PT  - JOURNAL ARTICLE
AU  - Vincent Escuyer
TI  - Use of whole genome sequencing for detection of antimicrobial resistance: Mycobacterium tuberculosis, a model organism
AID  - 10.29074/ascls.119.001784
DP  - 2019 Jan 01
TA  - American Society for Clinical Laboratory Science
PG  - ascls.119.001784
4099  - http://hwmaint.clsjournal.ascls.org/content/early/2019/10/08/ascls.119.001784.short
4100  - http://hwmaint.clsjournal.ascls.org/content/early/2019/10/08/ascls.119.001784.full
AB  - 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.