Accuracy and Effect of Rapid Line Probe Assay Testing for First- and Second-Line Tuberculosis in a High-Volume Programmatic Laboratory

Background: Rapid drug susceptibility testing (DST) is crucial to confirm eligibility for new tuberculosis (TB) regimens. Genotype MTBDRsl is a World Health Organization (WHO)-endorsed assay yet performance data on smear-negative sputum are scarce and programmatic adoption limited. Methods: Sputa from Xpert MTB/RIF-rifampicin resistant patients (n=951) were programmatically tested by Genotype MTBDRplus and Genotype MTBDRsl (both v2). Phenotypic DST was the reference standard for MTBDRsl. Discrepant results underwent Sanger sequencing. Findings: 89% (849/951) of sputa were culture-positive [56% (476/849) smear-negative]. MTBDRplus had non-actionable results (control and/or TB-detection bands absent or invalid; precluding resistance reporting) in 3% (11/373) and 19% (92/476; p=0.001) of smear-positives and -negatives, respectively. Of Xpert rifampicin-resistant specimens, 23% (172/746) were MTBDRplus isoniazid-susceptible. 85% (22/26) Xpert rifampicin-resistant, MTBDRplus rifampicin-susceptible specimens resolved in favour of Xpert by sequencing. MTBDRsl had at least one non-actionable result for 10% (35/342) and 40% (171/427; p=0.001) of smear-positives and -negatives, respectively. MTBDRsl sensitivity in smear-negatives was 84% (95% CI 67-93) for fluoroquinolones, 81% (54-95) for second-line injectables, and 57% (28-82) for resistance to both. Specificities were 93% (89-98), 88% (81-93), and 97% (91-99), respectively. Days to second-line susceptibility reporting with the advent of rapid direct testing improved vs. prior standard-of-care [6 (5-7) vs. 37 (35-46); p<0.001]. Interpretation: MTBDRplus is unsuitable for Xpert-detected rifampicin-resistance confirmation and isoniazid are likely still useful in many Xpert rifampicin-resistant patients. MTBDRsl is accurate for ruling-in second-line resistance, however, non-actionable result rates are unacceptably high (4/10 smear-negatives failed, which is not reflected in sensitivity estimates). Better second-line DSTs are needed. Funding Information: The work was funded by Stellenbosch University Faculty of Health Sciences, the National Research Foundation and Harry Crossley. RMW acknowledges funding from the South African Medical Research Council. GT acknowledges funding from the EDCTP2 programme supported by the European Union (grant SF1401, OPTIMAL DIAGNOSIS) and the National Institute of Allergy and Infection Diseases of the National Institutes of Health (U01AI152087). Declaration of Interests: All authors reported no conflict of interest. Ethics Approval Statement: This study was done in accordance with relevant guidelines and regulations, approved by the Health Research Ethics Committee of Stellenbosch University (N16/04/045) and the Western Cape Province Department of Health (2016RP18 637). Permission was granted to access anonymised residual specimens collected as part of routine diagnostic practice and informed consent waived.