{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:10:28Z","timestamp":1787962228940,"version":"build-2784847793"},"reference-count":17,"publisher":"American Society for Microbiology","issue":"11","license":[{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["23fk0108607h"],"award-info":[{"award-number":["23fk0108607h"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003478","name":"Ministry of Health, Labour and Welfare","doi-asserted-by":"publisher","award":["22HA2001"],"award-info":[{"award-number":["22HA2001"]}],"id":[{"id":"10.13039\/501100003478","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Genomic analysis of mycobacteria has become increasingly crucial for understanding drug-resistance mechanisms, molecular epidemiology, and pathogenesis. However, efficient extraction of high-molecular-weight genomic DNA from these organisms remains challenging because of their thick mycolic acid-rich cell walls. In this study, we report the chloroform-bead method, a universal DNA extraction protocol that combines chemical and mechanical disruptions to overcome these challenges. Multi-laboratory evaluation (16 sites) demonstrated the chloroform-bead method\u2019s superiority over conventional methods for\n                      <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                      (DNA yield: 17.9 vs 1.9 \u00b5g, purity A260\/A230: 1.86 vs 1.22, both\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      &lt; 0.001). Single-facility assessment extended these findings to &gt;32 nontuberculous mycobacterial species (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 1,058), showing performance comparable to\n                      <jats:italic toggle=\"yes\">M. tuberculosis<\/jats:italic>\n                      (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 1,000), with both achieving median yields of 22.2 \u00b5g DNA and consistent quality metrics. The chloroform-bead method significantly reduced the processing time from 2 to 3 days to 2 h while ensuring complete sample sterilization, eliminating the need for species-specific optimization. This streamlined and universally applicable protocol represents a practical advancement in mycobacterial DNA extraction methodology, ideal for high-throughput genomic studies and routine clinical diagnostics.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>Mycobacterial genomics is crucial for understanding pathogenesis and drug resistance; however, DNA extraction remains a significant challenge because of its unique cell wall. Traditional methods rely on enzymatic treatments, resulting in complex and time-consuming protocols with variable results. The chloroform-bead method introduces a paradigm shift by chemically and mechanically disrupting the mycolic acid layer and eliminating the need for enzymatic treatment. This standardized approach ensures consistent, high-quality DNA extraction across diverse mycobacterial species, thereby enhancing research capabilities and clinical applications.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00765-25","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T13:00:42Z","timestamp":1759410042000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["A universal, high-quality, and high-yield DNA purification method for mycobacteria, including\n                    <i>Mycobacterium tuberculosis<\/i>\n                    : large-scale assessment of the chloroform-bead method"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0240-8352","authenticated-orcid":true,"given":"Yoshiro","family":"Murase","sequence":"first","affiliation":[{"name":"Department of Mycobacterium Reference and Research, 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Appropriate statistics for ordinal level data: should we really be using t-test and Cohen\u2019sd for evaluating group differences on the NSSE and other surveys 177"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.3791\/2565"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2024.107053"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00765-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00765-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T14:09:35Z","timestamp":1762265375000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00765-25"}},"subtitle":[],"editor":[{"given":"Rosemary C.","family":"She","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,4]]},"references-count":17,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,11,4]]}},"alternative-id":["10.1128\/spectrum.00765-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00765-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,4]]},"assertion":[{"value":"2025-05-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-04","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-10-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00765-25"}}