Interpretation of duplex IS6110-16S qPCR results.

BackgroundNon-tuberculous mycobacteria (NTM) are environmental agents that can cause opportunistic pulmonary disease in humans and animals, often misdiagnosed as tuberculosis (TB). In this study, we describe the cases of NTM identified during the first national anti-TB drug resistance survey conducted in Mali and explore associated risk factors.MethodsSputum was collected from people presenting for pulmonary TB diagnosis from April to December 2019, regardless of age. Microscopy-positive patients were enrolled and tested using the Xpert MTB/RIF assay. A patient who tested negative for the Mycobacterium tuberculosis complex (MTBC) was tested for the presence of mycobacteria by amplification of the IS6110 and 16SrRNA (16S) genes through double quantitative real-time PCR, followed by nested PCR and Sanger sequencing of the IS6110-negative samples for NTM species identification.Results1,418 sputum smear-positive patients were enrolled, including 1,199 new cases, 211 previously treated cases, and 8 whose previous treatment history was unknown. Based on the results of Xpert MTB/RIF assay and in-house PCR methods, 1,331 (93.9%) patients were positive for MTBC, 48 (3.4%) for NTM, and no species identification was possible for 39 (2.7%). Advanced age of 65 and over with an OR 8.8 (95% CI 2.3–33.2 and p = 0.001) and previous TB treatment with an OR 3.4 (95% CI 1.2–9.6 and p = 0.016) were the risk factors statistically associated with NTM detection. M. avium complex (MAC) was the predominant NTM species, detected in 20 cases.ConclusionDetection of NTM in people presumed to have TB is an ongoing challenge, confounding correct TB diagnosis. Concomitant use of microscopy and GeneXpert testing among at-risk individuals could improve patient management.