{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T22:34:08Z","timestamp":1788820448588,"version":"build-2803163510"},"reference-count":45,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Healthcare"],"abstract":"<jats:p>Background: Drug-resistant tuberculosis (TB) remains a major challenge in high-burden settings, where timely identification of emerging resistance and effective governance responses are critical. While routine molecular diagnostics generate large volumes of resistance-associated mutation data, these outputs are typically used for individual patient management and remain underutilized for population-level surveillance and for the application of clinical governance approaches for improved TB care. Methods: We conducted a retrospective cross-sectional analysis of 1386 molecular diagnostic records for Mycobacterium tuberculosis, collected between March 2021 and December 2024, from 30 health facilities in the King Sabata Dalindyebo (K.S.D.) Local Municipality of Oliver Reginald (O.R.) Tambo District. Resistance-associated mutation proxies were identified for loci associated with isoniazid (katG, inhA), fluoroquinolone (gyrA), and second-line injectable agents (amikacin, kanamycin, and capreomycin) through mutations in the rrs locus. Mutation proxy prevalence was examined overall, by age group, over time, and across facilities. Persistence of resistance detection was assessed using consecutive-month analyses to characterize temporal continuity at the facility level. Results: At least one resistance-associated mutation proxy was detected in 72.7% of the analyzed records. Isoniazid resistance predominated, with katG mutation proxies identified in 52.2% and inhA in 20.2% of cases. Mutation proxies associated with fluoroquinolone and second-line injectable resistance were less frequently observed. Temporal analysis demonstrated variability over the study period, with a general decline in overall mutation proxy prevalence alongside a relative increase in inhA-associated mutations. Substantial heterogeneity in resistance patterns was observed across health facilities, with high-volume sites contributing the greatest absolute burden and selected facilities demonstrating sustained persistence of mutation detection over consecutive months. These findings highlight the magnitude, distribution, and persistence of resistance-associated mutation proxies within routine programmatic data. Conclusions: Routine molecular diagnostic data revealed a substantial and heterogeneous burden of drug-resistant Mycobacterium tuberculosis in K.S.D. Local Municipality, characterized by age-specific patterns, temporal shifts, and sustained facility-level persistence. Beyond descriptive epidemiology, routinely generated mutation proxy data can serve as early-warning indicators of clinical governance stress, signaling emerging pressures on TB care systems when resistance patterns persist or worsen. Interpreting these trends can support more anticipatory clinical governance, strengthen resistance surveillance, and guide prioritized interventions in high-burden, resource-constrained settings.<\/jats:p>","DOI":"10.3390\/healthcare14101280","type":"journal-article","created":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T20:14:16Z","timestamp":1778530456000},"page":"1280","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Routine Molecular Surveillance of Drug-Resistant Tuberculosis: Translating Mutation Proxies into Clinical Governance Intelligence in Rural Eastern Cape"],"prefix":"10.3390","volume":"14","author":[{"given":"Bulela","family":"Sonka","sequence":"first","affiliation":[{"name":"Walter Sisulu Tuberculosis Research Group, Faculty of Medicine and Health Sciences, School of Pathology, Walter Sisulu University, Mthatha 5100, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0388-787X","authenticated-orcid":false,"given":"Mojisola Clara","family":"Hosu","sequence":"additional","affiliation":[{"name":"Walter Sisulu Tuberculosis Research Group, Faculty of Medicine and Health Sciences, School of Pathology, Walter Sisulu University, Mthatha 5100, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ntandazo","family":"Dlatu","sequence":"additional","affiliation":[{"name":"Walter Sisulu Institute for Clinical Governance and Healthcare Administration, Faculty of Medicine and Health Sciences, School of Public Health, Walter Sisulu University, Mthatha 5100, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0918-7539","authenticated-orcid":false,"given":"Thokoe Vincent","family":"Makola","sequence":"additional","affiliation":[{"name":"Walter Sisulu Institute for Clinical Governance and Healthcare Administration, Faculty of Medicine and Health Sciences, School of Public Health, Walter