{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:29:33Z","timestamp":1787567373649,"version":"build-2736575974"},"reference-count":116,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"crossref","award":["CRSII5_177163"],"award-info":[{"award-number":["CRSII5_177163"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"award":["CRSII5_177163"],"award-info":[{"award-number":["CRSII5_177163"]}],"id":[{"id":"https:\/\/ror.org\/00yjd3n13","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"crossref","award":["CRSII5_213514"],"award-info":[{"award-number":["CRSII5_213514"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"award":["CRSII5_213514"],"award-info":[{"award-number":["CRSII5_213514"]}],"id":[{"id":"https:\/\/ror.org\/00yjd3n13","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"crossref","award":["10001893"],"award-info":[{"award-number":["10001893"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"award":["10001893"],"award-info":[{"award-number":["10001893"]}],"id":[{"id":"https:\/\/ror.org\/00yjd3n13","id-type":"ROR","asserted-by":"publisher"}]},{"name":"European Research Council","award":["883582"],"award-info":[{"award-number":["883582"]}]},{"award":["883582"],"award-info":[{"award-number":["883582"]}],"id":[{"id":"https:\/\/ror.org\/0472cxd90","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"crossref","award":["10000213"],"award-info":[{"award-number":["10000213"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"award":["10000213"],"award-info":[{"award-number":["10000213"]}],"id":[{"id":"https:\/\/ror.org\/00yjd3n13","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    Infectious diseases have affected humanity for millennia and are among the strongest selective forces. Tuberculosis (TB) is an ancient disease, caused by the human-adapted members of the\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    complex (MTBC). The outcome of TB infection and disease is highly variable, and co-evolution between human populations and MTBC strains may account for some of this variability. Particular human genetic ancestries have been associated with higher susceptibility to TB, but sociodemographic aspects of the disease can confound such associations. Here, we studied 1000 TB patients from Dar es Salaam, Tanzania, together with their respective MTBC isolates, by combining human and bacterial genomics with clinical data. We found that the genetic background of the TB patient population was strongly influenced by migrations of Bantu-speaking populations from West Africa, which contrasts with the corresponding MTBC genotypes that were mainly introduced from outside Africa. These findings suggest a recent evolutionary history of co-existence between the human and MTBC populations in Dar es Salaam. We detected no evidence of an effect of human genetic ancestry, or MTBC phylogenetic diversity alone, nor their interaction, on TB disease severity. There was also no evidence of an association between human variation genome-wide and TB disease severity. Treatment-seeking, social, and environmental factors are likely to be the main determinants of disease severity at the point of care in this patient population.\n                  <\/jats:p>","DOI":"10.7554\/elife.103533","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T12:25:32Z","timestamp":1736166332000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.103533","source":"Crossref","is-referenced-by-count":0,"title":["Human genetic ancestry, Mycobacterium tuberculosis diversity, and tuberculosis disease severity in Dar es Salaam, Tanzania"],"prefix":"10.7554","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3864-1503","authenticated-orcid":true,"given":"Michaela","family":"Zwyer","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Zhi Ming","family":"Xu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/002n09z45","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Institute of Bioinformatics","place":["Lausanne, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s376052","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","place":["Lausanne, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Amanda","family":"Ross","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Jerry","family":"Hella","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04js17g72","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Intervention and Clinical Trials, Ifakara Health Institute","place":["Ifakara, United Republic of Tanzania"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Mohamed","family":"Sasamalo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04js17g72","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Intervention and Clinical Trials, Ifakara Health Institute","place":["Ifakara, United Republic of Tanzania"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Maxime","family":"Rotival","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0495fxg12","id-type":"ROR","asserted-by":"publisher"}],"name":"Human Evolutionary Genetics Unit, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9","place":["Paris, France"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Hellen Charles","family":"Hiza","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Liliana