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

Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause ofnosocomial infection and is categorized as high priority by the World Health Organizationglobal priority list of antibiotic-resistant bacteria. In the past, livestock havebeen proposed as a putative reservoir for drug-resistant E. faecium strains that infecthumans, and isolates of the same lineage have been found in both reservoirs. Weundertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestockfarms, retail meat, and wastewater treatment plants in the United Kingdom.More than 600 isolates from these sources were sequenced, and their relatednessand antibiotic resistance genes were compared with genomes of almost 800 E. faeciumisolates from patients with bloodstream infection in the United Kingdom andIreland. E. faecium was isolated from 28/29 farms; none of these isolates wereVREfm, suggesting a decrease in VREfm prevalence since the last UK livestock surveyin 2003. However, VREfm was isolated from 1% to 2% of retail meat products andwas ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstratedthat the majority of human and livestock-related isolates were geneticallydistinct, although pig isolates from three farms were more genetically related to humanisolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms[SNPs]). Analysis of accessory (variable) genes added further evidence for distinctniche adaptation. An analysis of acquired antibiotic resistance genes and their variantsrevealed limited sharing between humans and livestock. Our findings indicatethat the majority of E. faecium strains infecting patients are largely distinct fromthose from livestock in this setting, with limited sharing of strains and resistancegenes.