Prasit PalittapongarnpimPravech AjawatanawongWasna ViratyosinNat SmittipatAreeya DisratthakitSurakameth MahasirimongkolHideki YanaiNorio YamadaSupalert NedsuwanWorarat ImasanguanPacharee KantipongBoonchai ChaiyasirinrojeJiraporn WongyaiLicht Toyo-okaJody PhelanJulian ParkhillTaane G. ClarkMartin L. HibberdWuthiwat RuengchaiPanawun PalittapongarnpimTada JuthayothinSissades TongsimaKatsushi TokunagaJapan Anti-Tuberculosis AssociationLondon School of Hygiene & Tropical MedicineUniversity of TokyoThailand Ministry of Public HealthMahidol UniversityThailand National Center for Genetic Engineering and BiotechnologyThe Research Institute of Tuberculosis, Japan Anti-Tuberculosis AssociationWellcome Sanger InstituteTB/HIV Research Foundation2019-08-282019-08-282018-12-01Scientific Reports. Vol.8, No.1 (2018)204523222-s2.0-85051061432https://repository.li.mahidol.ac.th/handle/20.500.14594/47499© 2018, The Author(s). Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.Mahidol UniversityMultidisciplinaryArticleSCOPUS10.1038/s41598-018-29986-3