{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:50:20Z","timestamp":1786117820130,"version":"build-2736575974"},"reference-count":35,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","award":["R37AI026170"],"award-info":[{"award-number":["R37AI026170"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Research Foundation centre of excellence","award":["MND210624615487"],"award-info":[{"award-number":["MND210624615487"]}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI114900"],"award-info":[{"award-number":["R01AI114900"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","award":["R21AI168940"],"award-info":[{"award-number":["R21AI168940"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The European & Developing Countries Clinical Trials Partnership (EDCTP) Fellowships","award":["TMA2018SF-2467"],"award-info":[{"award-number":["TMA2018SF-2467"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"ABSTRACT<\/jats:title>\n \n \n \n There is an urgent need for rapid, affordable diagnostic tools capable of detecting baseline and treatment-emergent resistance among patients with drug-resistant tuberculosis (DR-TB). Reporter mycobacteriophages provide a phenotypic solution enhanced by brighter luminescent reporters compatible with simple readouts. We applied the TM4::\n GeNL<\/jats:italic>\n reporter mycobacteriophage for rapid phenotypic drug susceptibility testing (pDST) on serial\n Mycobacterium tuberculosis<\/jats:italic>\n isolates from six DR-TB patients, including four with treatment-emergent resistance and two with baseline bedaquiline (BDQ)-resistant subpopulations. Susceptibility to BDQ, pretomanid (PMD), delamanid (DLM), and linezolid (LZD) was assessed by luminescence retention after TM4::\n GeNL<\/jats:italic>\n infection compared to no-drug control, with conventional pDST and whole-genome sequencing as the reference standard. Isolates with baseline and treatment-emergent resistance to BDQ and PMD had a mean relative luminescence unit (RLU) retention of 83.8% (95% CI, 52.1\u2013115.6), while susceptible clinical isolates retained 1.5% mean RLU (95% CI, 0.2\u20132.8). The TM4::\n GeNL<\/jats:italic>\n DST results were consistent with conventional pDST in detecting BDQ and PMD resistance. Three patients with BDQ treatment-emergent resistance had mutations in\n mmpR5<\/jats:italic>\n (\n Rv0678<\/jats:italic>\n ), with a range of variant frequencies (12.6%\u201392.3%). One isolate with treatment-emergent DLM\/PMD resistance had mutations in the\n fbiC<\/jats:italic>\n gene, with A487fs and S534stop variants at 25.0% and 12.0%, respectively. Sequencing of serial isolates from one patient on a regimen that included LZD identified an emergent mutation in\n rrl<\/jats:italic>\n (n.2814G > T, 53.8% frequency); however, the isolate was LZD susceptible by both TM4::\n GeNL<\/jats:italic>\n DST and conventional pDST. TM4::\n GeNL<\/jats:italic>\n reporter mycobacteriophage accurately detected baseline and treatment-emergent resistance to BDQ and PMD compared to conventional pDST. This rapid, phenotypic approach shows promise for accelerating detection of resistance to new and repurposed DR-TB drugs in clinical settings.\n <\/jats:p>\n <\/jats:sec>\n \n IMPORTANCE<\/jats:title>\n \n Ongoing transmission of drug-resistant tuberculosis (DR-TB), combined with limited access to rapid diagnostics for resistance to key drugs in modern regimens, poses a major challenge to global TB control. We applied TM4::\n GeNL<\/jats:italic>\n reporter mycobacteriophage for rapid phenotypic drug susceptibility testing on\n Mycobacterium tuberculosis<\/jats:italic>\n (\n Mtb<\/jats:italic>\n ) clinical isolates with baseline and treatment-emergent resistance to DR-TB drugs (bedaquiline, pretomanid, and delamanid), generating results within 48 h from a positive culture. Our findings provide evidence on the utility of the TM4::\n GeNL<\/jats:italic>\n mycobacteriophage to infect\n Mtb<\/jats:italic>\n clinical isolates and distinguish between drug-susceptible and resistant isolates. TM4::\n GeNL<\/jats:italic>\n reporter mycobacteriophage detected emerging resistance to bedaquiline and pretomanid within 48 h from a positive culture, with our results correlating well with conventional phenotypic drug susceptibility and whole-genome sequencing data. These findings support TM4::\n GeNL<\/jats:italic>\n reporter mycobacteriophage as a rapid, multiplexed alternative drug-susceptibility test for DR-TB.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1128\/spectrum.03900-25","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T13:02:31Z","timestamp":1784120551000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Rapid detection of treatment-emergent resistance to bedaquiline and pretomanid in\n Mycobacterium tuberculosis<\/i>\n using TM4::\n GeNL<\/i>\n reporter mycobacteriophages"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4355-5068","authenticated-orcid":false,"given":"Senamile L.","family":"Ngema","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2201-8028","authenticated-orcid":true,"given":"Saranathan","family":"Rajagopalan","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05cf8a891","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Albert Einstein College of Medicine","place":["Bronx, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rubeshan","family":"Perumal","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal","place":["Durban, South Africa"]},{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pulmonology and Critical Care, School of Clinical Medicine, College of Health Sciences, University of KwaZulu-Natal","place":["Durban, South Africa"]},{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"South African Medical Research Council (SAMRC)\u2013CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sashen","family":"Moodley","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"African Health Research Institute, University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin J.","family":"Guzman","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9177-8827","authenticated-orcid":false,"given":"Adrie J. C.","family":"Steyn","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"African Health Research Institute, University of KwaZulu-Natal","place":["Durban, South Africa"]},{"id":[{"id":"https:\/\/ror.org\/008s83205","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology, University of Alabama at Birmingham","place":["Birmingham, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"William R.","family":"Jacobs","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05cf8a891","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Albert Einstein College of Medicine","place":["Bronx, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kogieleum","family":"Naidoo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal","place":["Durban, South Africa"]},{"id":[{"id":"https:\/\/ror.org\/04qzfn040","id-type":"ROR","asserted-by":"publisher"}],"name":"South African Medical Research Council (SAMRC)\u2013CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"O'Donnell","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center","place":["New York, USA"]},{"id":[{"id":"https:\/\/ror.org\/01esghr10","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Epidemiology, Columbia University Medical Center","place":["New York, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3532-350X","authenticated-orcid":true,"given":"Michelle H.","family":"Larsen","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05cf8a891","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Immunology, Albert Einstein College of Medicine","place":["Bronx, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40249-023-01107-x"},{"key":"e_1_3_4_3_2","unstructured":"World Health Organization. 2024. 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