Ditthawat NonghanphithakAngkana ChaiprasertSaijai SmithtikarnPhalin KamolwatPetchawan PungrassamiVirasakdi ChongsuvivatwongSurakameth MahasirimongkolWipa ReechaipichitkulChaniya LeepiyasakulchaiJody E. PhelanDavid BlairTaane G. ClarkKiatichai FaksriLondon School of Hygiene &amp; Tropical MedicineJames Cook UniversityKhon Kaen UniversityThailand Ministry of Public HealthMahidol UniversityPrince of Songkla University2022-08-042022-08-042021-03-01Emerging Infectious Diseases. Vol.27, No.3 (2021), 813-82210806059108060402-s2.0-85101578452https://repository.li.mahidol.ac.th/handle/20.500.14594/78396Multidrug-resistant tuberculosis (MDR TB), pre-extensively drug-resistant tuberculosis (pre-XDR TB), and extensively drug-resistant tuberculosis (XDR TB) complicate disease control. We analyzed whole-genome sequence data for 579 phenotypically drug-resistant M. tuberculosis isolates (28% of available MDR/pre-XDR and all culturable XDR TB isolates collected in Thailand during 2014–2017). Most isolates were from lineage 2 (n = 482; 83.2%). Cluster analysis revealed that 281/579 isolates (48.5%) formed 89 clusters, including 205 MDR TB, 46 pre-XDR TB, 19 XDR TB, and 11 poly–drug-resistant TB isolates based on genotypic drug resistance. Members of most clusters had the same subset of drug resistance-associated mutations, supporting potential primary resistance in MDR TB (n = 176/205; 85.9%), pre-XDR TB (n = 29/46; 63.0%), and XDR TB (n = 14/19; 73.7%). Thirteen major clades were significantly associated with geography (p<0.001). Clusters of clonal origin contribute greatly to the high prevalence of drug-resistant TB in Thailand.Mahidol UniversityMedicineArticleSCOPUS10.3201/eid2703.204364