Long reads produced by Single Molecule Real Time Sequencing allow rapid identification of Antimicrobial Resistance Genes (ARGs) and linkage of them to their taxonomic origin or genetic context. In this study, we co-explored environmental microbiomes and resistomes in a veterinary teaching hospital using the Oxford Nanopore technology to find ARG-associated infectious disease risks.
Swabs from various hospital surfaces were minimally enriched in broth before DNA purification and MinION sequencing. Taxa, ARGs and mobile genetic elements (MGEs) were assigned to reads by metagenomic classifiers (Kraken, Centrifuge) and searchable sequence databases (Resfinder, ISfinder); results were compared to OTU analysis by 16S rRNA Illumina sequencing and ARG detection by Wafergen qPCR.
The MinION results compared favourably with the Illumina and Wafergen approaches. Long reads were obtained that carried single or multiple ARGs associated with bacterial pathogens or MGEs, indicating the presence of high risk ARGs. Potentially acquired ARG products included aminoglycoside transferases, extended-spectrum beta-lactamases, sulphonamide resistance synthases, macrolide esterases and tetracycline efflux pumps. The Intensive Care Unit (ICU) shared 77% of these high risk ARGs with the trolleys used to collect dirty laundry from the unit and 41% of them with the mop buckets used to clean the floor of the unit. These two waste collection points had much higher relative abundances of MGE-associated high risk ARGs, suggesting significant amplification and selection of the ARG-carrying bacterial populations in these environments. In contrast, a control floor surface from an office corridor that had no animal contact did not have any of these ARGs.
MinION sequencing allowed the exploration of ARG transfers between related environmental sites in veterinary facilities and identified waste collection points as amplifying reservoirs of clinically important ARGs. These findings will improve routine environmental surveillance programmes and biosecurity practices in veterinary hospitals, ultimately helping to prevent overuse of antimicrobials in animals.