Rapid Molecular Assays for the Diagnosis of Drug-Resistant Tuberculosis

Figures & data

Table 1 Minimum Characteristics of a Future Point of Care DR-TB Diagnostic Test

Test Specification	Requirement
Sensitivity and specificity (adults)	For pulmonary TB only, regardless of HIV status: Sensitivity: 95% for smear-positive and >60% for smear-negative, culture-positive samples Specificity: 95% compared to culture
Sensitivity and specificity (children)	For pulmonary TB only, regardless of HIV status: Sensitivity: 80% compared to culture of any sample type Specificity: 95% compared to culture
Drug resistance	Should be able to screen for resistance to currently available and new generation first- and second-line drugs First line: streptomycin, rifampicin, isoniazid, pyrazinamide and ethambutol Second line: levofloxacin, moxifloxacin, bedaquiline, linezolid, clofazimine, cycloserine, ethambutol, delamanid, pyrazinamide, amikacin, ethionamide, and p-aminosalicylic
Sample type	Adults: urine, saliva, exhaled breath, blood, or sputum Children: urine, saliva, blood Samples should not require refrigeration
Sample processing	Minimal protocol steps (maximum 3), ability to be performed at a bedside or in a BSL1 facility, processing that is not time-sensitive
Sample throughput	≥20 tests per day performed by one technical laboratory staff member
Robust	Shelf-life >24 months (including reagents), stable at high temperatures for shorter time periods, can be battery-powered, easy and environmentally friendly waste disposal, minimal maintenance requirement and utilised existing equipment (repurposed technology)
Cost	Affordable and easily accessible in high-burden countries, ideally <$10/test
Training	Used by health care workers with minimal training and minimum skill level
Time to results	3 hours maximum (patient must receive results the same day),
Result interpretation	Easy-to-read, unambiguous, simple “yes”, “no”, or “invalid” answer

Abbreviations: BSL1, biosafety level 1; HIV, human immunodeficiency virus; TB, tuberculosis.

Table 2 Performance of WHO-Endorsed Molecular Diagnostics for Drug-Resistant TB Diagnosis and Drug-Susceptibility Testing

Assay (Manufacturer) Year	Mtb and Drug Resistance (Sensitivity, Specificity) %	DR-TB Category	Cost Per Test	Time to Result	Specimen Types	Benefits	Limitations
GeneXpert assays
XPERT MTB/RIF (Cepheid) 2010	Mtb: (85, 98) Drug resistance: RIF (96, 98)	RR-TB	$10	2 hours	Raw sputum Concentrated sputum sediments	- One- step process- automated - Results available in <2 hours - Requires fewer biosafety measures than culture/LPA, so can be used in lower level - Laboratories - High sensitivity and specificity - Multi- platform: can be used for HIV, hepatitis C diagnosis and viral load monitoring - Can be used on extrapulmonary TB samples	- Reliant on electricity - Expensive - Cannot be used to track treatment progress - Requires annual calibration
XPERT MTB/RIF Ultra (Cepheid) 2017	Mtb (90, 96) Drug resistance: RIF (94, 98)	RR- TB	$10	2 hours	Raw sputum Concentrated sputum sediments
XPERT MTB/XDR (Cepheid) 2021	Mtb: none Drug resistance: INH (94.2, 98); FQ (93.1, 98.3); AMK (86.1, 98.9); ETH (98, 99.7); KAN (98.1, 97); CAP (70, 99.7)	RR- TB; MDR- TB; Pre- XDR- TB;	N/A	1.5 hours	Raw sputum Concentrated sputum sediments
Truenat assay
TRUENAT MTB- RIF Dx (Molbio) 2020	Mtb: none Drug resistance: RIF (84, 97)	RR- TB	$1240	1 hour	Sputum Extrapulmonary body fluids	- Results available in <1 hour - Multi- platform: can be used for hepatitis C, Human Papillomavirus, SARS- CoV2	- Several manual steps that need to be performed by skilled personnel
Moderate complexity automated NAATs
RealTime MTB RIF (Abbott) 2019	Mtb: none Drug resistance: RIF (94.8, 100); INH (88.3, 94.3)	RR-TB; MDR-TB	N/A	10.5hours	Raw sputum Bronchial alveolar lavage NALC sediment of sputum or bronchial alveolar lavage	-High sample throughput -Each assay has specific multi-platform benefits for HIV-1, HBV, HCV, HPV, SARS-CoV2	-Reliant on electricity -Expensive equipment and specialised training required
BD MAX MDR-TB (Becton Dickson) 2021	Mtb: none Drug resistance: RIF (90, 95); INH (82, 100)	RR-TB; MDR-TB	N/A	4 hours	Raw sputum Concentrated sputum sediments
Cobas MTB-RIF/INH (Roche) 2021	Mtb: none RIF (97.2, 98.6); INH (96.9, 99.4)	RR-TB; MDR-TB	N/A	4.5 hours	Raw sputum Sputum sediment Bronchoalveolar lavage
FluoroType MTBDR (Hain) 2021	Mtb: none Drug resistance: RIF (98.9, 100); INH (91.7, 100)	RR-TB; MDR-TB	N/A	3 hours	Decontaminated sputum
Line probe assays
GenoType MTBDRplus (Hain) 2008	Mtb: None Drug resistance: RIF (98.2, 97.8); INH (95.4, 98.8)	RR-TB; MDR-TB	$7,50	5 hours	Decontaminated sputum Cultured material (solid/liquid medium)	-Can be performed from pulmonary specimen and from culture material -Results are obtained in 5hrs -Fast detection of INH and RIF resistance, allows early, appropriate treatment, which reduces transmission and spread of MDR-TB.	-Cannot fully replace methods like conventional cultures -Not as fast as Xpert -Requires complex laboratory infrastructure and expensive equipment -Requires well-trained staff -Requires BSL3 -High number of uninterpretable results is high -Target coverage is limited to the main mutations
GenoType MTBDRsl (Hain) 2016	Mtb: none Drug resistance: FLQ (100, 98.9); AMK (93.8, 98.5); CAP (86.2, 95.9)	RR-TB; MDR-TB	$7,50	5 hours	Decontaminated sputum Cultured material (solid/liquid medium)

Abbreviations: HIV, human immunodeficiency virus; Mtb, Mycobacterium tuberculosis; TB, tuberculosis; RR-TB, rifampicin-resistant tuberculosis; MDR-TB, multidrug-resistant tuberculosis; N/A, not applicable; RIF, rifampicin; INH, isoniazid; FLQ, fluoroquinolone; AMK, amikacin; KAN, kanamycin; ETH, ethionamide; CAP, capreomycin.