Journal article
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance
NL Sherry, KA Horan, SA Ballard, A Gonҫalves da Silva, CL Gorrie, MB Schultz, K Stevens, M Valcanis, ML Sait, TP Stinear, BP Howden, T Seemann
Nature Communications | Published : 2023
Abstract
Realising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public health microbiology. Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI’s AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles. In these analyses, abritAMR displays 99.9% accuracy, 97...
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Awarded by Department of Health, State Government of Victoria
Funding Acknowledgements
MDU PHL is funded by the Victorian Government Department of Health. BPH receives an investigator grant from National Health and Medical Research Council Australia (GNT1196103). NLS received an Australian Government Research Training Program (RTP) scholarship. We sincerely thank the NCBI's AMRFinderPlus team for their dedication to producing and maintaining high-quality tools and database for detection of AMR mechanisms from WGS data. We also thank Cheryll Sia for sharing her insights on genotype-phenotype correlations for fluoroquinolone resistance in Salmonella.