Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance

PLoS Genet. 2021 Nov 30;17(11):e1009919. doi: 10.1371/journal.pgen.1009919. eCollection 2021 Nov.

Abstract

Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model (HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / genetics*
  • Bacteriocins / biosynthesis*
  • Drug Resistance, Bacterial / genetics*
  • Evolution, Molecular*
  • Gammaproteobacteria / drug effects
  • Gammaproteobacteria / genetics*
  • Genes, Bacterial*
  • Markov Chains
  • Phylogeny
  • Plasmids*

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Bacteriocins
  • ROM protein, Bacteria

Grants and funding

B.G.Z. was supported by grants from the European Joint Program One Health EJP, ARDIG Grant Agreement No 77380; from the European Union’s Horizon 2020 research and innovation program. M.A.A. was supported by the Universidad Complutense de Madrid (Grant ID CT27/16-CT28/16 and EB14/19). E.P.C.R. acknowledges the financial support of Equipe FRM (EQU201903007835) and the Laboratoire d’Excellence IBEID (ANR-10-LABX-62-IBEID). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.