Using genomics to explore the epidemiology of vancomycin resistance in a sewage system

VanHAX-mediated glycopeptide resistance has been high in Copenhagen’s Lynetten sewer system for over 20 years. A study mapped 505 shotgun metagenomic data sets to 831 different glycopeptide resistance genes, finding only vanHAX and vanHBX genes differentially abundant. The study also found that vanHAX could only be linked to the phylum level and plasmids found in enterococci species. The study suggests that Hi-C technology is valuable for linking antimicrobial resistance genes to bacterial taxa, but faces challenges in reliably mapping the linked read to a genomic region with sufficient taxonomic information.