{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:56:01Z","timestamp":1787032561952,"version":"build-2736575974"},"posted":{"date-parts":[[2025,12,18]]},"group-title":"Microbiology","reference-count":31,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"Bill and Melinda Gates Foundation grant","award":["OPP1170003"],"award-info":[{"award-number":["OPP1170003"]}]},{"name":"U.S. Department of Veterans Affairs (VA) grant","award":["1I01BX004527-01A1"],"award-info":[{"award-number":["1I01BX004527-01A1"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health grant","doi-asserted-by":"crossref","award":["UM1AI179699"],"award-info":[{"award-number":["UM1AI179699"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health grant","doi-asserted-by":"crossref","award":["R01AI158963"],"award-info":[{"award-number":["R01AI158963"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,12,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  The standard pharmacodynamic marker in murine tuberculosis drug studies is colony-forming units (\n                  <jats:bold>CFU<\/jats:bold>\n                  ). A faster PCR-based marker of bacterial burden is 16S rRNA. For unclear reasons, treatment reduces CFU more than 16S rRNA. We evaluated this CFU-16S gap and estimated the fraction potentially attributable to slow decay of 16S rRNA from dead\n                  <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                  (\n                  <jats:bold>\n                    <jats:italic>Mtb<\/jats:italic>\n                  <\/jats:bold>\n                  ) versus transition to a viable but not culturable on solid agar (\n                  <jats:bold>\n                    VBNC\n                    <jats:sub>SA<\/jats:sub>\n                  <\/jats:bold>\n                  ) population.\n                <\/jats:p>\n                <jats:p>\n                  We quantified the CFU-16S gap during and following treatment in six BALB\/c mouse studies and one\n                  <jats:italic>in vitro<\/jats:italic>\n                  study. Applying a two-population ordinary differential equation-based model of\n                  <jats:italic>Mtb<\/jats:italic>\n                  death and 16S rRNA decay, we estimated the fraction of the gap potentially attributable to dead\n                  <jats:italic>Mtb.<\/jats:italic>\n                  Using meta-regression, we estimated the association between CFU or 16S rRNA with relapse.\n                <\/jats:p>\n                <jats:p>\n                  For all regimens, CFU fell more than 16S rRNA, ranging from isoniazid-rifampin-pyrazinamide-ethambutol (CFU decreased 39-times more than 16S rRNA at week 4) to bedaquiline-pretomanid-moxifloxacin-pyrazinamide (CFU decreased &gt;500,000-times more). The two-population model suggested that the fraction of the CFU-16S gap attributable to residual 16S rRNA from dead\n                  <jats:italic>Mtb<\/jats:italic>\n                  is modest and decreases over time. After treatment, 16S rRNA often fell while CFU rose. Four-week CFU change explained most variation in relapse (R\u00b2=0.90) while four-week 16S rRNA change did not (R\u00b2=0.24).\n                <\/jats:p>\n                <jats:p>\n                  CFU-16S gap is only partially explained by slow decay of residual 16S, suggesting development of a VBNC\n                  <jats:sub>SA<\/jats:sub>\n                  population. However, continued decrease in 16S rRNA after treatment cessation and its limited association with relapse suggests VBNC\n                  <jats:sub>SA<\/jats:sub>\n                  may be a transient rather than persistent state.\n                <\/jats:p>","DOI":"10.64898\/2025.12.18.695164","type":"posted-content","created":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T02:30:16Z","timestamp":1766111416000},"source":"Crossref","is-referenced-by-count":3,"title":["Mind the gap: Understanding discordance between culture- and a non-culture-based measure of bacterial burden in murine tuberculosis treatment models"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-3420-8343","authenticated-orcid":false,"given":"Samuel T.","family":"Tabor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-2723-3556","authenticated-orcid":false,"given":"Allan D.","family":"Friesen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew J.","family":"Reichlen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Dide-Agossou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"McGrath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Peterson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vitaly V.","family":"Ganusov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory T.","family":"Robertson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9565-7923","authenticated-orcid":false,"given":"Martin I.","family":"Voskuil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas D.","family":"Walter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025122012200883000_2025.12.18.695164v1.1","unstructured":"World Health Organization. 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