Sisulu University, Mthatha 5100, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7308-4239","authenticated-orcid":false,"given":"Lindiwe Modest","family":"Faye","sequence":"additional","affiliation":[{"name":"Walter Sisulu Tuberculosis Research Group, Faculty of Medicine and Health Sciences, School of Pathology, Walter Sisulu University, Mthatha 5100, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/s41579-024-01025-1","article-title":"Drug-resistant tuberculosis: A persistent global health concern","volume":"22","author":"Farhat","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Mancuso, G., Midiri, A., De Gaetano, S., Ponzo, E., and Biondo, C. (2023). Tackling drug-resistant tuberculosis: New challenges from the old pathogen Mycobacterium tuberculosis. Microorganisms, 11.","DOI":"10.20944\/preprints202308.2059.v1"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e00180-19","DOI":"10.1128\/cmr.00180-19","article-title":"The changing paradigm of drug-resistant tuberculosis treatment: Successes, pitfalls, and future perspectives","volume":"35","author":"Dookie","year":"2022","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Liebenberg, D., Gordhan, B.G., and Kana, B.D. (2022). Drug-resistant tuberculosis: Implications for transmission, diagnosis, and disease management. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.943545"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.2147\/IDR.S457308","article-title":"Identification of Mycobacterium tuberculosis resistance to common antibiotics: An overview of current methods and techniques","volume":"17","author":"Xiong","year":"2024","journal-title":"Infect. Drug Resist."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Bartolomeu-Gon\u00e7alves, G., Souza, J.M., Fernandes, B.T., Spoladori, L.F., Correia, G.F., Castro, I.M., Borges, P.H., Silva-Rodrigues, G., Tavares, E.R., and Yamauchi, L.M. (2024). Tuberculosis diagnosis: Current, ongoing, and future approaches. Diseases, 12.","DOI":"10.3390\/diseases12090202"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2627072","DOI":"10.1080\/22221751.2026.2627072","article-title":"Rapid drug resistance prediction in positive Mycobacterium tuberculosis clinical samples using an extensive targeted next-generation sequencing panel","volume":"15","author":"Rosendal","year":"2026","journal-title":"Emerg. Microbes Infect."},{"key":"ref_8","unstructured":"(2026, March 09). King Sabatha Dalindyebo Municipality Draft Annual Report 2024\/2025, Available online: https:\/\/ksd.gov.za\/download\/documents\/reports\/annual_reports\/KSDM-Draft-Annual-Report-2024-2025.pdf."},{"key":"ref_9","unstructured":"King Sabata Dalindyebo Local Municipality (2013). Map 2: The KSD and Its 35 Wards. Integrated Development Plan 2013\u20132014, King Sabata Dalindyebo Local Municipality."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"153563","DOI":"10.1016\/j.bbrc.2026.153563","article-title":"Decoding antibiotic resistance in tuberculosis: Role of RRDR and non-RRDR mutations in diagnostic perspectives","volume":"812","author":"Hazarika","year":"2026","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Mujuni, D., Kasemire, D.L., Ibanda, I., Kabugo, J., Nsawotebba, A., Phelan, J.E., Majwala, R.K., Tugumisirize, D., Nyombi, A., and Orena, B. (2022). Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: A two and a half-year\u2019s review. BMC Infect. Dis., 22.","DOI":"10.1186\/s12879-022-07339-w"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e213","DOI":"10.1016\/S2589-7500(21)00038-8","article-title":"WHO SMART guidelines: Optimizing country-level use of guideline recommendations in the digital age","volume":"3","author":"Mehl","year":"2021","journal-title":"Lancet Digit. Health"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4944","DOI":"10.4102\/phcfm.v17i1.4944","article-title":"Access to Tuberculosis Care in South Africa during the COVID-19 Pandemic: A Scoping Review","volume":"17","author":"Appel","year":"2025","journal-title":"Afr. J. Prim. Health Care Fam. Med."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1136\/jech-2021-217529","article-title":"Tuberculosis in times of COVID-19","volume":"76","author":"Zimmer","year":"2022","journal-title":"J. Epidemiol. Commun. Health"},{"key":"ref_15","unstructured":"Vitrosens Biotechnology (2026, April 12). TB in the Post-COVID Era: Why Diagnostic Gaps Are Widening and How Point-of-Care Molecular Testing Can Help. Vitrosens Biotechnology 2026, 27 March. Available online: https:\/\/vitrosens.com\/tb-post-covid-diagnostic-gaps-molecular-testing\/."