Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field

Abstract

The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.

The evolving biology of Mycobacterium tuberculosis drug resistance

“…The updated model has implications for how we track drug susceptibility and resistance. Increasingly around the world, slow and labor-intensive microbiological drug susceptibility testing is being replaced by faster DNA-based methods, either PCR or next-generation sequencing (NGS) ( Dookie et al., 2022 ; Rowlinson and Musser, 2022 ). For example, a recent study reported the whole genome sequences of more than 12,000 Mtb clinical isolates, along with sensitivity data for 13 different drugs ( The CRyPTIC Consortium, 2022 ).…”

“…NGS sequencing and analysis are not always straightforward ( Villellas et al., 2017 ; Kaniga et al., 2022 ), and global standards for the application of NGS data to drug susceptibility testing and data reporting are still emerging. Further, there are cases of discordance between whole genome sequencing and drug sensitivity data ( Dookie et al., 2022 ), though these are rare and the extent to which they are due to experimental errors is not yet clear. Finally, NGS generally provides only a snapshot of a bulk sample, without conveying the subtleties of the heterogeneous subpopulations described above.…”

Drug resistant tuberculosis: Implications for transmission, diagnosis, and disease management

“…Whole genome sequencing (WGS) has the capability to identify all genetic mutations in a sample (Katale et al, 2020), but the use of such technology needs to be refined before it can be implemented in a diagnostic setting. WGS testing would need to be performed directly on sputum in a form that is cheap, fast and accessible but thus far, no such technique that can be deployed at programmatic levels has been reported (Dookie et al, 2022). An additional consideration is that the use of WGS for clinical decision making requires accurate information about genotype to phenotype correlations (Faksri et al, 2019).…”

“…An additional consideration is that the use of WGS for clinical decision making requires accurate information about genotype to phenotype correlations (Faksri et al, 2019). In the absence of definitive information in this regard, a combination of genotypic and phenotypic approaches will most likely be needed (Dookie et al, 2022). An alternative to WGS is targeted sequencing, which also makes use of next-generation technology to provide information on drug resistance loci directly from clinical samples (MacLean et al, 2020;Dookie et al, 2022).…”

“…In the absence of definitive information in this regard, a combination of genotypic and phenotypic approaches will most likely be needed (Dookie et al, 2022). An alternative to WGS is targeted sequencing, which also makes use of next-generation technology to provide information on drug resistance loci directly from clinical samples (MacLean et al, 2020;Dookie et al, 2022). Despite the fact that this technique provides simpler data than WGS, it has the ability to detect low frequency variants (MacLean et al, 2020;Dookie et al, 2022).…”