Genomic surveillance of Enterococcus faecium reveals limited sharing of strains and resistance genes between livestock and humans

Theodore Gouliouris, Kathy E. Raven, Catherine Ludden, Beth Blane, Jukka Corander, Carolyne Horner, Juan Hernandez-Garcia, Paul Wood, Nazreen Hadjirin, Milorad Radakovic, Mark A. Holmes, Marcus de Goffau, Nicholas M. Brown, Julian Parkhill, Sharon J Peacock

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of
nosocomial infection and is categorized as high priority by the World Health Organization
global priority list of antibiotic-resistant bacteria. In the past, livestock have
been proposed as a putative reservoir for drug-resistant E. faecium strains that infect
humans, and isolates of the same lineage have been found in both reservoirs. We
undertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestock
farms, retail meat, and wastewater treatment plants in the United Kingdom.
More than 600 isolates from these sources were sequenced, and their relatedness
and antibiotic resistance genes were compared with genomes of almost 800 E. faecium
isolates from patients with bloodstream infection in the United Kingdom and
Ireland. E. faecium was isolated from 28/29 farms; none of these isolates were
VREfm, suggesting a decrease in VREfm prevalence since the last UK livestock survey
in 2003. However, VREfm was isolated from 1% to 2% of retail meat products and
was ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstrated
that the majority of human and livestock-related isolates were genetically
distinct, although pig isolates from three farms were more genetically related to human
isolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms
[SNPs]). Analysis of accessory (variable) genes added further evidence for distinct
niche adaptation. An analysis of acquired antibiotic resistance genes and their variants
revealed limited sharing between humans and livestock. Our findings indicate
that the majority of E. faecium strains infecting patients are largely distinct from
those from livestock in this setting, with limited sharing of strains and resistance
Original languageEnglish
Publication statusPublished - 6 Nov 2018

Keywords / Materials (for Non-textual outputs)

  • vancomycin-resistant
  • Enterococcus faecium
  • One Health
  • livestock
  • genome sequencing
  • vancomycin resistant


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