{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:02:02Z","timestamp":1785427322310,"version":"3.56.0"},"posted":{"date-parts":[[2026,4,4]]},"group-title":"Microbiology","reference-count":42,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T00:00:00Z","timestamp":1775260800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["75N93019C00071"],"award-info":[{"award-number":["75N93019C00071"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01AI134195"],"award-info":[{"award-number":["R01AI134195"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Whole genome sequencing of\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (Mtb) populations from clinical samples has increasingly identified genes undergoing selection within and between hosts that drive differential infection and treatment outcomes. However, the intrahost Mtb mutational landscape\u2014especially in the context of human immunodeficiency virus coinfection and antiretroviral therapy (ART)\u2014remains less clear, as do the potential impacts of such mutations on Mtb infection dynamics. Here, we performed whole genome sequencing of Mtb populations isolated from 477 infected tissues across 20 non-human primates, including animals co-infected with simian immunodeficiency virus (SIV) with or without virological suppression by ART. We identified 116 mutations that emerged during infection, including those that are overrepresented within individual tissues and a subset that are shared across tissues during Mtb dissemination. We further find differential mutation trajectories across treatment groups, with higher mutation rate and bacterial outgrowth in SIV-infected hosts and increased prevalence of oxidative damage-associated mutations in coinfected animals on ART. Finally, we demonstrate a common pattern of mutation in Mtb lipid metabolism and polyketide synthase genes and identify a subset of NHP-derived mutations that have also independently arisen in human clinical isolates. Together, our population-based sequencing uncovers Mtb diversification during early infection, captures discrete bacterial dissemination events and infers differential immune pressures faced by Mtb in the setting of SIV-Mtb coinfection and ART suppression.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Importance<\/jats:title>\n                  <jats:p>\n                    Tuberculosis remains a leading cause of death worldwide, especially in people living with HIV. How HIV infection and antiretroviral therapy impacts\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    (Mtb) intrahost evolution remains unclear. Using whole genome sequencing from hundreds of infected tissues from non-human primates, we find that simian immunodeficiency virus co-infected hosts and those receiving antiretroviral therapy exact different immune pressures on Mtb leading to different mutation rates and types of DNA damage that are incurred. Mtb mutations were enriched in genes involved in lipid metabolisms and some of these are also seen in human TB strains. This work highlights the role of immune pressure to alter bacterial pathways that may enable Mtb adaptation to the host.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.04.03.714442","type":"posted-content","created":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T01:50:11Z","timestamp":1775353811000},"source":"Crossref","is-referenced-by-count":0,"title":["Population-level genome sequencing reveals distinct Mycobacterium tuberculosis intrahost mutational trajectories in simian immunodeficiency virus co-infected and antiretroviral treated non-human primates"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3158-7337","authenticated-orcid":false,"given":"Michael C.","family":"Chao","sequence":"first","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Chase","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shoko","family":"Wakabayashi","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Vickers","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byron","family":"Roman","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Forrest","family":"Hopkins","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0605-5849","authenticated-orcid":false,"given":"Peter H.","family":"Culviner","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximillan G.","family":"Marin","sequence":"additional","affiliation":[{"name":"Department of Data Science, Dana-Farber Cancer Institute, Boston, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline","family":"Maiello","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States"},{"name":"Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7635-9699","authenticated-orcid":false,"given":"Collin R.","family":"Diedrich","sequence":"additional","affiliation":[{"name":"Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States"},{"name":"Department of Pediatrics, Children\u2019s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8610-2766","authenticated-orcid":false,"given":"Zandrea","family":"Ambrose","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States"},{"name":"Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5169-3714","authenticated-orcid":false,"given":"Philana Ling","family":"Lin","sequence":"additional","affiliation":[{"name":"Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States"},{"name":"Department of Pediatrics, Children\u2019s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7565-9975","authenticated-orcid":false,"given":"Sarah M.","family":"Fortune","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026070906151989000_2026.04.03.714442v2.1","unstructured":"World Health Organization. Global Tuberculosis Report 2024. https:\/\/www.who.int\/publications\/m\/item\/top-findings-and-messages-in-the-2024-report."},{"key":"2026070906151989000_2026.04.03.714442v2.2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0034156"},{"key":"2026070906151989000_2026.04.03.714442v2.3","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000238406.93249.cd"},{"key":"2026070906151989000_2026.04.03.714442v2.4","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir421"},{"key":"2026070906151989000_2026.04.03.714442v2.5","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1093\/cid\/ciae499","article-title":"Risk of Tuberculosis After Achieving HIV Virological Suppression on Antiretroviral Therapy: A Danish Nationwide Prospective Cohort Study","volume":"80","year":"2025","journal-title":"Clinical Infectious Diseases"},{"key":"2026070906151989000_2026.04.03.714442v2.6","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.128"},{"key":"2026070906151989000_2026.04.03.714442v2.7","doi-asserted-by":"crossref","unstructured":"Diedrich, C. R. et al. Antiretroviral treatment does not prevent extrapulmonary tuberculosis during SIV\/Mtb coinfection in macaques. JCI Insight 11, (2026).","DOI":"10.1172\/jci.insight.199314"},{"key":"2026070906151989000_2026.04.03.714442v2.8","doi-asserted-by":"crossref","first-page":"1007958","DOI":"10.3389\/fcimb.2022.1007958","article-title":"Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine","volume":"12","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"2026070906151989000_2026.04.03.714442v2.9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012956"},{"key":"2026070906151989000_2026.04.03.714442v2.