{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T22:25:27Z","timestamp":1794349527618,"version":"4.9.0"},"reference-count":76,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100014334","name":"JICA Ogata Sadako Research Institute for Peace and Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014334","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004156","name":"Mahidol University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004156","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.isci.2026.117699","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T20:57:14Z","timestamp":1790110634000},"page":"117699","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Association between human genomes and mycobacterial genomes contributes to severity and transmissibility of pulmonary tuberculosis"],"prefix":"10.1016","volume":"29","author":[{"given":"Pornpen","family":"Tantivitayakul","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Punna","family":"Kunhapan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manon","family":"Boonbangyang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kridsadakorn","family":"Chaichoompu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alisa","family":"Wilantho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waritta","family":"Sawaengdee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wuthiwat","family":"Ruangchai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuttapong","family":"Thawornwattana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideki","family":"Yanai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukanya","family":"Wattanapokayakit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Areeya","family":"Disratthakit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reiko","family":"Miyahara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Supalert","family":"Nedsuwan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Worarat","family":"Imasanguan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pacharee","family":"Kantipong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boonchai","family":"Chaiyasirinroje","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin L.","family":"Hibberd","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katsushi","family":"Tokunaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surakameth","family":"Mahasirimongkol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5057-6719","authenticated-orcid":false,"given":"Prasit","family":"Palittapongarnpim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2026.117699_bib1","series-title":"Global Tuberculosis Report 2025","year":"2025"},{"key":"10.1016\/j.isci.2026.117699_bib2","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/s41598-022-05524-0","article-title":"Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis Lineage 1 in endemic regions of Asia and Africa","volume":"12","author":"Netikul","year":"2022","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2026.117699_bib3","article-title":"Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2","volume":"7","author":"Thawornwattana","year":"2021","journal-title":"Microb. Genom."},{"key":"10.1016\/j.isci.2026.117699_bib4","doi-asserted-by":"crossref","DOI":"10.1038\/emi.2016.111","article-title":"Risk factors for pulmonary cavitation in tuberculosis patients from China","volume":"5","author":"Zhang","year":"2016","journal-title":"Emerg. Microb. Infect."},{"key":"10.1016\/j.isci.2026.117699_bib5","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1097\/MCP.0000000000000672","article-title":"Human global and population-specific genetic susceptibility to Mycobacterium tuberculosis infection and disease","volume":"26","author":"M\u00f6ller","year":"2020","journal-title":"Curr. Opin. Pulm. Med."},{"key":"10.1016\/j.isci.2026.117699_bib6","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1089\/jir.2013.0050","article-title":"Innate defects of the IL-12\/IFN-gamma axis in susceptibility to infections by mycobacteria and salmonella","volume":"34","author":"Ramirez-Alejo","year":"2014","journal-title":"J. Interferon Cytokine Res."},{"key":"10.1016\/j.isci.2026.117699_bib7","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/s41586-024-07866-3","article-title":"Tuberculosis in otherwise healthy adults with inherited TNF deficiency","volume":"633","author":"Arias","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117699_bib8","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aau8714","article-title":"Tuberculosis and impaired IL-23-dependent IFN-gamma immunity in humans homozygous for a common TYK2 missense variant","volume":"3","author":"Boisson-Dupuis","year":"2018","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.isci.2026.117699_bib9","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20220484","article-title":"Inherited human ITK deficiency impairs IFN-gamma immunity and underlies tuberculosis","volume":"220","author":"Ogishi","year":"2023","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.isci.2026.117699_bib10","doi-asserted-by":"crossref","DOI":"10.3390\/ijms26199544","article-title":"Genetic Susceptibility to Tuberculosis and the Utility of Polygenic Scores in Population Stratification","volume":"26","author":"Dashian","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.isci.2026.117699_bib11","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev-genom-021623-101844","article-title":"Genomic Interactions Between Mycobacterium tuberculosis and Humans","volume":"25","author":"Palittapongarnpim","year":"2024","journal-title":"Annu. Rev. Genom. Hum. