{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T21:31:07Z","timestamp":1780608667007,"version":"3.54.1"},"reference-count":54,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T00:00:00Z","timestamp":1759449600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82373649"],"award-info":[{"award-number":["82373649"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,3]]},"abstract":"<jats:p>The application of pan-genomics in understanding <jats:italic>Mycobacterium tuberculosis<\/jats:italic> complex (MTBC) transmission remains understudied, particularly in high-burden settings such as China. We constructed an <jats:italic>M. tuberculosis<\/jats:italic> complex pan-genome (MTB_pan) using 307 complete genomes representing all eight lineages from the National Center for Biotechnology Information (NCBI). Core and accessory genomes were analysed, lineage-associated genes were identified and functional annotations were assessed using Pfam domains. Transmission dynamics were evaluated by comparing pan-genome- and H37Rv-based approaches for isolates collected from China, focusing on alignment rates, clustering efficiency and SNP distances. The MTB_pan (5.75 Mb) consisted of 3,893 core and 958 accessory genes, with 176 accessory genes significantly associated with specific lineages. These genes were enriched in PE\/PPE\/PGRS families, mobile genetic elements (e.g. IS6110) and pentapeptide repeats. The median alignment rate based on MTB_pan reached 99.8%, which was significantly higher than that based on H37Rv. The clustering rate of isolates based on MTB_pan (19.93%) was higher than that based on H37Rv (18.90%). The pairwise SNP distances below 50 SNPs within lineage 2 decreased significantly, while those within lineage 4 showed no significant differences. Compared to a single reference genome, clustering using the pan-genome improved the identification of same-province transmission events. Therefore, the pan-genomic analysis is a more powerful analytical tool that enables the establishment of a high-resolution picture of tuberculosis transmission in different epidemiological settings, which will enable more precise outbreak mapping and support data-driven tuberculosis control strategies.<\/jats:p>","DOI":"10.1099\/mgen.0.001460","type":"journal-article","created":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T16:16:37Z","timestamp":1759508197000},"source":"Crossref","is-referenced-by-count":1,"title":["Pan- and core genome analysis of Mycobacterium tuberculosis in high-resolution transmission and genetic diversity studies"],"prefix":"10.1099","volume":"11","author":[{"given":"Zhengwei","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, PR 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