Diagnostic technique

Efficacy in Rural/Urban




WHO/CDC recommendation

Light Microscopy of sputum smear


Low cost, easy accessible traditional method.

Low sensitivity. Not suitable for drug resistant strains

[3] [61] .

Discontinued by WHO.

Fluorescence microscopy


One of the traditional method.

High setting and cost. Not much difference in sensitivity from light microscopy

[62] [63] [64] [65] .

Discontinued by WHO.

LED fluorescence microscopy


Higher sensitivity compared to traditional microscopy. Useful in peripheral area for detection.

The low sensitivity HIV-positive individuals particularly those with low CD4 T cell counts. Not suitable for drug resistant test.

[66] [67] [68] .

WHO has recommended use of LED microscopy which can generate both light and fluorescence wavelength instead of conventional light or fluorescence microscopes [55] .

Culture and Drug susceptibility test

Urban lab settings with biosafety level 3 lab (BSL3) requirements

More sensitive than microscopy. Drug resistance can be confirmed.

Time taking, expensive, Lab setting and expertise needed. Risk of cross contamination and biohazard.

[3] [69] [70] .

Commercial liquid culture medium and rapid speciation strip recommended by WHO [23] [71] .

Immunological technique-(ELISA /RDTs)

Quick serodiagnostc tests in rural and urban settings

Quick commercial tests, ease to use.

Low sensitivity, False positive results

[5] [72] .

Recommended to discontinue commercial serodiagnostic tests by WHO [18] .

DNA based test-LPA

Commercial kits available for rural and urban setting with biosafety level 2 lab (BSL2) requirement

High sensitivity test. Less sample requirement. Drug resistance can be detected and correlated to gene mutation.

Mainly recommended for MDR-TB but not for XDR-TB.

[27] [28] [29] [73] .

The use of commercial line probe assays is recommended by WHO in MDR-TB endemic area as well as combination with cultivation for DST [71] .

DNA based test-RTPCR

Fast commercial Xpert method and GenXpert instruments for rural and urban area

rtPCR based technique Xpert MTB/RIF can detect and identify drug resistance directly from sputum. Highly sensitive, cost effective, less time taking, drug resistance detection, lower biosafety requirements.

Only detects Rifampicin resistance

[31] [74] [75] .

WHO has endorsed the Xpert technology in 2010 [19] [32] .

DNA based test-Microarray technique

Urban laboratory settings

Highly sensitive and advanced method for in depth genomic studies of positive samples. Simultaneously detect all gene mutations.

Requires advanced lab settings.

[33] [34] .

Not recommended for routine diagnostics.