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib12","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/s41467-023-36282-w","article-title":"Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease","volume":"14","author":"Phelan","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117699_bib13","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1038\/jhg.2017.82","article-title":"Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis","volume":"62","author":"Omae","year":"2017","journal-title":"J. Hum. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib14","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-50078-3","article-title":"A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages","volume":"9","author":"Ajawatanawong","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2026.117699_bib15","doi-asserted-by":"crossref","first-page":"S38","DOI":"10.1016\/S1472-9792(13)70009-X","article-title":"Evaluation of large genotypic Mycobacterium tuberculosis clusters: contributions from remote and recent transmission","volume":"93","author":"Teeter","year":"2013","journal-title":"Tuberculosis"},{"key":"10.1016\/j.isci.2026.117699_bib16","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.3201\/eid1407.060468","article-title":"Determinants of cluster size in large, population-based molecular epidemiology study of tuberculosis, northern Malawi","volume":"14","author":"Glynn","year":"2008","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib17","doi-asserted-by":"crossref","first-page":"S636","DOI":"10.1093\/infdis\/jix361","article-title":"Tuberculosis Infectiousness and Host Susceptibility","volume":"216","author":"Turner","year":"2017","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib18","doi-asserted-by":"crossref","first-page":"e117","DOI":"10.1016\/S1473-3099(20)30148-1","article-title":"Cavitary tuberculosis: the gateway of disease transmission","volume":"20","author":"Urbanowski","year":"2020","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib19","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/s41588-018-0117-9","article-title":"Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam","volume":"50","author":"Holt","year":"2018","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib20","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1038\/s41559-018-0680-6","article-title":"China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis","volume":"2","author":"Liu","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.isci.2026.117699_bib21","doi-asserted-by":"crossref","first-page":"6099","DOI":"10.1038\/s41467-021-26248-1","article-title":"Population structure, biogeography and transmissibility of Mycobacterium tuberculosis","volume":"12","author":"Freschi","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117699_bib22","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0132692","article-title":"Collectin CL-LK Is a Novel Soluble Pattern Recognition Receptor for Mycobacterium tuberculosis","volume":"10","author":"Troegeler","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117699_bib23","doi-asserted-by":"crossref","first-page":"6182","DOI":"10.1038\/s41467-023-41937-9","article-title":"Global burden of disease due to rifampicin-resistant tuberculosis: a mathematical modeling analysis","volume":"14","author":"Menzies","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117699_bib24","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1086\/425005","article-title":"The effect of initial drug resistance on treatment response and acquired drug resistance during standardized short-course chemotherapy for tuberculosis","volume":"39","author":"Seung","year":"2004","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0152933","article-title":"Prevalence, Risk Factors, and Treatment Outcomes of Isoniazid- and Rifampicin-Mono-Resistant Pulmonary Tuberculosis in Lima, Peru","volume":"11","author":"Villegas","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117699_bib26","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1007\/s00228-012-1429-9","article-title":"NAT2 genotype guided regimen reduces isoniazid-induced liver injury and early treatment failure in the 6-month four-drug standard treatment of tuberculosis: a randomized controlled trial for pharmacogenetics-based therapy","volume":"69","author":"Azuma","year":"2013","journal-title":"Eur. J. Clin. Pharmacol."},{"key":"10.1016\/j.isci.2026.117699_bib27","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1056\/NEJM193407052110106","article-title":"Certain Factors Influencing the Mortality of Sanatorium Treated Cases of Pulmonary Tuberculosis","volume":"211","author":"Langmuir AD","year":"1934","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.isci.2026.117699_bib28","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1007\/s00018-011-0728-0","article-title":"Alpha T-catenin (CTNNA3): a gene in the hand is worth two in the nest","volume":"68","author":"Smith","year":"2011","journal-title":"Cell. Mol. Life Sci."},{"key":"10.1016\/j.isci.2026.117699_bib29","doi-asserted-by":"crossref","DOI":"10.1080\/21688370.2018.1463896","article-title":"alphaT-catenin: A developmentally dispensable, disease-linked member of the alpha-catenin family","volume":"6","author":"Chiarella","year":"2018","journal-title":"Tissue Barriers"},{"key":"10.1016\/j.isci.2026.117699_bib30","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/s12866-022-02461-w","article-title":"Impact of pathobiological diversity of Mycobacterium tuberculosis on clinical features and lethal outcome of tuberculosis","volume":"22","author":"Mokrousov","year":"2022","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.isci.2026.117699_bib31","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.tube.2015.02.040","article-title":"Sublineages of Mycobacterium tuberculosis Beijing genotype strains and unfavorable outcomes of anti-tuberculosis treatment","volume":"95","author":"Hang","year":"2015","journal-title":"Tuberculosis"},{"key":"10.1016\/j.isci.2026.117699_bib32","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s12916-019-1487-2","article-title":"A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic","volume":"18","author":"Klopper","year":"2020","journal-title":"BMC Med."