Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom

Abstract

The rise in rates of human infection caused by vancomycin-resistant Enterococcus faecium (VREfm) strains between 1988 to the 2000s in Europe was suggested to be associated with acquisition from livestock. As a result, the European Union banned the use of the glycopeptide drug avoparcin as a growth promoter in livestock feed. While some studies reported a decrease in VREfm in livestock, others reported no reduction. Here, we report the first livestock VREfm prevalence survey in the UK since 2003 and the first large-scale study using whole-genome sequencing to investigate the relationship between E. faecium strains in livestock and humans. We found a low prevalence of VREfm in retail meat and limited evidence for recent sharing of strains between livestock and humans with bloodstream infection. There was evidence for limited sharing of genes encoding antibiotic resistance between these reservoirs, a finding which requires further research.

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

“…The acquisition of copper resistance genes may have contributed to the adaptation of E. faecium to environmental constraints imposed by pig farming. Recently, Gouliouris et al also described the same copper resistance operon as overrepresented in pig isolates, thus confirming that this set of plasmid-borne genes has played an important role in E. faecium survival in farms (35). Those plasmid genes were identified in our set of complete plasmid sequences and were present in a RepA_N conjugative plasmid (140 kbp) identified in pig and nonhospitalized isolates.…”

Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food-Producing Animals

“…The absence of IS1216V within the Tn1546 elements of the isolates from this study is characteristic for VREfm identified previously in strains in Europe in the late 1990s and 2000s, indicating that the vanA-type resistance mechanism may be very conserved among livestock enterococci in Switzerland. The lack of the diversity observed in Tn1546 structures, which is typical for human clinical isolates, suggests a limited sharing of resistance genes between livestock and human VRE, as observed previously for livestock and human enterococci isolates analysed in the United Kingdom [58].…”

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

“…Since copper was used as a growth-promoter agent in piglets and high 23 levels of copper are toxic for most bacterial species, the acquisition of copper resistance genes may have contributed to the adaptation of E. faecium to environmental constraints imposed by pig farming. Recently, Gouliouris et al 2018 also described the same copper-resistance operon to be overrepresented in pig isolates and thus confirming that this set of plasmid-encoding genes have played an important role in E. faecium survival in farms (Gouliouris et al 2018). We also identified a choloylglycine-hydrolase gene widely present in poultry isolates.…”

“…Pig and poultry isolates were grouped in a limited number of distinct SCs, with 88% of pig isolates grouping in SC 29 and 30 and 93% of poultry isolates grouping in SC24, 25 and 35 ( Supplemental Table S1). This clearly indicates host-specific evolution of E. faecium in distinct ecotypes, something that was suggested decades ago based on DNA fingerprint data (Willems et al 2000) and later confirmed using MLST ) and whole-genome sequencing (Gouliouris et al 2018) . If we consider SCs 29 and 30 as genuine pig-associated lineages then the isolates from patients (n=11) and non-hospitalized persons (n=33) in these SC groups may represent spillover events from these farm animals.…”

“…Human community isolates from non-hospitalized patients are widely dispersed over the phylogenetic tree outside clade A1. In previous reports, isolates from non-hospitalized persons dominated clade B (Lebreton et al 2013) and were supplemented by isolates from other sources Gouliouris et al 2018). In the current study, most isolates from non-hospitalized persons cluster outside clade B and cluster near isolates from a variety of different sources, which may indicate either frequent exchange or easy adaptation to different ecological niches.…”