Current Methods and Role of Next-Generation Sequencing in the Diagnosis of Antimicrobial Resistance in Tuberculosis

Rapid diagnosis of tuberculosis (TB) and identification of antimicrobial resistance (AR) are critical to improving patient outcomes, especially for multidrug- and extensively drug-resistant TB (DR-TB) infections. Diagnosis can take weeks with traditional culture and growth-based antimicrobial susceptibility testing, delaying appropriate treatment, impacting transmission of resistant strains, and leading to additional health care costs. Next-generation sequencing (NGS) techniques are revolutionizing the diagnostic laboratory and provide rapid, comprehensive, and accurate detection of AR in one test. With NGS, the whole genome can be sequenced in as little as 4 days from identification of TB in a positive culture. Subsequent bioinformatic analysis of sequence data assesses nucleotide changes compared to a wild-type reference genome and can identify mutations known to cause AR. Additionally, data can be analyzed to determine the species and provide a genotype. Targeted NGS methods designed to detect DR-TB directly from clinical specimens hold promise for the future.