K","family":"Rutaihwa","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05tcsqz68","id-type":"ROR","asserted-by":"publisher"}],"name":"FIND, Foundation for Innovative New Diagnostics","place":["Geneva, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"resources","vocabulary":"credit"}]},{"given":"Sonia","family":"Borrell","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Klaus","family":"Reither","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8240-939X","authenticated-orcid":true,"given":"Jacques","family":"Fellay","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/002n09z45","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Institute of Bioinformatics","place":["Lausanne, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s376052","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","place":["Lausanne, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/05a353079","id-type":"ROR","asserted-by":"publisher"}],"name":"Precision Medicine Unit, Lausanne University Hospital and University of Lausanne","place":["Lausanne, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2949-9557","authenticated-orcid":true,"given":"Damien","family":"Portevin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Lluis","family":"Quintana-Murci","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0495fxg12","id-type":"ROR","asserted-by":"publisher"}],"name":"Human Evolutionary Genetics Unit, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9","place":["Paris, France"]},{"id":[{"id":"https:\/\/ror.org\/04ex24z53","id-type":"ROR","asserted-by":"publisher"}],"name":"Chair of Human Genomics and Evolution, Coll\u00e8ge de France","place":["Paris, France"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7783-9048","authenticated-orcid":true,"given":"Sebastien","family":"Gagneux","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8090-2287","authenticated-orcid":true,"given":"Daniela","family":"Brites","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03adhka07","id-type":"ROR","asserted-by":"publisher"}],"name":"Swiss Tropical and Public Health Institute","place":["Allschwil, Switzerland"]},{"id":[{"id":"https:\/\/ror.org\/02s6k3f65","id-type":"ROR","asserted-by":"publisher"}],"name":"University of Basel","place":["Basel, Switzerland"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2026,3,24]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.tube.2010.08.004","type":"journal-article","article-title":"Mycobacterium tuberculosis strains with the Beijing genotype demonstrate variability in virulence associated with transmission","volume":"90","author":"Aguilar L","year":"2010","journal-title":"Tuberculosis"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"3347","DOI":"10.3748\/wjg.v24.i30.3347","type":"journal-article","article-title":"Host genetic factors affecting hepatitis B infection outcomes: Insights from genome-wide association studies","volume":"24","author":"Akcay","year":"2018","journal-title":"World Journal of Gastroenterology"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","type":"journal-article","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Research"},{"key":"bib4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-246","type":"journal-article","article-title":"Enhancements to the ADMIXTURE algorithm for individual ancestry estimation","volume":"12","author":"Alexander","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"bib5","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1164\/arrd.1960.81.6.839","type":"journal-article","article-title":"The after-history of pulmonary tuberculosis: VI. the first fifteen years following diagnosis","volume":"81","author":"Alling","year":"1960","journal-title":"The American Review of Respiratory Disease"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","type":"journal-article","article-title":"A global reference for human genetic variation","volume":"526","author":"Altshuler","year":"2015","journal-title":"Nature"},{"key":"bib7","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.99062","type":"journal-article","article-title":"Soluble immune mediators orchestrate protective in vitro granulomatous responses across Mycobacterium tuberculosis complex lineages","volume":"13","author":"Arbu\u00e9s","year":"2025","journal-title":"eLife"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.ijid.2018.05.014","type":"journal-article","article-title":"Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa","volume":"73","author":"Asare","year":"2018","journal-title":"International Journal of Infectious Diseases"},{"key":"bib9","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2022.100151","type":"journal-article","article-title":"Higher native Peruvian genetic ancestry proportion is associated with tuberculosis progression risk","volume":"2","author":"Asgari","year":"2022","journal-title":"Cell Genomics"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.1002\/mco2.250","type":"journal-article","article-title":"Genome\u2010wide association study of tuberculosis in the western Chinese Han and Tibetan