},{"key":"10.1016\/j.isci.2026.117699_bib33","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/S0954-6111(98)90297-9","article-title":"Radiographic spectrum of adult pulmonary tuberculosis in a developed country","volume":"92","author":"Wilcke","year":"1998","journal-title":"Respir. Med."},{"key":"10.1016\/j.isci.2026.117699_bib34","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1186\/1471-2334-13-484","article-title":"Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease","volume":"13","author":"Wampande","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib35","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1038\/nsmb.3064","article-title":"The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD","volume":"22","author":"Sun","year":"2015","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.isci.2026.117699_bib36","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007613","article-title":"Transmission phenotype of Mycobacterium tuberculosis strains is mechanistically linked to induction of distinct pulmonary pathology","volume":"15","author":"Verma","year":"2019","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.isci.2026.117699_bib37","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003468","article-title":"Ethnic variation in inflammatory profile in tuberculosis","volume":"9","author":"Coussens","year":"2013","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.isci.2026.117699_bib38","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.ncrna.2024.12.005","article-title":"Long non-coding RNA transcripts in Mycobacterium tuberculosis-host interactions","volume":"11","author":"Vijayaraghavan","year":"2025","journal-title":"Noncoding. RNA Res."},{"key":"10.1016\/j.isci.2026.117699_bib39","article-title":"Long Non-coding RNAs in Tuberculosis: From Immunity to Biomarkers","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.isci.2026.117699_bib40","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1136\/thoraxjnl-2019-213281","article-title":"Association between bacterial homoplastic variants and radiological pathology in tuberculosis","volume":"75","author":"Grandjean","year":"2020","journal-title":"Thorax"},{"key":"10.1016\/j.isci.2026.117699_bib41","article-title":"Hypervirulent Mycobacterium tuberculosis strain triggers necrotic lung pathology associated with enhanced recruitment of neutrophils in resistant C57BL\/6 mice","volume":"12","author":"Almeida","year":"2017","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117699_bib42","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1128\/CVI.00250-12","article-title":"Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig","volume":"19","author":"Kato-Maeda","year":"2012","journal-title":"Clin. Vaccine Immunol."},{"key":"10.1016\/j.isci.2026.117699_bib43","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41564-017-0090-6","article-title":"Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis","volume":"3","author":"Ates","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.isci.2026.117699_bib44","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adw5194","article-title":"Loss of the PPE71-esxX-esxY-PPE38 locus drives adaptive transcriptional responses and hypervirulence of Mycobacterium tuberculosis lineage 2","volume":"11","author":"Koleske","year":"2025","journal-title":"Sci. Adv."},{"key":"10.1016\/j.isci.2026.117699_bib45","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/s41467-020-14508-5","article-title":"TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages","volume":"11","author":"Bottai","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117699_bib46","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1016\/S1473-3099(06)70602-8","article-title":"Sputum processing methods to improve the sensitivity of smear microscopy for tuberculosis: a systematic review","volume":"6","author":"Steingart","year":"2006","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.isci.2026.117699_bib47","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/2049-6958-7-34","article-title":"Endobronchial tuberculosis: histopathological subsets and microbiological results","volume":"7","author":"Ozkaya","year":"2012","journal-title":"Multidiscip. Respir. Med."},{"key":"10.1016\/j.isci.2026.117699_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0059461","article-title":"Increased production of IL-4 and IL-12p40 from bronchoalveolar lavage cells are biomarkers of Mycobacterium tuberculosis in the sputum","volume":"8","author":"Nolan","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117699_bib49","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1186\/s13054-022-04208-5","article-title":"A genome-wide association study of survival in patients with sepsis","volume":"26","author":"Hernandez-Beeftink","year":"2022","journal-title":"Crit. Care"},{"key":"10.1016\/j.isci.2026.117699_bib50","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1007\/s12010-024-05006-1","article-title":"Prognostic Value of Insulin Growth Factor-Like Receptor 1 (IGFLR1) in Stage II and III Colorectal Cancer and Its Association with Immune Cell Infiltration","volume":"197","author":"Jin","year":"2025","journal-title":"Appl. Biochem. Biotechnol."},{"key":"10.1016\/j.isci.2026.117699_bib51","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112106","article-title":"Hypoxia-controlled EphA3 marks a human endometrium-derived multipotent mesenchymal stromal cell that supports vascular growth","volume":"9","author":"To","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117699_bib52","doi-asserted-by":"crossref","first-page":"4470","DOI":"10.1158\/0008-5472.CAN-14-0218","article-title":"Targeting EphA3 inhibits cancer growth by disrupting the tumor stromal microenvironment","volume":"74","author":"Vail","year":"2014","journal-title":"Cancer Res."