Bridging the gap between bioinformatics and the clinical and public health microbiology
laboratory: An ISO-accredited genomics workflow for antimicrobial resistance

Realising the promise of genomics to revolutionise routine AMR diagnosis and surveillance has
been a long-standing challenge in clinical and public health microbiology. We have directly
addressed this issue by creating and validating abritAMR, an ISO-accredited bioinformatics
platform for genomics-based bacterial AMR gene detection. abritAMR utilises the NCBI
AMRFinderPlus for detection of AMR genes and mutations, with additional features to classify
AMR determinants into an antibiotic class. We validated abritAMR by comparing with multiplex
PCR or gold-standard reference genomes, together representing 1500 different bacteria across
29 genera and covering 415 antibiotic resistance alleles.