population","volume":"4","author":"Bai","year":"2023","journal-title":"MedComm"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"1568","DOI":"10.3201\/eid1009.040046","type":"journal-article","article-title":"Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis","volume":"10","author":"Baker","year":"2004","journal-title":"Emerging Infectious Diseases"},{"key":"bib12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13480-z","type":"journal-article","article-title":"Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania","volume":"10","author":"Band","year":"2019","journal-title":"Nature Communications"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1001\/archinte.167.4.335","type":"journal-article","article-title":"Risk of tuberculosis from exposure to tobacco smoke: a systematic review and meta-analysis","volume":"167","author":"Bates","year":"2007","journal-title":"Archives of Internal Medicine"},{"key":"bib14","doi-asserted-by":"publisher","DOI":"10.1126\/science.aay5012","type":"journal-article","article-title":"Insights into human genetic variation and population history from 929 diverse genomes","volume":"367","author":"Bergstr\u00f6m","year":"2020","journal-title":"Science"},{"key":"bib15","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abq2616","type":"journal-article","article-title":"Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture","volume":"9","author":"Bird","year":"2023","journal-title":"Science Advances"},{"key":"bib16","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aau8714","type":"journal-article","article-title":"Tuberculosis and impaired IL-23-dependent IFN-\u03b3 immunity in humans homozygous for a common TYK2 missense variant","volume":"3","author":"Boisson-Dupuis","year":"2018","journal-title":"Science Immunology"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","type":"journal-article","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1038\/s41586-023-05754-w","type":"journal-article","article-title":"Entwined African and Asian genetic roots of medieval peoples of the Swahili coast","volume":"615","author":"Brielle","year":"2023","journal-title":"Nature"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1111\/imr.12264","type":"journal-article","article-title":"Co-evolution of Mycobacterium tuberculosis and Homo sapiens","volume":"264","author":"Brites","year":"2015","journal-title":"Immunological Reviews"},{"key":"bib20","type":"software","article-title":"Picard toolkit","volume-title":"Github","author":"broadinstitute","year":"2019","unstructured":"broadinstitute. 2019. Picard toolkit. Github. 1.8.x. https:\/\/broadinstitute.github.io\/picard\/."},{"key":"bib21","type":"software","article-title":"Picard","volume-title":"Github","author":"broadinstitute","year":"2025","unstructured":"broadinstitute. 2025. Picard. Github. fc0b084. https:\/\/github.com\/broadinstitute\/picard."},{"key":"bib22","volume-title":"The History and Geography of Human Genes","author":"Cavalli-Sforza","year":"1994","type":"book"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"205","DOI":"10.5603\/ARM.2018.0032","type":"journal-article","article-title":"Chest X ray score (Timika score): an useful adjunct to predict treatment outcome in tuberculosis","volume":"86","author":"Chakraborthy","year":"2018","journal-title":"Advances in Respiratory Medicine"},{"key":"bib24","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8","type":"journal-article","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nrg3114","type":"journal-article","article-title":"Human genetic susceptibility to infectious disease","volume":"13","author":"Chapman","year":"2012","journal-title":"Nature Reviews Genetics"},{"key":"bib26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200632","type":"journal-article","article-title":"Geospatial distribution of Mycobacterium tuberculosis genotypes in Africa","volume":"13","author":"Chihota","year":"2018","journal-title":"PLOS ONE"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/cid\/cir788","type":"journal-article","article-title":"Relationship between Mycobacterium tuberculosis phylogenetic lineage and clinical site of tuberculosis","volume":"54","author":"Click","year":"2012","journal-title":"Clinical Infectious Diseases"},{"key":"bib28","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms5812","type":"journal-article","article-title":"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains","volume":"5","author":"Coll","year":"2014","journal-title":"Nature Communications"},{"key":"bib29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000600","type":"journal-article","article-title":"The past and future of tuberculosis research","volume":"5","author":"Comas","year":"2009","journal-title":"PLOS Pathogens"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/ng.590","type":"journal-article","article-title":"Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved","volume":"42","author":"Comas","year":"2010","journal-title":"Nature Genetics"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"3260","DOI":"10.1016\/j.cub.2015.10.061","type":"journal-article","article-title":"Population genomics of Mycobacterium tuberculosis in ethiopia contradicts the virgin soil hypothesis for human tuberculosis in Sub-Saharan Africa","volume":"25","author":"Comas","year":"2015","journal-title":"Current