Prevalence of non-tuberculous mycobacteria among people presumed to have tuberculosis, positive for acid-fast bacilli in Mali

Background: Non-tuberculosis mycobacteria (NTMs) are environmental agents that can cause opportunistic pulmonary disease in humans and animals which is often misdiagnosed as tuberculosis (TB). In this study, we describe the cases of NTMs identified during the first national anti-TB drug-resistance survey conducted in Mali, and associated risk factors. Methods: Sputum was collected from people presenting for pulmonary TB diagnosis, from April to December 2019, regardless of age. Microscopy-positive patients were enrolled and were tested by GeneXpert MTB/RIF. Cases that tested negative for the Mycobacterium tuberculosis complex (MTBc) were tested for presence of mycobacteria by amplification of the IS6110 and 16SrRNA genes through double quantitative real-time PCR, followed by nested PCR and Sanger sequencing of the IS6110-negative samples for NTM species identification. Results: A total of 1,418 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 GeneXpert MTB/RIF and in-house PCR methods, 1331 (93.9%) patients were positive for MTBc, 48 (3.4%) for NTMs and for 39 (2.7%) no species identification was possible. Advanced age (65 and over) (OR 8.8, p=0.001) and previous TB treatment (OR 3.4 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. Conclusion: Detection of NTMs 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 lessen confusion. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Global Fund against tuberculosis ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: ETHICS COMMITTEE (EC) OF THE EX-National Institute of Public Research Health (NIPRH)/DECISION NO. 08/2018/EC-NIPRH OF 21 MARCH 2018 I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors