{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T05:01:11Z","timestamp":1784869271859,"version":"3.55.0"},"reference-count":26,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:00:00Z","timestamp":1784678400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"crossref","award":["209080321235"],"award-info":[{"award-number":["209080321235"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/microorganisms14071596","type":"journal-article","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T09:20:39Z","timestamp":1784712039000},"page":"1596","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diagnostic Discordance During MDR-TB Treatment: Retrospective Identification of Mycobacterium avium Complex-Associated Nontuberculous Mycobacterium by Whole-Genome Sequencing"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6279-6409","authenticated-orcid":false,"given":"Ivy","family":"Rukasha","sequence":"first","affiliation":[{"name":"Division of Medical Microbiology, Department of Pathology, School of Medicine, University of Limpopo, Polokwane 0727, South Africa"},{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5351-7834","authenticated-orcid":false,"given":"Kabelo Gabriel","family":"Kaapu","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Department of Pathology, School of Medicine, University of Limpopo, Polokwane 0727, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nakamozi Francine","family":"Nemaguvhuni","sequence":"additional","affiliation":[{"name":"Multidrug Resistant Tuberculosis Unit, Tshilidzini Hospital, Limpopo Department of Health, Limpopo 0950, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8569-0183","authenticated-orcid":false,"given":"Felicia","family":"Wells-Hunter","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6402-6993","authenticated-orcid":false,"given":"Abhinav","family":"Sharma","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody Emile","family":"Phelan","sequence":"additional","affiliation":[{"name":"Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutlisi Jacqueline","family":"Kolobe","sequence":"additional","affiliation":[{"name":"Department of Microbiology, National Health Laboratory Service, Polokwane 0699, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8560-8581","authenticated-orcid":false,"given":"Molebogeng Ruth","family":"Lekalakala-Mokaba","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Department of Pathology, School of Medicine, University of Limpopo, Polokwane 0727, South Africa"},{"name":"Department of Microbiology, National Health Laboratory Service, Polokwane 0699, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5741-7358","authenticated-orcid":false,"given":"Robin Mark","family":"Warren","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7445-6620","authenticated-orcid":false,"given":"Emilyn","family":"Costa Concei\u00e7\u00e3o","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa"},{"name":"Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Cape Town 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"108054","DOI":"10.1016\/j.ijid.2025.108054","article-title":"Longitudinal epidemiology of pulmonary nontuberculous mycobacteria and tuberculosis in Singapore (2006\u20132024): Emerging dominance of Mycobacterium abscessus","volume":"160","author":"Pereira","year":"2025","journal-title":"Int. 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