Biology"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"e43","DOI":"10.1016\/j.ddmec.2010.09.004","type":"journal-article","article-title":"Does M. tuberculosis genomic diversity explain disease diversity?","volume":"7","author":"Coscolla","year":"2010","journal-title":"Drug Discovery Today. Disease Mechanisms"},{"key":"bib33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003468","type":"journal-article","article-title":"Ethnic variation in inflammatory profile in tuberculosis","volume":"9","author":"Coussens","year":"2013","journal-title":"PLOS Pathogens"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1016\/j.tube.2014.03.012","type":"journal-article","article-title":"The role of ancestry in TB susceptibility of an admixed South African population","volume":"94","author":"Daya","year":"2014","journal-title":"Tuberculosis"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1086\/591504","type":"journal-article","article-title":"Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia","volume":"198","author":"de Jong","year":"2008","journal-title":"The Journal of Infectious Diseases"},{"key":"bib36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0000744","type":"journal-article","article-title":"Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa","volume":"4","author":"de Jong","year":"2010","journal-title":"PLOS Neglected Tropical Diseases"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1016\/S1473-3099(09)70282-8","type":"journal-article","article-title":"Tuberculosis and diabetes mellitus: convergence of two epidemics","volume":"9","author":"Dooley","year":"2009","journal-title":"The Lancet. Infectious Diseases"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1111\/j.1365-2249.2004.02551.x","type":"journal-article","article-title":"Correlation of virulence, lung pathology, bacterial load and delayed type hypersensitivity responses after infection with different Mycobacterium tuberculosis genotypes in a BALB\/c mouse model","volume":"137","author":"Dormans","year":"2004","journal-title":"Clinical and Experimental Immunology"},{"key":"bib39","doi-asserted-by":"publisher","DOI":"10.1101\/2023.03.14.23287284","type":"preprint","article-title":"The effect of M. tuberculosis lineage on clinical phenotype","volume-title":"medRxiv","author":"Du","year":"2023"},{"key":"bib40","doi-asserted-by":"publisher","first-page":"1266","DOI":"10.1093\/bioinformatics\/btu014","type":"journal-article","article-title":"Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)","volume":"30","author":"Durbin","year":"2014","journal-title":"Bioinformatics"},{"key":"bib41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003318","type":"journal-article","article-title":"HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis","volume":"9","author":"Fenner","year":"2013","journal-title":"PLOS Genetics"},{"key":"bib42","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac209","type":"journal-article","article-title":"Demographic and selection histories of populations across the sahel\/savannah belt","volume":"39","author":"Fortes-Lima","year":"2022","journal-title":"Molecular Biology and Evolution"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"e830","DOI":"10.1093\/cid\/ciaa1402","type":"journal-article","article-title":"Subclinical tuberculosis disease-a review and analysis of prevalence surveys to inform definitions, burden, associations, and screening methodology","volume":"73","author":"Frascella","year":"2021","journal-title":"Clinical Infectious Diseases"},{"key":"bib44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002355","type":"journal-article","article-title":"Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution","volume":"7","author":"Fumagalli","year":"2011","journal-title":"PLOS Genetics"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1073\/pnas.0511240103","type":"journal-article","article-title":"Variable host-pathogen compatibility in Mycobacterium tuberculosis","volume":"103","author":"Gagneux","year":"2006","journal-title":"PNAS"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1038\/nrmicro.2018.8","type":"journal-article","article-title":"Ecology and evolution of Mycobacterium tuberculosis","volume":"16","author":"Gagneux","year":"2018","journal-title":"Nature Reviews. Microbiology"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1534\/genetics.107.077495","type":"journal-article","article-title":"Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data","volume":"177","author":"Garrigan","year":"2007","journal-title":"Genetics"},{"key":"bib48","doi-asserted-by":"publisher","first-page":"2113","DOI":"10.1038\/s41564-024-01758-y","type":"journal-article","article-title":"Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry","volume":"9","author":"Gr\u00f6schel","year":"2024","journal-title":"Nature Microbiology"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"560","DOI":"10.3201\/eid3003.231466","type":"journal-article","article-title":"Newly identified mycobacterium africanum lineage 10, Central Africa","volume":"30","author":"Guyeux","year":"2024","journal-title":"Emerging Infectious