Direct targeted next-generation sequencing for diagnosis of drug-resistant tuberculosis from clinical samples - An update.

Timely detection of drug resistance is a pre-requisite to tuberculosis management globally. While phenotypic drug susceptibility testing (pDST) by liquid or solid method takes time, current genotypic DST assays can be performed directly from clinical specimens but target only a limited number of resistance variants. Targeted Next Generation Sequencing (tNGS) is a rapid, cost-effective method using direct sample to perform the sequencing than compared to whole genome sequencing (WGS) which requires culture. tNGS provides comprehensive drug resistance profiling with turnaround time of 3-4 days when done directly from clinical samples. For respiratory samples with rifampicin resistance, tNGS could be used for the rapid detection of additional drug resistance including newer and repurposed drugs like Bedaquiline, Delamanid, Pretomanid, Linezolid and Clofazimine for which no rapid molecular tests are currently available. A variety of clinical samples can be used and there are wide choices available for DNA extraction. The targets for tNGS could be amplified using commercial kits or in house primers. tNGS could be performed using different platforms like Illumina, Oxford Nanopore Technology and/or Ion torrent and diverse bio-informatic pipeline options. Positioning of a tNGS with portability system in the current TB diagnostic algorithm and its use in the clinical management of patients' needs further evaluation and efforts.