{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T17:30:13Z","timestamp":1787074213388,"version":"build-2736575974"},"reference-count":31,"publisher":"American Chemical Society (ACS)","issue":"25","license":[{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFC2311200"],"award-info":[{"award-number":["2024YFC2311200"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Pretomanid (PMD) is a key antibiotic of the newest multidrug-resistant or rifampicin-resistant tuberculosis treatment regimen \u201cBPaL\u201d, but knowledge of its resistance mutations is still limited, especially in China, as it was approved only in late 2024. We analyzed a collection of Mycobacterium tuberculosis (MTB) isolates from China including the whole-genome sequencing and drug susceptibility testing data and extended analysis to other 2165 isolates from lineage 4. We found in-frame deletion variants in the ddn genome sequence in the isolates collected in Xinjiang Uyghur Autonomous Region, China, with a high level of PMD resistance without pre-exposure to PMD belonging to sublineage 4.5. The extended analysis found that in-frame deletion variants occurred more frequently in sublineage 4.5. Some isolates contain multiple ancestral components after historical evolution, which may cause in-frame deletion variants to spread in some settings. Furthermore, molecular dynamics simulations and free energy calculations of the key mutants indicated that the impaired mutant structures result in unfavorable domination binding, which poses less probability for PMD activation for targeting other critical MTB targets and also leads to insufficient generation of NO (nitric oxide) to kill MTB. Currently, PMD resistance is mainly due to ddn gene mutations, especially frameshift mutations. However, our findings underscore the importance of surveillance for in-frame deletions, especially in regions with a high prevalence of sublineage 4.5, and the high level of PMD resistance conferred by deletions raises crucial concerns about the future effectiveness of the BPaL regimen.<\/jats:p>","DOI":"10.1021\/acsomega.5c00610","type":"journal-article","created":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T07:43:18Z","timestamp":1750664598000},"page":"26551-26559","source":"Crossref","is-referenced-by-count":2,"title":["High-Level Primary\nPretomanid-Resistant with\n                    <i>ddn<\/i>\n                    In-Frame Deletion of\n                    <i>Mycobacterium tuberculosis<\/i>\n                    and Its Association with\nLineage 4.5 in China"],"prefix":"10.1021","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9758-3959","authenticated-orcid":true,"given":"Shaojun","family":"Pei","sequence":"first","affiliation":[{"name":"Peking University , , ,","place":["Beijing, China, 100191"]},{"name":"Brigham and Women\u2019s Hospital , , , ,","place":["Boston, Massachusetts, United States, 02120"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9396-329X","authenticated-orcid":true,"given":"Wei","family":"Yang","sequence":"additional","affiliation":[{"name":"National Clinical Research Center for Infectious Diseases, Shenzhen Third People\u2019s Hospital , ,","place":["Shenzhen, China, 518112"]},{"name":"The Chinese University of Hong Kong , , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xichao","family":"Ou","sequence":"additional","affiliation":[{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]},{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]},{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeyuan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Tianjin Medical University , , ,","place":["Tianjin, China, 300070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zekun","family":"Wang","sequence":"additional","affiliation":[{"name":"Peking University , , ,","place":["Beijing, China, 100191"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zexuan","family":"Song","sequence":"additional","affiliation":[{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]},{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengfen","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]},{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyuan","family":"Zhuang","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong , , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Li","sequence":"additional","affiliation":[{"name":"Monash University , , , ,","place":["Melbourne, Victoria, Australia, 3800"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanlin","family":"Zhao","sequence":"additional","affiliation":[{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]},{"name":"Chinese Center for Disease Control and Prevention , , ,","place":["Beijing, China, 102206"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2025,6,23]]},"reference":[{"key":"2026081811255237200_cit1","unstructured":"WHO\n          . Global Tuberculosis Report 2022. 2022. https:\/\/www.who.int\/teams\/global-tuberculosis-programme\/tb-reports\/global-tuberculosis-report-2022 (accessed Oct 27, 2022)."