Diseases"},{"key":"bib50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006976","type":"journal-article","article-title":"Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations","volume":"13","author":"Hollfelder","year":"2017","journal-title":"PLOS Genetics"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/s41588-018-0117-9","type":"journal-article","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":"Nature Genetics"},{"key":"bib52","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00216-2017","type":"journal-article","article-title":"Alcohol consumption as a risk factor for tuberculosis: meta-analyses and burden of disease","volume":"50","author":"Imtiaz","year":"2017","journal-title":"The European Respiratory Journal"},{"key":"bib53","type":"software","article-title":"SeqPrep","volume-title":"Github","author":"John","year":"2011","unstructured":"John JS. 2011. SeqPrep. Github. 575507b. https:\/\/github.com\/jstjohn\/SeqPrep."},{"key":"bib54","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.129684.111","type":"journal-article","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Research"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"142","DOI":"10.5588\/ijtld.23.0254","type":"journal-article","article-title":"Outcomes for people with TB by disease severity at presentation","volume":"28","author":"Leavitt","year":"2024","journal-title":"The International Journal of Tuberculosis and Lung Disease"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/j.cell.2013.08.034","type":"journal-article","article-title":"Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway","volume":"155","author":"Lee","year":"2013","journal-title":"Cell"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","type":"journal-article","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","type":"journal-article","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"bib59","type":"web-resource","article-title":"Dar es Salaam, Tanzania Metro Area Population (1950\u20132026). Macrotrends","author":"Llc","year":"2026","unstructured":"Llc M. 2026. Dar es Salaam, Tanzania Metro Area Population (1950\u20132026). Macrotrends. https:\/\/www.macrotrends.net\/global-metrics\/cities\/22894\/dar-es-salaam\/population [Accessed February 23, 2026]."},{"key":"bib60","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1038\/ng.3679","type":"journal-article","article-title":"Reference-based phasing using the haplotype reference consortium panel","volume":"48","author":"Loh","year":"2016","journal-title":"Nature Genetics"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1046\/j.1365-2249.2003.02171.x","type":"journal-article","article-title":"A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes","volume":"133","author":"L\u00f3pez","year":"2003","journal-title":"Clinical and Experimental Immunology"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/s0732-8893(99)00007-3","type":"journal-article","article-title":"Malnutrition in tuberculosis","volume":"34","author":"Macallan","year":"1999","journal-title":"Diagnostic Microbiology and Infectious Disease"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nature18964","type":"journal-article","article-title":"The simons genome diversity project: 300 genomes from 142 diverse populations","volume":"538","author":"Mallick","year":"2016","journal-title":"Nature"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"5511","DOI":"10.1128\/IAI.72.9.5511-5514.2004","type":"journal-article","article-title":"Differential monocyte activation underlies strain-specific Mycobacterium tuberculosis pathogenesis","volume":"72","author":"Manca","year":"2004","journal-title":"Infection and Immunity"},{"key":"bib65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008728","type":"journal-article","article-title":"Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution?","volume":"16","author":"McHenry","year":"2020","journal-title":"PLOS Genetics"},{"key":"bib66","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2020.104204","type":"journal-article","article-title":"Genetics and evolution of tuberculosis pathogenesis: new perspectives and approaches","volume":"81","author":"McHenry","year":"2020","journal-title":"Infection, Genetics and Evolution"},{"key":"bib67","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10111487","type":"journal-article","article-title":"Interaction between M. tuberculosis lineage and human genetic variants reveals novel pathway associations with severity of TB","volume":"10","author":"McHenry","year":"2021","journal-title":"Pathogens"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","type":"journal-article","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Research"},{"key":"bib69","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2164-8","type":"journal-article","article-title":"Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity","volume":"19","author":"Menardo","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"bib70","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.28318.2","type":"journal-article","article-title":"Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim","volume":"10","author":"Menardo","year":"2021","journal-title":"F1000Research"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.vetmic.2005.11.035","type":"journal-article","article-title":"Wildlife