Comparative Genomic investigation of Enterococcus faecium and Enterococcus faecalis across One-Health Sectors

Enterococci are Gram-positive bacteria often isolated from a variety of environments including soil, water, plant ecosystems and the intestinal tract of humans and animals. Although considered commensals in humans, Enterococcus spp. are important opportunistic pathogens. The ubiquitous presence of enterococci across One Health sectors makes these bacteria ideal candidates to study antimicrobial resistance (AMR) in this continuum. In this study, 246 Enterococcus faecium and 376 Enterococcus faecalis genomes recovered from human clinical samples, livestock (bovine, poultry and swine), municipal wastewater and environmental sources were investigated using comparative genomic approaches to determine their phylogenomic relatedness across sectors, carriage of antimicrobial resistance genes (ARGs) and their dissemination potential. The ARG profiling of E. faecium and E. faecalis genomes identified 31 and 34 different ARGs respectively, with 62% and 68% of isolates having plasmid-associated ARGs. Among these, tetracycline resistance genes [tet(L) and tet(M)] were commonly identified in E. faecium and E. faecalis across genomes from different sources followed by macrolide [erm(B)] and aminoglycoside [(aph(3’)-IIIa and ant(6)-Ia)] resistance genes. The bi-functional aac(6')-Ie/aph(2'')-Ia gene associated with IS256 elements was identified in E. faecium genomes from clinical and municipal isolates on five different plasmids. Vancomycin resistance gene vanA was found on pV24-3 and pF856 in clinical genomes. One E. faecium isolate from bovine feces carrying plasmid pFSIS1608820 harboring ant(9)-Ia, cfr, ermA, ermB, fexA and optrA was identified. The core E. faecium genome tree formed two main clades; clade ‘A’ and ‘B’ where genomes in clade A carried more virulence genes and ARGs as compared to clade B genomes. The majority of clinical samples were clustered in clade A, while no segregation across clades of isolates from other sources was identified. In conclusion, ARGs associated with clinically important antibiotics were exclusive to human and municipal wastewater isolates reflecting the natural-selection of resistance under selective pressure of antimicrobials. In addition, similar AMR profiles of livestock-associated isolates showed that along with ARGs conferring resistance against antimicrobials used in those sectors, co-localized AGRs belonging to other drug classes not being used in those sectors were being co-selected. Moreover, strong association of identified ARGs with mobile genetic elements showed their significant role in dissemination of antimicrobial resistance.