},{"key":"10.1016\/j.isci.2026.117699_bib53","doi-asserted-by":"crossref","first-page":"4871","DOI":"10.1073\/pnas.0305627101","article-title":"Stable association between strains of Mycobacterium tuberculosis and their human host populations","volume":"101","author":"Hirsh","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2026.117699_bib54","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/imr.12264","article-title":"Co-evolution of Mycobacterium tuberculosis and Homo sapiens","volume":"264","author":"Brites","year":"2015","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.isci.2026.117699_bib55","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.84394","article-title":"Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture","volume":"13","author":"Schurz","year":"2024","journal-title":"eLife"},{"key":"10.1016\/j.isci.2026.117699_bib56","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2022.105352","article-title":"Genetic architecture of tuberculosis susceptibility: A comprehensive research synopsis, meta-analyses, and epidemiological evidence","volume":"104","author":"Jiao","year":"2022","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.isci.2026.117699_bib57","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1038\/ng.3704","article-title":"Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages","volume":"48","author":"Stucki","year":"2016","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib58","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117699_bib59","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117699_bib60","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117699_bib61","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117699_bib62","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.isci.2026.117699_bib63","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1111\/2041-210X.12410","article-title":"Popart: full-feature software for haplotype network construction","volume":"6","author":"Leigh","year":"2015","journal-title":"Methods Ecol. Evol."},{"key":"10.1016\/j.isci.2026.117699_bib64","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"10.1016\/j.isci.2026.117699_bib65","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1038\/ng.3656","article-title":"Next-generation genotype imputation service and methods","volume":"48","author":"Das","year":"2016","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib66","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13029-019-0072-6","article-title":"IPCAPS: an R package for iterative pruning to capture population structure","volume":"14","author":"Chaichoompu","year":"2019","journal-title":"Source Code Biol. Med."},{"key":"10.1016\/j.isci.2026.117699_bib67","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.isci.2026.117699_bib68","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nmeth.1681","article-title":"FaST linear mixed models for genome-wide association studies","volume":"8","author":"Lippert","year":"2011","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117699_bib69","series-title":"Definitions and Reporting Framework for Tuberculosis","year":"2013"},{"key":"10.1016\/j.isci.2026.117699_bib70","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-29986-3","article-title":"Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates","volume":"8","author":"Palittapongarnpim","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2026.117699_bib71","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117699_bib72","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/s13073-020-00817-3","article-title":"Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies","volume":"12","author":"Napier","year":"2020","journal-title":"Genome Med."},{"key":"10.1016\/j.isci.2026.117699_bib73","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117699_bib74","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.02692-18","article-title":"Genomewide Association Study Confirming the Association of NAT2 with Susceptibility to Antituberculosis Drug-Induced Liver Injury in Thai Patients","volume":"63","author":"Suvichapanich","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.isci.2026.117699_bib75","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/jhg.2016.10","article-title":"NAT2 variants are associated with drug-induced liver injury caused by anti-tuberculosis drugs in Indonesian patients with tuberculosis","volume":"61","author":"Yuliwulandari","year":"2016","journal-title":"J. Hum. Genet."},{"key":"10.1016\/j.isci.2026.117699_bib76","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s41439-020-0101-7","article-title":"Haplotype-specific PCR for NAT2 diplotyping","volume":"7","author":"Wichukchinda","year":"2020","journal-title":"Hum. Genome Var."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226030804?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226030804?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T21:46:54Z","timestamp":1794347214000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004226030804"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":76,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["S2589004226030804"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2026.117699","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Association between human genomes and mycobacterial genomes contributes to severity and transmissibility of pulmonary tuberculosis","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2026.117699","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"117699"}}