Diagnostic Discordance During MDR-TB Treatment: Retrospective Identification of Mycobacterium avium Complex-Associated Nontuberculous Mycobacterium by Whole-Genome Sequencing

Nontuberculous mycobacteria (NTM) pose significant diagnostic challenges in high tuberculosis (TB)-burden settings, particularly when routine molecular assays suggest multidrug-resistant TB (MDR-TB). Current diagnostic algorithms in high TB-burden settings are primarily designed to detect members of the Mycobacterium tuberculosiscomplex (MTBC) and may inadequately distinguish NTM when discordant laboratory findings are encountered. The value of this case lies not in demonstrating that whole-genome sequencing (WGS) should guide real-time treatment, but in illustrating how diagnostic uncertainty can arise when routine MTBC-focused tests fail to identify NTM and how genomic surveillance can contribute to species-level characterization in such settings. We report a complex case which was initially diagnosed as rifampicin- and isoniazid-resistant MTBC and subsequently managed according to programmatic MDR-TB guidelines. Persistent acid-fast bacilli positivity in the presence of negative MTBC antigen testing during follow-up raised suspicion of NTM involvement. Whole-genome sequencing (WGS), performed retrospectively on a follow-up isolate, identified an NTM belonging to the Mycobacterium avium complex (MAC) which was phylogenetically closest to genomes provisionally designated Mycobacterium europaeum_A and distinct from Mycobacterium europaeum sensu stricto, a member of the Mycobacterium simiae complex. The identification of a MAC-associated NTM provided an explanation for the observed diagnostic discordance but could not determine whether the organism represented colonization, sequential infection, or concurrent infection. Although WGS did not inform clinical management, it provided high-resolution species identification and highlighted important limitations of MTBC-focused diagnostic workflows when discordant microbiological findings are encountered. This case underscores the need for the targeted investigation of NTM in patients with acid-fast bacilli-positive cultures and negative MTBC antigen testing and supports the use of genomic surveillance to improve species-level identification and understanding of NTM epidemiology in high TB-burden settings such as Limpopo Province, South Africa.