Table 3.

Current challenges to the design of molecular assays for resistance detection to new and repurposed anti-tuberculosis compounds and research priorities.

Drug	Gene targets (No.)	Challenges for molecular assay inclusion	Research priorities
Pyrazinamide	pncA (1)	• Length of gene• Not all mutations associated with resistance• Indels including whole-gene deletion	• WGS of resistant isolates and phenotypic testing and data synthesis to identify additional, high-confidence resistance mutations • Repository of resistant isolates with phenotypic and genotypic data • Lineage effects
Bedaquiline	pepQ, Rv0678, mmpL5, mmpS5, atpE (5)	• Number of genes • Length of genes • Mutations spread throughout genes • Additional, unknown resistance mechanisms • Not all mutations associated with resistance	• WGS of resistant isolates and phenotypic data synthesis to identify and characterize additional mutations associated with resistance • Determination how results for efflux pump mechanisms may differ before and following drug exposure • Repository of resistant isolates with phenotypic and genotypic data • Lineage effects
Linezolid	rplC, rrl (2)	• Additional, unknown resistance mechanisms	• WGS of resistant isolates and phenotypic data synthesis to identify and characterize additional mutations associated with resistance • Repository of resistant isolates with phenotypic and genotypic data
Pretomanid	fgd1, ddn, fbiA, fbiB, fbiC, Rv2983 (6)	• Number of genes • Length of genes • Mutations spread throughout genes	• WGS of resistant isolates and phenotypic data synthesis to identify and characterize additional mutations associated with resistance • Repository of resistant isolates with phenotypic and genotypic data • Lineage effects