Table 2.

Summary of clinically available rapid molecular resistance testing assays for Mycobacterium tuberculosis

Molecular Testing Method	Turn-around time	Sensitivity	Specificity	Advantages	Limitations
Line probe assay ▪INNO-LipA® Rif.TB ▪Genotype®MTBDR ▪Genotype®MTBDR plus	6 – 48 hours	Rifampin resistance: -culture isolates:   95–100% - clinical specimens:   80–100% Isoniazid resistance:   72–92%	Rifampin resistance: - culture isolates:   92–100% - clinical specimens:   100% Isoniazid resistance:   95–100%	- rapid -sensitivity in detecting rifampin resistance mutations	- inability to differentiate silent mutations from those responsible for rifampin resistance - limited accuracy in detecting isoniazid resistance mutations
RT-PCR coupled with molecular beacons	2 hours	Rifampin resistance:   86–100% Isoniazid resistance:   76–94%	Rifampin resistance:   95–100% Isoniazid resistance:   100%	- rapid - accuracy in detecting rifampin resistance mutations within the target region - high throughput - elimination of cross- contamination - hands-free processing - capacity to detect novel mutations	- expensive - inability to detect mutations outside of pre-specified target region - limited accuracy in detecting isoniazid resistance mutations
Pyrosequencing	2 – 48 hours	Rifampin resistance: 92–100% Isoniazid resistance: 64–81%	Rifampin resistance: 92–100% Isoniazid resistance: 100%	- provides exact DNA sequences - high throughput	- accuracy limited in lengthy DNA sequences - limited accuracy in detecting isoniazid resistance mutations