Although the availability of bioinformatics tools for analysis and clinical reporting of Mycobacterium tuberculosis sequence data is improving, there remains a need for accessible, flexible bioinformatics tools that can be easily tailored for clinical reporting needs in different settings and that are suitable for accreditation to international standards.
We developed tbtAMR, a flexible yet comprehensive data-driven tool for analysis of M. tuberculosis genomic data.
tbtAMR takes short-read sequencing data (fastq files) or an annotated vcf file (from short-read or long-read sequencing), maps genomic variants (single nucleotide polymorphisms, insertions or deletions, large structural changes, and gene loss or loss of function), identifies resistance-associated mutations from the WHO catalogue (or user-defined database), and interprets and classifies drug resistance to produce an output file ready for clinical reporting.
tbtAMR accurately predicted lineages and phenotypic susceptibility for first-line (sensitivity 94.6% [95% CI 94.2-95.0], specificity 97.5% [97.3-97.7]) and second-line (sensitivity 83.7% [82.7-84.7], specificity 98.0% [97.9-98.1]) drugs.
We have accredited this tool to ISO standards in our laboratory, and it has been implemented for routine reporting of antimicrobial resistance from genomic sequence data in a clinically relevant timeframe.
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