tuberculosis in South African conservation areas: implications and challenges","volume":"112","author":"Michel","year":"2006","journal-title":"Veterinary Microbiology"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1093\/bfgp\/elq037","type":"journal-article","article-title":"Genome-wide association studies and susceptibility to infectious diseases","volume":"10","author":"Newport","year":"2011","journal-title":"Briefings in Functional Genomics"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"2076","DOI":"10.1093\/bioinformatics\/btu168","type":"journal-article","article-title":"VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants","volume":"30","author":"Obenchain","year":"2014","journal-title":"Bioinformatics"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1016\/j.meegid.2011.10.005","type":"journal-article","article-title":"\u201cLethal\u201d combination of Mycobacterium tuberculosis Beijing genotype and human CD209 -336G allele in Russian male population","volume":"12","author":"Ogarkov","year":"2012","journal-title":"Infection, Genetics and Evolution"},{"key":"bib75","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4163","type":"journal-article","article-title":"The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists","volume":"5","author":"Patin","year":"2014","journal-title":"Nature Communications"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1126\/science.aal1988","type":"journal-article","article-title":"Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America","volume":"356","author":"Patin","year":"2017","journal-title":"Science"},{"key":"bib77","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evad054","type":"journal-article","article-title":"Evolutionary genetics and admixture in african populations","volume":"15","author":"Pfennig","year":"2023","journal-title":"Genome Biology and Evolution"},{"key":"bib78","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36282-w","type":"journal-article","article-title":"Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease","volume":"14","author":"Phelan","year":"2023","journal-title":"Nature Communications"},{"key":"bib79","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2350-13-5","type":"journal-article","article-title":"A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians","volume":"13","author":"Png","year":"2012","journal-title":"BMC Medical Genetics"},{"key":"bib80","type":"software","article-title":"Pysam","volume-title":"Github","author":"pysam-developers","year":"2026","unstructured":"pysam-developers. 2026. Pysam. Github. 7929385. https:\/\/github.com\/pysam-developers\/pysam."},{"key":"bib81","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1136\/thx.2010.136242","type":"journal-article","article-title":"A simple, valid, numerical score for grading chest x-ray severity in adult smear-positive pulmonary tuberculosis","volume":"65","author":"Ralph","year":"2010","journal-title":"Thorax"},{"key":"bib82","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1016\/j.gde.2006.10.008","type":"journal-article","article-title":"African human diversity, origins and migrations","volume":"16","author":"Reed","year":"2006","journal-title":"Current Opinion in Genetics & Development"},{"key":"bib83","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1128\/JCM.02142-08","type":"journal-article","article-title":"Major Mycobacterium tuberculosis lineages associate with patient country of origin","volume":"47","author":"Reed","year":"2009","journal-title":"Journal of Clinical Microbiology"},{"key":"bib84","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2019.00112","type":"journal-article","article-title":"Multiple introductions of Mycobacterium tuberculosis lineage 2\u2013Beijing into africa over centuries","volume":"7","author":"Rutaihwa","year":"2019","journal-title":"Frontiers in Ecology and Evolution"},{"key":"bib85","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1126\/science.1227721","type":"journal-article","article-title":"Genomic variation in seven Khoe-San groups reveals adaptation and complex African history","volume":"338","author":"Schlebusch","year":"2012","journal-title":"Science"},{"key":"bib86","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1056\/NEJM198903023200901","type":"journal-article","article-title":"A prospective study of the risk of tuberculosis among intravenous drug users with human immunodeficiency virus infection","volume":"320","author":"Selwyn","year":"1989","journal-title":"The New England Journal of Medicine"},{"key":"bib87","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/molbev\/msz224","type":"journal-article","article-title":"Along the indian ocean coast: genomic variation in mozambique provides new insights into the bantu expansion","volume":"37","author":"Semo","year":"2020","journal-title":"Molecular Biology and Evolution"},{"key":"bib88","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22207-y","type":"journal-article","article-title":"Genetic substructure and complex demographic history of South African Bantu speakers","volume":"12","author":"Sengupta","year":"2021","journal-title":"Nature