},{"key":"2026081811255237200_cit2","unstructured":"WHO\n          . WHO Consolidated Guidelines on Tuberculosis. Module\n4: Treatment\ue5f8Drug-Resistant Tuberculosis Treatment, 2022 Update. 2022. https:\/\/www.who.int\/publications\/i\/item\/9789240063129 (accessed Dec 15, 2022)."},{"issue":"10","key":"2026081811255237200_cit3","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1056\/NEJMoa1901814","article-title":"Nix-TB Trial Team. Treatment\nof Highly Drug-Resistant Pulmonary Tuberculosis","volume":"382","author":"Conradie","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"2026081811255237200_cit4","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.str.2011.11.001","article-title":"Structure of Ddn, the\ndeazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824","volume":"20","author":"Cellitti","year":"2012","journal-title":"Structure"},{"key":"2026081811255237200_cit5","doi-asserted-by":"publisher","first-page":"2831","DOI":"10.1007\/s00253-016-8038-y","article-title":"Discovery\nand characterization of an F420-dependent glucose-6-phosphate dehydrogenase\n(Rh-FGD1) from Rhodococcus jostii RHA1","volume":"101","author":"Nguyen","year":"2017","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"2026081811255237200_cit6","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.jgar.2022.09.001","article-title":"Pretomanid\ndevelopment and its clinical roles in treating tuberculosis","volume":"31","author":"Fekadu","year":"2022","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"2026081811255237200_cit7","doi-asserted-by":"publisher","first-page":"3828","DOI":"10.1038\/s41467-023-39300-z","article-title":"DprE2 is a molecular\ntarget of the\nanti-tubercular nitroimidazole compounds pretomanid and delamanid","volume":"14","author":"Abrahams","year":"2023","journal-title":"Nat. Commun."},{"key":"2026081811255237200_cit8","doi-asserted-by":"publisher","first-page":"5316","DOI":"10.1128\/AAC.00308-15","article-title":"Mutations in genes for\nthe F420 biosynthetic pathway and a nitroreductase enzyme are the\nprimary resistance determinants in spontaneous in vitro-selected PA-824-resistant\nmutants of Mycobacterium tuberculosis","volume":"59","author":"Haver","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026081811255237200_cit9","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1093\/jac\/dkt364","article-title":"Mutation\nrate and the emergence of drug resistance in Mycobacterium\ntuberculosis","volume":"69","author":"McGrath","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"2026081811255237200_cit10","doi-asserted-by":"publisher","first-page":"19431","DOI":"10.1038\/s41598-021-98862-4","article-title":"Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid\nand pretomanid","volume":"11","author":"Go\u0301mez-Gonza\u0301lez","year":"2021","journal-title":"Sci. Rep."},{"key":"2026081811255237200_cit11","unstructured":"WHO\n          . Catalogue of Mutations in Mycobacterium Tuberculosis\nComplex and Their Association with Drug Resistance, 2nd ed. 2023. https:\/\/www.who.int\/publications\/i\/item\/9789240082410 (accessed Nov 20, 2023)."},{"key":"2026081811255237200_cit12","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1093\/jac\/dkac070","article-title":"Ancient and recent differences\nin the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid","volume":"77","author":"Bateson","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"2026081811255237200_cit13","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01026-22","article-title":"The ddn Trp20Stop\nMutation and Its Association with Lineage 4.5 and Resistance to Delamanid\nand Pretomanid in Mycobacterium tuberculosis","volume":"66","author":"Mansjo\u0308","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026081811255237200_cit14","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/s12941-024-00697-0","article-title":"Prevalence and genetic basis of Mycobacterium\ntuberculosis resistance to pretomanid in China","volume":"23","author":"Zhao","year":"2024","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"2026081811255237200_cit15","doi-asserted-by":"publisher","first-page":"mgen000955","DOI":"10.1099\/mgen.0.000955","article-title":"Distribution\nand origins of Mycobacterium tuberculosis L4 in Southeast\nAsia","volume":"9","author":"Ashton","year":"2023","journal-title":"Microb. Genom."},{"key":"2026081811255237200_cit16","doi-asserted-by":"publisher","first-page":"e265","DOI":"10.1016\/S2666-5247(21)00301-3","article-title":"The 2021 WHO catalogue\nof Mycobacterium tuberculosis complex mutations associated\nwith drug resistance: A genotypic analysis","volume":"3","author":"Walker","year":"2022","journal-title":"Lancet Microbe"},{"key":"2026081811255237200_cit17","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1039\/C6MB00033A","article-title":"Protonation state of\nF 420 H 2 in the prodrug-activating deazaflavin dependent nitroreductase\n(Ddn) from Mycobacterium tuberculosis","volume":"12","author":"Mohamed","year":"2016","journal-title":"Mol. BioSyst."