{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:11:54Z","timestamp":1785427914098,"version":"3.56.0"},"posted":{"date-parts":[[2025,8,15]]},"group-title":"Microbiology","reference-count":48,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T00:00:00Z","timestamp":1755216000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R01AI158963"],"award-info":[{"award-number":["R01AI158963"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Immune correlates of protection against infection with\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (\n                  <jats:bold>Mtb<\/jats:bold>\n                  ) or against tuberculosis (\n                  <jats:bold>TB<\/jats:bold>\n                  ) remain poorly defined. The ratio of colony forming units (\n                  <jats:bold>CFUs<\/jats:bold>\n                  ) to chromosomal equivalents (\n                  <jats:bold>CEQs<\/jats:bold>\n                  ),\n                  <jats:italic>Z<\/jats:italic>\n                  = CFUs\/CEQs, recovered either from the whole lung (mice) or individual lesions (monkeys or rabbits) of Mtb-infected animals has been used as a metric for how effectively Mtb is killed in vivo. However, the contribution of bacterial killing to changes in the CFU\/CEQ ratio during an infection has not been rigorously investigated. We developed alternative mathematical models to study the dynamics of CFUs, CEQs, and their ratio during an Mtb infection. We find that the ratio\n                  <jats:italic>Z<\/jats:italic>\n                  alone cannot be used to infer the death rate of bacteria, unless the dynamics of CEQs and CFUs are entirely uncoupled, which is biologically unreasonable and inconsistent with the view that CEQs reflect an accumulated burden of both viable and non-viable bacteria. Importantly, we estimate a decay rate of 3.6%\n                  <jats:italic>\/<\/jats:italic>\n                  day (a half life of about 20 days) of Mtb H37Rv CEQs in B6 mice that is similar to 4%\n                  <jats:italic>\/<\/jats:italic>\n                  day, previously found for Mtb Erdman in cynomolgus macaques. While the estimated Mtb DNA decay rate seems small, we found that estimated rates of Mtb replication and death\/killing are still extremely sensitive even to slow decay of Mtb DNA, in part, because Mtb replication and death rates are also small especially during chronic phases of infection. By applying our models to data on Mtb dynamics during the first 3 weeks of infection in macaques, we provide evidence of substantial killing of Mtb bacteria, prior to arrival of adaptive immunity to the site of infection, challenging the previously established notion of non-dying bacteria in the absence of T cell immunity and granuloma formation. We also propose experiments that will allow more accurately to measure the rate of Mtb DNA loss, helping more rigorously quantify impact of immunity on within-host Mtb dynamics.\n                <\/jats:p>","DOI":"10.1101\/2025.08.15.670581","type":"posted-content","created":{"date-parts":[[2025,8,16]],"date-time":"2025-08-16T07:00:16Z","timestamp":1755327616000},"source":"Crossref","is-referenced-by-count":1,"title":["Immortal genome assumption significantly underestimates replication and death rates of\n                  <i>Mycobacterium tuberculosis<\/i>\n                  in mice and monkeys"],"prefix":"10.64898","author":[{"given":"Allan D.","family":"Friesen","sequence":"first","affiliation":[{"name":"Host-Pathogen Interactions program, Texas Biomedical Research Institute, San Antonio, TX 78277"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6572-1691","authenticated-orcid":false,"given":"Vitaly V.","family":"Ganusov","sequence":"additional","affiliation":[{"name":"Host-Pathogen Interactions program, Texas Biomedical Research Institute, San Antonio, TX 78277"},{"name":"Molecular Microbiology and Immunology department, University of Texas at San Antonio, San Antonio, TX 78249"},{"name":"Department of Microbiology, University of Tennessee, Knoxville, TN 37996"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026060105450709000_2025.08.15.670581v2.1","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20180518"},{"key":"2026060105450709000_2025.08.15.670581v2.2","doi-asserted-by":"publisher","DOI":"10.1128\/aac.02516-18"},{"key":"2026060105450709000_2025.08.15.670581v2.3","doi-asserted-by":"crossref","unstructured":"Wessler, T. , Joslyn, L. R. , Borish, H. J. , Gideon, H. P. , Flynn, J. L. , Kirschner, D. E. & Linderman, J. J. 2019 A computational model tracks whole-lung mycobacterium tuberculosis infection and predicts factors that inhibit dissemination. PLoS Computational Biology, 16.","DOI":"10.1101\/713701"},{"key":"2026060105450709000_2025.08.15.670581v2.4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1011825"},{"key":"2026060105450709000_2025.08.15.670581v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2022.04.004"},{"key":"2026060105450709000_2025.08.15.670581v2.6","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.73.1.546-551.2005"},{"key":"2026060105450709000_2025.08.15.670581v2.7","doi-asserted-by":"crossref","unstructured":"Chakraborty, D. , Batabyal, S. & Ganusov, V. V. 2024 A brief overview of mathematical modeling of the within-host dynamics of mycobacterium tuberculosis. Frontiers Appl. Math. Stat., 10.","DOI":"10.3389\/fams.2024.1355373"},{"key":"2026060105450709000_2025.08.15.670581v2.8","doi-asserted-by":"crossref","unstructured":"Sarathy, J. P. 2024 Molecular and microbiological methods for the identification of nonreplicating mycobacterium tuberculosis. PLOS Pathogens, 