Communications"},{"key":"bib89","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010490","type":"journal-article","article-title":"Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns","volume":"18","author":"Silva","year":"2022","journal-title":"PLOS Pathogens"},{"key":"bib90","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1136\/bmj.307.6907.759","type":"journal-article","article-title":"Tuberculosis and poverty","volume":"307","author":"Spence","year":"1993","journal-title":"BMJ"},{"key":"bib91","doi-asserted-by":"publisher","first-page":"e570","DOI":"10.1016\/S2666-5247(24)00022-3","type":"journal-article","article-title":"Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains","volume":"5","author":"Stanley","year":"2024","journal-title":"The Lancet. Microbe"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/s40142-017-0130-9","type":"journal-article","article-title":"Genomics of human pulmonary tuberculosis: from genes to pathways","volume":"5","author":"Stein","year":"2017","journal-title":"Current Genetic Medicine Reports"},{"key":"bib93","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-881","type":"journal-article","article-title":"KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes","volume":"15","author":"Steiner","year":"2014","journal-title":"BMC Genomics"},{"key":"bib94","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1038\/ng.3704","type":"journal-article","article-title":"Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages","volume":"48","author":"Stucki","year":"2016","journal-title":"Nature Genetics"},{"key":"bib95","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1146\/annurev.genom.4.070802.110226","type":"journal-article","article-title":"Patterns of human genetic diversity: implications for human evolutionary history and disease","volume":"4","author":"Tishkoff","year":"2003","journal-title":"Annual Review of Genomics and Human Genetics"},{"key":"bib96","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1126\/science.1172257","type":"journal-article","article-title":"The genetic structure and history of Africans and African Americans","volume":"324","author":"Tishkoff","year":"2009","journal-title":"Science"},{"key":"bib97","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1007\/s00438-017-1296-2","type":"journal-article","article-title":"Population structure and infectious disease risk in southern Africa","volume":"292","author":"Uren","year":"2017","journal-title":"Molecular Genetics and Genomics"},{"key":"bib98","type":"software","article-title":"Compositions: compositional data analysis 2022","volume-title":"CRAN","author":"van den Boogaart","year":"2022","unstructured":"van den Boogaart KG, Tolosana-Delgado R, Bren M. 2022. Compositions: compositional data analysis 2022. CRAN. 2.0-9. https:\/\/cran.r-project.org\/web\/packages\/compositions\/index.html."},{"key":"bib99","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaz0183","type":"journal-article","article-title":"Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa","volume":"6","author":"Wang","year":"2020","journal-title":"Science Advances"},{"key":"bib100","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1080\/00365540701558698","type":"journal-article","article-title":"TBscore: Signs and symptoms from tuberculosis patients in a low-resource setting have predictive value and may be used to assess clinical course","volume":"40","author":"Wejse","year":"2008","journal-title":"Scandinavian Journal of Infectious Diseases"},{"key":"bib101","type":"report","volume-title":"Global Tuberculosis Report","author":"WHO","year":"2023","unstructured":"WHO. 2023. World Health Organization. Global Tuberculosis Report. https:\/\/www.who.int\/teams\/global-programme-on-tuberculosis-and-lung-health\/tb-reports\/global-tuberculosis-report-2023."},{"key":"bib102","doi-asserted-by":"publisher","DOI":"10.1186\/s12916-018-1180-x","type":"journal-article","article-title":"Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis","volume":"16","author":"Wiens","year":"2018","journal-title":"BMC Medicine"},{"key":"bib103","type":"web-resource","article-title":"Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance","author":"World Health Organization","year":"2021","unstructured":"World Health Organization. 2021. Catalogue of mutations in Mycobacterium tuberculosis complex and their association with drug resistance. https:\/\/www.who.int\/publications\/i\/item\/9789240028173 [Accessed June 25, 2021]."},{"key":"bib104","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009628","type":"journal-article","article-title":"Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations","volume":"18","author":"Xu","year":"2022","journal-title":"PLOS Computational Biology"},{"key":"bib105","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-025-02164-x","type":"journal-article","article-title":"Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania","volume":"18","author":"Xu","year":"2025","journal-title":"BMC Medical Genomics"},{"key":"bib106","first-page":"7","type":"journal-article","article-title":"Diagnostic checking in regression relationships","volume":"2","author":"Zeileis","year":"2002","journal-title":"R