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Sharma, S. (2025). Deprioritized and disrupted: Tuberculosis care in the shadow of COVID-19. Front. Public Health, 13.","DOI":"10.3389\/fpubh.2025.1651902"},{"key":"ref_17","unstructured":"World Health Organization (2021). Catalogue of Mutations in Mycobacterium Tuberculosis Complex and Their Association with Drug Resistance, WHO."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Girdwood, S., Pandey, M., Machila, T., Warrier, R., Gautam, J., Mukumbwa-Mwenechanya, M., Benade, M., Nichols, K., Shibemba, L., and Mwewa, J. (2023). The integration of tuberculosis and HIV testing on GeneXpert can substantially improve access and same-day diagnosis and benefit tuberculosis programmes: A diagnostic network optimization analysis in Zambia. PLoS Glob. Public Health, 3.","DOI":"10.1371\/journal.pgph.0001179"},{"key":"ref_19","unstructured":"Reis, K., Lu, X., Seepamore, B., Wolf, A., Zulu, M., Nyilana, H., Guzman, K., Cheung, K., Friedland, G., and Yushkov, J. Characterizing the dual burden of stigma in people with multidrug-resistant tuberculosis (MDR-TB) and HIV co-infection in South Africa: A mixed methods, prospective cohort study. JAIDS J. Acquir. Immune Defic. Syndr., Online ahead of print."},{"key":"ref_20","first-page":"16","article-title":"Prevalence of gene mutations associated with isoniazid resistance in drug-resistant tuberculosis: A study from Limpopo, South Africa","volume":"7","author":"Premjith","year":"2025","journal-title":"J. Med. Lab. Sci. Technol. S. Afr."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Nono, V.N., Nantia, E.A., Mutshembele, A., Teagho, S.N., Simo, Y.W.K., Takong, B.S., Djieugoue, Y.J., Assolo, Y.P., Ongboulal, S.M., and Awungafac, S.N. (2025). Prevalence of katG and inhA mutations associated with isoniazid resistance in Mycobacterium tuberculosis clinical isolates in Cameroon. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-03816-9"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1513\/AnnalsATS.202312-1076OC","article-title":"The hidden epidemic of isoniazid-resistant tuberculosis in South Africa","volume":"21","author":"Klopper","year":"2024","journal-title":"Ann. Am. Thorac. Soc."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e01280-20","DOI":"10.1128\/AAC.02091-20","article-title":"Systematic review of mutations associated with isoniazid resistance points to continuing evolution and subsequent evasion of molecular detection and potential for emergence of multidrug resistance in clinical strains of Mycobacterium tuberculosis","volume":"65","author":"Valafar","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e506","DOI":"10.1016\/S2666-5247(23)00110-6","article-title":"Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: A genomic epidemiology study","volume":"4","author":"Goig","year":"2023","journal-title":"Lancet Microbe"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Dagne, B., Desta, K., Fekade, R., Amare, M., Tadesse, M., Diriba, G., Zerihun, B., Getu, M., Sinshaw, W., and Seid, G. (2021). The epidemiology of first- and second-line drug resistance in common Mycobacterium tuberculosis complex species: Evidence from selected tuberculosis treatment-initiating centers in Ethiopia. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0245687"},{"key":"ref_26","first-page":"94","article-title":"Mathematical model of tuberculosis with drug resistance to the first and second line of treatment","volume":"21","author":"Gupta","year":"2018","journal-title":"J. New Theory"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1007\/s15010-022-01941-5","article-title":"Resistance Patterns among Drug-Resistant Tuberculosis Patients and Trends-over-Time Analysis of National Surveillance Data in Gabon, Central Africa","volume":"51","author":"Abdul","year":"2023","journal-title":"Infection"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Monde, N., Munyeme, M., Chongwe, G., Wensman, J.J., Zulu, M., Siziya, S., Tembo, R., Siame, K.K., Shambaba, O., and Malama, S. (2023). First and Second-Line Anti-Tuberculosis Drug-Resistance Patterns in Pulmonary Tuberculosis Patients in Zambia. Antibiotics, 12.","DOI":"10.3390\/antibiotics12010166"},{"key":"ref_29","unstructured":"World Health Organization (2026, April 11). The 9-Month All-Oral Regimen. WHO TB Knowledge Sharing Platform 2022. Available online: https:\/\/tbksp.who.int\/fr\/node\/582."