TY - JOUR T1 - Use of whole genome sequencing for detection of antimicrobial resistance: Mycobacterium tuberculosis, a model organism JF - American Society for Clinical Laboratory Science JO - Clin Lab Sci DO - 10.29074/ascls.119.001784 SP - ascls.119.001784 AU - Vincent Escuyer Y1 - 2019/01/01 UR - http://hwmaint.clsjournal.ascls.org/content/early/2019/10/08/ascls.119.001784.abstract N2 - Increasing rates of antimicrobial resistance is a public health crisis. The emergence of resistant pathogens is multi-factorial but is at least partially due to inappropriate antibiotic prescribing and lack of stewardship interventions. Effective stewardship programs require timely antimicrobial resistance testing. This can be challenging for pathogens that grow slowly or not at all in culture. Next generation sequencing approaches, such as isolate whole genome sequencing (WGS), offer a more rapid alternative for such pathogens. Mycobacterium tuberculosis (TB) is a model organism for WGS to predict susceptibility due to its highly conserved and stable genome, extremely slow growth in culture and increasing resistance rates to a limited armamentarium of anti-TB drugs. Studies have shown excellent concordance between conventional phenotypic susceptibility testing and use of WGS to predict susceptibility to at least 2 first-line anti-TB agents, rifampin and isoniazid. More data is needed for other agents, including a more comprehensive curated database of mutations paired with phenotypic data, before WGS can completely replace phenotypic testing. ER -