Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant
Enterococcus(VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalisand Enterococcus faeciumare recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results
VRE isolates, including
E. faecalis( n= 24), E. faecium( n= 11), E. casseliflavus(n = 2) and E. gallinarum(n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faeciumand E. faecaliswere both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium( p< 0.001) and E. faecalis( p< 0.001) and with the number of AMR genes in E. faecium( p= 0.005). Genes conferring vancomycin resistance, including vanA and vanM ( E. faecium), vanG ( E. faecalis), and vanC ( E. casseliflavus/ E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavusand E. gallinarum,respectively. Virulence genes were more common in E. faecalisand E. faecium, than E. casseliflavusand E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalisgenomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions
There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs.
E. faecalisand E. faeciumhave smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.