Bringing tuberculosis genomics to the clinic: development and validation of a comprehensive pipeline to predict antimicrobial susceptibility from genomic data, accredited to ISO standards

Abstract

BackgroundWhole-genome sequencing is increasingly contributing to the clinical management of tuberculosis. 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 aimed to develop a robust software tool to identify M tuberculosis lineages and antimicrobial resistance from genomic data, tailored for clinical reporting and accessible to clinical microbiology laboratories.MethodsWe developed tbt..