20.","DOI":"10.1371\/journal.ppat.1012595"},{"key":"2026060105450709000_2025.08.15.670581v2.9","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0285-3"},{"key":"2026060105450709000_2025.08.15.670581v2.10","doi-asserted-by":"publisher","DOI":"10.1038\/nm.1915"},{"key":"2026060105450709000_2025.08.15.670581v2.11","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-146-2-297"},{"key":"2026060105450709000_2025.08.15.670581v2.12","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00862"},{"key":"2026060105450709000_2025.08.15.670581v2.13","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3412"},{"key":"2026060105450709000_2025.08.15.670581v2.14","doi-asserted-by":"publisher","DOI":"10.1128\/aac.02266-17"},{"key":"2026060105450709000_2025.08.15.670581v2.15","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00159-19"},{"key":"2026060105450709000_2025.08.15.670581v2.16","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.07.579301"},{"key":"2026060105450709000_2025.08.15.670581v2.17","unstructured":"Aitchison, J. & Brown, J. A. C. 1957 The Lognormal Distribution: With Special Reference to Its Uses in Economics. No. 5 in University of Cambridge Department of Applied Economics Monographs. Cambridge, UK: Cambridge University Press."},{"key":"2026060105450709000_2025.08.15.670581v2.18","doi-asserted-by":"publisher","DOI":"10.1063\/1.2159468"},{"key":"2026060105450709000_2025.08.15.670581v2.19","doi-asserted-by":"publisher","DOI":"10.1021\/j100540a008"},{"key":"2026060105450709000_2025.08.15.670581v2.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08506-6"},{"key":"2026060105450709000_2025.08.15.670581v2.21","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10020460"},{"key":"2026060105450709000_2025.08.15.670581v2.22","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01125-14"},{"key":"2026060105450709000_2025.08.15.670581v2.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2023.102332"},{"key":"2026060105450709000_2025.08.15.670581v2.24","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra1405427"},{"key":"2026060105450709000_2025.08.15.670581v2.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.10.003"},{"key":"2026060105450709000_2025.08.15.670581v2.26","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2236"},{"key":"2026060105450709000_2025.08.15.670581v2.27","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00312-17"},{"key":"2026060105450709000_2025.08.15.670581v2.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.coi.2023.102365"},{"key":"2026060105450709000_2025.08.15.670581v2.29","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-54741-w"},{"key":"2026060105450709000_2025.08.15.670581v2.30","doi-asserted-by":"publisher","DOI":"10.18609\/vac\/2022.027"},{"key":"2026060105450709000_2025.08.15.670581v2.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-019-0142-2"},{"key":"2026060105450709000_2025.08.15.670581v2.32","doi-asserted-by":"crossref","unstructured":"Allen, L. J. S. 2010 An Introduction to Stochastic Processes with Applications to Biology. Boston, MA: Pearson.","DOI":"10.1201\/b12537"},{"key":"2026060105450709000_2025.08.15.670581v2.33","unstructured":"Kampen, N. V. 2007 Stochastic Processes in Physics and Chemistry (3rd ed.). Elsevier."},{"key":"2026060105450709000_2025.08.15.670581v2.34","doi-asserted-by":"crossref","unstructured":"Yam, Y.-K. , Alvarez, N. , Go, M. L. & Dick, T. 2020 Extreme drug tolerance of Mycobacterium abscessus \u201cpersisters\u201d. Frontiers in Microbiology, 11.","DOI":"10.3389\/fmicb.2020.00359"},{"key":"2026060105450709000_2025.08.15.670581v2.35","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.073379-0"},{"key":"2026060105450709000_2025.08.15.670581v2.36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006885"},{"key":"2026060105450709000_2025.08.15.670581v2.37","doi-asserted-by":"publisher","DOI":"10.1126\/science.1099390"},{"key":"2026060105450709000_2025.08.15.670581v2.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22833-6"},{"key":"2026060105450709000_2025.08.15.670581v2.39","doi-asserted-by":"publisher","DOI":"10.51429\/EJMM30209"},{"key":"2026060105450709000_2025.08.15.670581v2.40","doi-asserted-by":"publisher","DOI":"10.1164\/ajrccm.160.1.9811006"},{"key":"2026060105450709000_2025.08.15.670581v2.41","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00284-23"},{"key":"2026060105450709000_2025.08.15.670581v2.42","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01010-23"},{"key":"2026060105450709000_2025.08.15.670581v2.43","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.18.695164"},{"key":"2026060105450709000_2025.08.15.670581v2.44","doi-asserted-by":"crossref","unstructured":"Kemp, P. F. 1995 Can we estimate bacterial growth rates from ribosomal RNA content? In Molecular ecology of aquatic microbes, pp. 279\u2013302. Springer.","DOI":"10.1007\/978-3-642-79923-5_16"},{"key":"2026060105450709000_2025.08.15.670581v2.45","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004303"},{"key":"2026060105450709000_2025.08.15.670581v2.46","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(68)90425-7"},{"key":"2026060105450709000_2025.08.15.670581v2.47","doi-asserted-by":"publisher","DOI":"10.1126\/science.aac4812"},{"key":"2026060105450709000_2025.08.15.670581v2.48","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00598-23"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.08.15.670581","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:45:17Z","timestamp":1780317917000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.08.15.670581"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,15]]},"references-count":48,"URL":"https:\/\/doi.org\/10.1101\/2025.08.15.670581","relation":{},"subject":[],"published":{"date-parts":[[2025,8,15]]},"subtype":"preprint"}}