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e00713-25","DOI":"10.1128\/msystems.00713-25","article-title":"The diverse phenotypic and mutational landscape induced by fluoroquinolone treatment","volume":"10","author":"Mohiuddin","year":"2025","journal-title":"mSystems"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/s41572-024-00504-2","article-title":"Multidrug-resistant tuberculosis","volume":"10","author":"Dheda","year":"2024","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e559","DOI":"10.1016\/S1473-3099(24)00144-0","article-title":"The epidemiology, transmission, diagnosis, and management of drug-resistant tuberculosis\u2014Lessons from the South African experience","volume":"24","author":"Naidoo","year":"2024","journal-title":"Lancet Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/s41598-023-27516-4","article-title":"Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multidrug-resistant tuberculosis","volume":"13","author":"Napier","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"17552","DOI":"10.1038\/s41598-020-74432-y","article-title":"Prevalence and factors associated with multidrug-resistant tuberculosis in South India","volume":"10","author":"Shivekar","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.jgar.2025.02.014","article-title":"Second-line drug resistance among multidrug-resistant tuberculosis patients in Ethiopia: A laboratory-based surveillance","volume":"42","author":"Diriba","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"227","DOI":"10.4103\/lungindia.lungindia_204_19","article-title":"Pattern of InhA and KatG mutations in isoniazid monoresistant Mycobacterium tuberculosis isolates","volume":"37","author":"Charan","year":"2020","journal-title":"Lung India"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"96","DOI":"10.47310\/jpms2026150213","article-title":"Age-independent molecular resistance patterns in tuberculosis patients: A cross-sectional analytical study","volume":"15","author":"Naik","year":"2026","journal-title":"J. Pioneer. Med. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Adisa, R., Ayandokun, T.T., and Ige, O.M. (2021). Knowledge about tuberculosis, treatment adherence and outcome among ambulatory patients with drug-sensitive tuberculosis in two directly-observed treatment centres in Southwest Nigeria. BMC Public Health, 21.","DOI":"10.1186\/s12889-021-10698-9"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.ijregi.2022.01.004","article-title":"Prevalence of tuberculosis, including multidrug-resistant and extensively drug-resistant tuberculosis, and association with occupation in adults at Sirindhorn Hospital, Bangkok","volume":"2","author":"Puengpipattrakul","year":"2022","journal-title":"IJID Reg."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.3390\/idr16060095","article-title":"Drug-resistant tuberculosis hotspots in Oliver Reginald Tambo District Municipality, Eastern Cape, South Africa","volume":"16","author":"Faye","year":"2024","journal-title":"Infect. Dis. Rep."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Daneshi, S., Mehni, E.B., Kamali, M., Barfar, E., Barahouei, F.B., Hushmandi, K., and Raesi, R. (2025). Prevalence and contributing factors of drug-resistant tuberculosis in Iran: A systematic review. BMC Infect. Dis., 25.","DOI":"10.1186\/s12879-025-11439-8"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e40659","DOI":"10.2196\/40659","article-title":"The environmental and socioeconomic effects and prediction of patients with tuberculosis in different age groups in Southwest China: A population-based study","volume":"9","author":"Wei","year":"2023","journal-title":"JMIR Public Health Surveill."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Omoteso, O.A., Fadaka, A.O., Walker, R.B., and Khamanga, S.M. (2025). Innovative strategies for combating multidrug-resistant tuberculosis: Advances in drug delivery systems and treatment. Microorganisms, 13.","DOI":"10.20944\/preprints202503.0157.v1"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Shah, H.D., Nazli Khatib, M., Syed, Z.Q., Gaidhane, A.M., Yasobant, S., Narkhede, K., Bhavsar, P., Patel, J., Sinha, A., and Puwar, T. (2022). Gaps and interventions across the diagnostic care cascade of TB patients at the level of patient, community, and health system: A qualitative review of the literature. Trop. Med. Infect. Dis., 7.","DOI":"10.3390\/tropicalmed7070136"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Saktiawati, A.M.I., Vasiliu, A., Saluzzo, F., and Akkerman, O.W. (2024). Strategies to enhance diagnostic capabilities for the new drug-resistant tuberculosis drugs. Pathogens, 13.","DOI":"10.20944\/preprints202410.1500.v1"}],"container-title":["Healthcare"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-9032\/14\/10\/1280\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T04:38:28Z","timestamp":1779251908000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-9032\/14\/10\/1280"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,8]]},"references-count":45,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["healthcare14101280"],"URL":"https:\/\/doi.org\/10.3390\/healthcare14101280","relation":{},"ISSN":["2227-9032"],"issn-type":[{"value":"2227-9032","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,8]]}}}