News"},{"key":"bib107","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06539-w","type":"journal-article","article-title":"Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese","volume":"9","author":"Zheng","year":"2018","journal-title":"Nature Communications"},{"key":"bib108","doi-asserted-by":"publisher","DOI":"10.12688\/openreseurope.14029.2","type":"journal-article","article-title":"A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics","volume":"1","author":"Zwyer","year":"2021","journal-title":"Open Research Europe"},{"key":"bib109","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010893","type":"journal-article","article-title":"Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania","volume":"19","author":"Zwyer","year":"2023","journal-title":"PLOS Pathogens"},{"key":"bib110","type":"software","article-title":"TB-dar_mtb","volume-title":"Software Heritage","author":"Zwyer","year":"2026","unstructured":"Zwyer M. 2026. TB-dar_mtb. Software Heritage. swh:1:rev:7df5cba38dfee39493433d209a5dd41908bc5c1d. https:\/\/archive.softwareheritage.org\/swh:1:dir:d3e82d79496f15682ee1d98d4f9a15275fccbdf8;origin=https:\/\/github.com\/mzwyer\/TB-Dar_Mtb;visit=swh:1:snp:cca76154ca9ac26628c945fcc74f6d99694f6880;anchor=swh:1:rev:7df5cba38dfee39493433d209a5dd41908bc5c1d."},{"key":"dataset1","type":"dataset","article-title":"Tuberculosis epidemic in Dar es Salaam, Tanzania","volume-title":"EBI European Nucleotide Archive","author":"Zwyer","year":"2022","unstructured":"Zwyer M, Hella J, Sasamalo M, Reither K, Fellay J, Portevin D, Gagneux S, Brites D. 2022. Tuberculosis epidemic in Dar es Salaam, Tanzania. EBI European Nucleotide Archive. https:\/\/www.ebi.ac.uk\/ena\/browser\/view\/PRJEB49562. PRJEB49562."},{"key":"dataset2","type":"dataset","article-title":"TB-DAR Whole Genome Sequencing Study","volume-title":"European Genome-phenome Archive","author":"Zwyer","year":"2021","unstructured":"Zwyer M, Hella J, Sasamalo M, Reither K, Fellay J, Portevin D, Gagneux S, Brites D. 2021. TB-DAR Whole Genome Sequencing Study. European Genome-phenome Archive. https:\/\/ega-archive.org\/datasets\/EGAD00001008400. EGAD00001008400."},{"key":"dataset3","type":"dataset","article-title":"TB-DAR Genotyping Study","volume-title":"European Genome-phenome Archive","author":"Zwyer","year":"2023","unstructured":"Zwyer M, Hella J, Sasamalo M, Reither K, Fellay J, Portevin D, Gagneux S, Brites D. 2023. TB-DAR Genotyping Study. European Genome-phenome Archive. https:\/\/ega-archive.org\/datasets\/EGAD00010002507. EGAD00010002507."},{"key":"dataset4","type":"dataset","article-title":"TB-DAR Genotyping Study","volume-title":"European Genome-phenome Archive","author":"Zwyer","year":"2023","unstructured":"Zwyer M, Hella J, Sasamalo M, Reither K, Fellay J, Portevin D, Gagneux S, Brites D. 2023. TB-DAR Genotyping Study. European Genome-phenome Archive. https:\/\/ega-archive.org\/studies\/EGAS00001007216. EGAS00001007216."},{"key":"dataset5","type":"dataset","article-title":"TB-DAR Whole Genome Sequencing Study","volume-title":"European Genome-phenome Archive","author":"Zwyer","year":"2021","unstructured":"Zwyer M, Hella J, Sasamalo M, Reither K, Fellay J, Portevin D, Gagneux S, Brites D. 2021. TB-DAR Whole Genome Sequencing Study. European Genome-phenome Archive. https:\/\/ega-archive.org\/studies\/EGAS00001005850. EGAS00001005850."},{"key":"dataset6","type":"dataset","article-title":"Biogeography of MTB lineage 1 and 3","volume-title":"EBI European Nucleotide Archive","author":"Menardo","year":"2021","unstructured":"Menardo F, Brites D, Gagneux S. 2021. Biogeography of MTB lineage 1 and 3. EBI European Nucleotide Archive. https:\/\/www.ebi.ac.uk\/ena\/browser\/view\/PRJNA670836. PRJNA670836."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/103533\/elife-103533-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/103533\/elife-103533-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/103533","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:07:29Z","timestamp":1787562449000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/103533"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,24]]},"references-count":116,"alternative-id":["10.7554\/eLife.103533"],"URL":"https:\/\/doi.org\/10.7554\/elife.103533","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.08.10.607244","asserted-by":"subject"}],"references":[{"id-type":"accession","id":"PRJNA670836","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.103533.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.103533.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.103533.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"accession","id":"PRJEB49562","asserted-by":"subject"},{"id-type":"accession","id":"EGAD00001008400","asserted-by":"subject"},{"id-type":"accession","id":"EGAD00010002507","asserted-by":"subject"},{"id-type":"accession","id":"EGAS00001007216","asserted-by":"subject"},{"id-type":"accession","id":"EGAS00001005850","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:d3e82d79496f15682ee1d98d4f9a15275fccbdf8;origin=https:\/\/github.com\/mzwyer\/TB-Dar_Mtb;visit=swh:1:snp:cca76154ca9ac26628c945fcc74f6d99694f6880;anchor=swh:1:rev:7df5cba38dfee39493433d209a5dd41908bc5c1d","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,24]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP103533"}}