},{"key":"2026081811255237200_cit18","doi-asserted-by":"publisher","first-page":"4421","DOI":"10.1080\/07391102.2022.2069156","article-title":"Molecular dynamic assisted investigation\non impact of mutations in deazaflavin dependent nitroreductase against\npretomanid: a computational study","volume":"41","author":"Singh","year":"2023","journal-title":"J. Biomol.\nStruct. Dyn."},{"key":"2026081811255237200_cit19","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1111\/j.1742-4658.2011.08404.x","article-title":"Substrate specificity\nof the deazaflavin-dependent nitroreductase from Mycobacterium\ntuberculosis responsible for the bioreductive activation\nof bicyclic nitroimidazoles","volume":"279","author":"Gurumurthy","year":"2012","journal-title":"FEBS J."},{"key":"2026081811255237200_cit20","doi-asserted-by":"publisher","first-page":"001288","DOI":"10.1099\/mic.0.001288","article-title":"Assay development and\ninhibition of the Mt-DprE2 essential reductase from\nMycobacterium tuberculosis","volume":"169","author":"Batt","year":"2023","journal-title":"Microbiology"},{"key":"2026081811255237200_cit21","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1021\/acs.jpclett.9b00208","article-title":"Laser Ablation\nAssists Cyclization Reactions of Hydantoic Acid: A Proof for the Near-Attack\nConformation Theory?","volume":"10","author":"Kolesnikova","year":"2019","journal-title":"J. Phys. Chem. Lett."},{"key":"2026081811255237200_cit22","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/128_2006_084","article-title":"QM\/MM methods\nfor biological systems","volume-title":"Atomistic Approaches\nin Modern Biology: From Quantum Chemistry to Molecular Simulations","author":"Senn","year":"2007"},{"key":"2026081811255237200_cit23","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1016\/j.csbj.2023.03.002","article-title":"Unveiling the methyl\ntransfer mechanisms in the epigenetic machinery DNMT3A-3 L: A comprehensive\nstudy integrating assembly dynamics with catalytic reactions","volume":"21","author":"Yang","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2026081811255237200_cit24","doi-asserted-by":"publisher","first-page":"12652","DOI":"10.3390\/ijms241612652","article-title":"Insights\ninto the Inhibitory\nMechanisms of the Covalent Drugs for DNMT3A","volume":"24","author":"Yang","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"2026081811255237200_cit25","doi-asserted-by":"publisher","first-page":"6908","DOI":"10.1021\/acs.biochem.6b00683","article-title":"Hydrophobic Shielding\nDrives Catalysis of Hydride Transfer in a Family of F(420)\u00adH(2)-Dependent\nEnzymes","volume":"55","author":"Mohamed","year":"2016","journal-title":"Biochemistry"},{"key":"2026081811255237200_cit26","doi-asserted-by":"publisher","first-page":"1392","DOI":"10.1126\/science.1164571","article-title":"PA-824\nkills nonreplicating Mycobacterium tuberculosis by\nintracellular NO release","volume":"322","author":"Singh","year":"2008","journal-title":"Science"},{"key":"2026081811255237200_cit27","doi-asserted-by":"publisher","first-page":"2203","DOI":"10.1038\/s41467-022-29832-1","article-title":"CinA mediates\nmultidrug\ntolerance in Mycobacterium tuberculosis","volume":"13","author":"Kreutzfeldt","year":"2022","journal-title":"Nat.\nCommun."},{"key":"2026081811255237200_cit28","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01755-19","article-title":"Adduct Formation of Delamanid with NAD in Mycobacteria","volume":"64","author":"Hayashi","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"2026081811255237200_cit29","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1111\/mmi.12127","article-title":"A novel F(420) -dependent anti-oxidant\nmechanism protects Mycobacterium tuberculosis against\noxidative stress and bactericidal agents","volume":"87","author":"Gurumurthy","year":"2013","journal-title":"Mol.\nMicrobiol."},{"key":"2026081811255237200_cit30","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models\nand Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"2026081811255237200_cit31","doi-asserted-by":"publisher","first-page":"gkad359","DOI":"10.1093\/nar\/gkad359","article-title":"Tree Visualization\nBy One Table (tvBOT): a web application for visualizing,\nmodifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res."}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.5c00610","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/10\/25\/26551\/40837072\/ao5c00610.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/10\/25\/26551\/40837072\/ao5c00610.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T17:18:01Z","timestamp":1787073481000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/10\/25\/26551\/3654670\/High-Level-Primary-Pretomanid-Resistant-with-ddn"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,23]]},"references-count":31,"journal-issue":{"issue":"25","published-online":{"date-parts":[[2025,6,23]]},"published-print":{"date-parts":[[2025,7,1]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.5c00610","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,23]]}}}