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

Manuel Ares-Arroyo,Eduardo P C Rocha,Bruno Gonzalez-Zorn,Josep Casadesús

doi:10.1371/journal.pgen.1009919

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.

Highlights

Plasmids are extrachromosomal self-replicating molecules of DNA able to transfer between bacteria mainly by conjugation [1]
Our analysis revealed that ColE1 replicons are associated with the emergence of antimicrobial resistant species categorized by the WHO as “high priority pathogens for the research and development of new antibiotics” [54]: ampicillin-resistant H. influenzae, fluoroquinolone-resistant Salmonella, and carbapenem-resistant and ESBL-producing Enterobacteriaceae (Fig 6B)
Our results reveal that the co-integration of ColE1 plasmids is a widespread phenomenon in Enterobacterales, in many cases mediated by ESBL/carbapenemase-encoding transposons (NDM-1, CTX-M-14, KPC-2, KPC-3) (S9 Fig and S3 Text)

Summary

Introduction

Plasmids are extrachromosomal self-replicating molecules of DNA able to transfer between bacteria mainly by conjugation [1]. Plasmids usually encode antimicrobial resistance determinants among their cargo genes and are considered to be the main spreaders of resistance in clinical environments [3] Among their extraordinary diversity, there is a family of plasmids that has become very popular due to its widespread use in biotechnology since the 1970s: the ColE1-like plasmids (ColE1 plasmids hereinafter) [4]. The ColE1-like group of replicons refers to every plasmid whose mechanism of replication resembles the original plasmid pColE1, most of which have been related to colicin production All these plasmids share the same characteristics, traditionally described as small, multicopy and mobilizable replicons [6], generally associated to the MOBP5/HEN family of relaxases [7]. We showed that these small multicopy plasmids are encapsidated in phages with up to 10,000 times more efficiency than large plasmids, suggesting that phages could be major vectors of antimicrobial resistance genes borne in ColE1 plasmids [8]

Methods

Results

Conclusion