Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Abstract

Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium , type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.

Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

“…Enterococcus faecium is a gram-positive, aerobic bacterium found in a variety of environments, such as soil, water, and the intestinal tract of humans and other animals 4 . These bacteria were considered safe without causing significant infections but, after the 1980s, they evolved as severe nosocomial pathogens 5 – 8 .…”

Comparative Genomic Analysis of Enterococci across Sectors of the One Health Continuum

“…Our core-genome tree topology partitioned into two clades. In contrast, in a recent study by Sanderson et al [ 36 ], clade B formed a paraphyletic clade rather than a monophyletic clade. Our findings also agree with previous studies [ 35 , 36 ], as more ARGs and virulence genes were associated with clade A than clade B isolates.…”

“…In contrast, in a recent study by Sanderson et al [ 36 ], clade B formed a paraphyletic clade rather than a monophyletic clade. Our findings also agree with previous studies [ 35 , 36 ], as more ARGs and virulence genes were associated with clade A than clade B isolates. Furthermore, most of the genomes associated with CL isolates clustered in clade A. Phylogenetically, E. faecalis genomes did not cleanly partition into clades by source and instead formed multiple clades that originated from multiple sources.…”

Dissemination of Enterococcal Genetic Lineages: A One Health Perspective

“…faecalis and E. faecium exhibit conserved genomes, although they possess a significant accessory genome (up to 38% in E. faecium), which contributes to remarkable genomic plasticity [16]. The evolution of enterococci was predominantly influenced by recombination and proficiency in acquiring novel genes through HGT facilitated by MGEs, such as plasmids, transposons [16,17], genomic islands (GI), and prophages [18]. The genome plasticity of clinical E. faecium can be explained by the lack of genome defense mechanisms limiting HGT, such as CRISPR-Cas and restriction-modification systems [16].…”