
  6. Eduardo P C Rocha: Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France. ORCID
  7. M Pilar Garcillán-Barcia: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain. ORCID
  8. Fernando de la Cruz: Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, C/Albert Einstein 22, 39011, Santander, Spain. delacruz@unican.es.
PMID: 32681114 DOI: 10.1038/s41467-020-17278-2

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.

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MeSH Term

Algorithms
Gammaproteobacteria
Gene Transfer, Horizontal
Genomics
Phylogeny
Plasmids
Journal Article Research Support, Non-U.S. Gov't
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