Table 3 Comparison of popular methods for the detection of drug-resistant tuberculosis

Culture-based methods

Solid-based media

High sensitivity and specificity

Cumbersome, time-consuming, laborious, need to standardization, need to skilled laboratory technicians, need to high-biosafety laboratories

Unreliability of HIV-positive cases, low sensitivity for extrapulmonary TB, less sensitive and slower than liquid culture

Relatively-expensive

[52, 53]

Liquid-based media

Rapid automated, facilitate the processing of large numbers of specimens, high reproducibility, high sensitivity and specificity

Complexity, bio-safety concern, need for standardization, need for equipment

Inability to check the colony morphology of the growing bacteria, invisible contamination, overgrowth of NTM, need of expensive complex systems

High-cost

[54, 55]

Colorimetric- based method

Rapid, inexpensive

Low sensitivity and specificity

NTM can produce cord factor, applied for culture isolates, isoniazid can lead to false-positive, need to large inoculum size

Low-cost

[56, 57]

Molecular-based methods

GeneXpert

A rapid, high reproducibility, high sensitivity and specificity, reliability of results for HIV-infected individuals, and extrapulmonary TB

Complexity, need for specialized laboratories, operator dependency

inability to detect isoniazid mono-resistance, mutation out of the rpoB was not detected, shelf life of the cartridges is only 18 months, very stable electricity supply is required, the instrument needs to be recalibrated annually

High-cost

[58, 59]

Line probe assays

Detection of MTB complex, screening of resistance to isoniazid, rifampin, and MDR-TB, high sensitivity and specificity

Limited number of gene targets, high rate of uninterpretable results, risk of cross contamination due to its open-tube format

Applicable for smear-positive and culture isolates, time consuming due hybridization process, need to trained technicians

High-cost

[60, 61]

HRM

Rapid, simple, closed-tube, homogenous, affordable method, cost-efficient

Variability of sensitivity and specificity for individual clinical diagnostic setting, misdiagnosis of small insertions and deletions, lack of databases

Poor accuracy in genotyping, safe amplicon length (more than 400 bp) depends on good PCR, instruments, and dyes

Low-cost

[18, 62,63,64]