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-025-01159-w"},{"key":"2026070906151989000_2026.04.03.714442v2.11","doi-asserted-by":"crossref","first-page":"e265","DOI":"10.1016\/S2666-5247(21)00301-3","article-title":"The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis","volume":"3","year":"2022","journal-title":"Lancet Microbe"},{"key":"2026070906151989000_2026.04.03.714442v2.12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001755"},{"key":"2026070906151989000_2026.04.03.714442v2.13","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1196-0"},{"key":"2026070906151989000_2026.04.03.714442v2.14","doi-asserted-by":"crossref","first-page":"102747","DOI":"10.1016\/j.ebiom.2020.102747","article-title":"Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment","volume":"55","year":"2020","journal-title":"EBioMedicine"},{"key":"2026070906151989000_2026.04.03.714442v2.15","doi-asserted-by":"crossref","unstructured":"Vargas, R. et al. In-host population dynamics of Mycobacterium tuberculosis complex during active disease. Elife 10, (2021).","DOI":"10.7554\/eLife.61805"},{"key":"2026070906151989000_2026.04.03.714442v2.16","doi-asserted-by":"publisher","DOI":"10.1038\/ng.811"},{"key":"2026070906151989000_2026.04.03.714442v2.17","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aba4901"},{"key":"2026070906151989000_2026.04.03.714442v2.18","doi-asserted-by":"publisher","DOI":"10.1038\/nm.4205"},{"key":"2026070906151989000_2026.04.03.714442v2.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22705-z"},{"key":"2026070906151989000_2026.04.03.714442v2.20","doi-asserted-by":"publisher","DOI":"10.1128\/mra.01232-24"},{"key":"2026070906151989000_2026.04.03.714442v2.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.7.3578"},{"key":"2026070906151989000_2026.04.03.714442v2.22","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1099\/mic.0.033621-0","article-title":"A distinct physiological role of MutY in mutation prevention in mycobacteria","volume":"156","year":"2010","journal-title":"Microbiology (Reading)"},{"key":"2026070906151989000_2026.04.03.714442v2.23","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1443"},{"key":"2026070906151989000_2026.04.03.714442v2.24","doi-asserted-by":"publisher","DOI":"10.1165\/rcmb.2010-0319OC"},{"key":"2026070906151989000_2026.04.03.714442v2.25","doi-asserted-by":"publisher","DOI":"10.1084\/jem.174.5.1209"},{"key":"2026070906151989000_2026.04.03.714442v2.26","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.tube.2010.09.006","article-title":"The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes","volume":"91","year":"2011","journal-title":"Tuberculosis (Edinb)"},{"key":"2026070906151989000_2026.04.03.714442v2.27","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAC1000"},{"key":"2026070906151989000_2026.04.03.714442v2.28","doi-asserted-by":"publisher","DOI":"10.1101\/2025.05.01.651750"},{"key":"2026070906151989000_2026.04.03.714442v2.29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010705"},{"key":"2026070906151989000_2026.04.03.714442v2.30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008413"},{"key":"2026070906151989000_2026.04.03.714442v2.31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009611"},{"key":"2026070906151989000_2026.04.03.714442v2.32","doi-asserted-by":"crossref","unstructured":"Correa-Macedo, W. et al. Alveolar macrophages from persons living with HIV show impaired epigenetic response to Mycobacterium tuberculosis. J Clin Invest 131, (2021).","DOI":"10.1172\/JCI148013"},{"key":"2026070906151989000_2026.04.03.714442v2.33","unstructured":"Simonson, A. W. et al. Intravenous BCG-mediated protection against tuberculosis requires CD4+ T cells and CD8\u03b1+ lymphocytes. J Exp Med 222, (2025)."},{"key":"2026070906151989000_2026.04.03.714442v2.34","doi-asserted-by":"crossref","unstructured":"Martin, C. J. et al. Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis. mBio 8, (2017).","DOI":"10.1128\/mBio.00312-17"},{"key":"2026070906151989000_2026.04.03.714442v2.35","doi-asserted-by":"publisher","DOI":"10.1080\/1040841X.2024.2370979"},{"key":"2026070906151989000_2026.04.03.714442v2.36","doi-asserted-by":"crossref","unstructured":"Cook, G. M. , Hards, K. , Vilch\u00e8ze, C. , Hartman, T. & Berney, M. Energetics of Respiration and Oxidative Phosphorylation in Mycobacteria. Microbiol Spectr 2, (2014).","DOI":"10.1128\/microbiolspec.MGM2-0015-2013"},{"key":"2026070906151989000_2026.04.03.714442v2.37","doi-asserted-by":"publisher","DOI":"10.3109\/10409238.2014.896859"},{"key":"2026070906151989000_2026.04.03.714442v2.38","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1038\/s41564-024-01697-8","article-title":"Propionate prevents loss of the PDIM virulence lipid in Mycobacterium tuberculosis","volume":"9","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026070906151989000_2026.04.03.714442v2.39","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.26278-0"},{"key":"2026070906151989000_2026.04.03.714442v2.40","unstructured":"Smith, C. M. et al. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. Elife 11, (2022)."},{"key":"2026070906151989000_2026.04.03.714442v2.41","doi-asserted-by":"crossref","first-page":"e107","DOI":"10.1002\/imt2.107","article-title":"Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp","volume":"2","year":"2023","journal-title":"Imeta"},{"key":"2026070906151989000_2026.04.03.714442v2.42","unstructured":"World Health Organization. Catalogue of Mutations in Mycobacterium Tuberculosis Complex and Their Association with Drug Resistance, Second Edition. (Geneva, 2023)."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.04.03.714442","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T13:15:30Z","timestamp":1783602930000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.04.03.714442"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,4]]},"references-count":42,"URL":"https:\/\/doi.org\/10.64898\/2026.04.03.714442","relation":{},"subject":[],"published":{"date-parts":[[2026,4,4]]},"subtype":"preprint"}}