Tuberculosis in Thailand

An observational study was conducted to assess the multidrug-resistant tuberculosis (MDR-TB) outbreak in Tha Maka district, with a retrospective laboratory-based molecular epidemiological analysis. Culture-positive MDR-TB samples collected between 2010 and 2020—primarily from 2014 to 2019—were analyzed using molecular methods including Line Probe Assay (LPA), GeneXpert MTB/RIF, and real-time PCR to confirm drug resistance. Drug susceptibility testing was performed using the WHO-endorsed proportional method and LPA, while whole-genome sequencing (WGS) was conducted using the Illumina NextSeq 500 platform. A total of 188 drug-resistant TB (DR-TB) cases were evaluated, comprising 168 MDR-TB (88.8%), 7 pre-extensively drug-resistant TB (pre-XDR-TB; 3.7%), and 13 extensively drug-resistant TB (XDR-TB; 6.9%).

The genomic analysis revealed a striking dominance of Lineage 2 (East Asian lineage), which accounted for 92% of all isolates, with the L2.2.M3 sub-lineage making up 84.4% of these. Minor representation came from Lineage 1 (Indo-Oceanic, 5.9%) and Lineage 4 (Euro-American, 2.1%). Genomic clustering showed that at a ≤5 single nucleotide polymorphism (SNP) threshold, three clusters emerged, the largest consisting of 38 isolates—all belonging to L2.2.M3. When the SNP threshold was relaxed to ≤12, 96 isolates clustered within the L2.2.M3 group, encompassing some pre-XDR and XDR cases.

Geographic and temporal data further demonstrated that L2.2.M3 had widespread and sustained transmission across most sub-districts from 2013 to 2019, unlike other sub-lineages, which appeared sporadically and were geographically confined. The dominance, genetic clustering, and persistent distribution of L2.2.M3 suggest that this strain is highly transmissible and well-adapted for clonal expansion within the Thai population, underlining its role as a key driver of the MDR-TB outbreak in the region.

Source: Thipkrua, N., Disrathakit, A., Chongsuvivatwong, V., Mahasirimongkol, S., Ruangchai, W., Palittapongarnpim, P., Chaiprasert, A., Pungrassami, P., Kamolwat, P., Suthum, K. and Tossapornpong, K., 2025. A large geno-spatial cluster of multi-drug resistant tuberculosis outbreak in a western district of Thailand. Infection, Genetics and Evolution, 128, p.105715.