Abstract
Tuberculosis (TB) remains a global public health challenge, including in Thailand, where it is
most commonly caused by Mycobacterium tuberculosis. While TB morbidity and mortality
rates in Thailand have been steadily declining, the current “passive” approach to TB control
has resulted in a reduction rate that remains too slow to achieve the national goal of "End
TB" by 2030, in alignment with the Sustainable Development Goals. We believe that if large
outbreak clusters can be identified and resources can be strategically allocated to target
highly drug-resistant strains with prompt treatment or preventive measures in a more
“proactive” manner, TB transmission could be more effectively reduced.
This project aims to develop a bioinformatics pipeline for whole-genome sequencing (WGS)
analysis of M. tuberculosis to detect large outbreak clusters, identify strains, and characterise
drug resistance patterns. The findings will support targeted TB investigations, and
prioritisation efforts, as well as capacity-building initiatives for healthcare professionals to
enhance the efficiency and effectiveness of TB diagnosis, treatment, and outbreak
investigations. Chiang Rai province, designated as a high-burden TB area with significant strain
diversity, has been selected as the study site. The project has a total duration of two years.
In year 1, the project collected and performed preliminary analyses on whole-genome
sequences of M. tuberculosis isolates from Chiang Rai and other provinces in Thailand. The
analysis identified four predominant lineages in Chiang Rai: L1, L2, L3, and L4. L2 exhibited a
significantly higher overall drug resistance rate than L1. The spatial distribution of each
lineage varied across Chiang Rai, but all regions faced comparable levels of drug-resistant TB.
Over the past two decades (1999–2023), no significant increase or decrease was observed in
the proportion of any particular lineage or drug-resistant strain. Data suggest that L1 is more
frequently found among elderly patients, while L2 is more common in pediatric and
working-age populations. Lineages L3 and L4 were detected across all age groups.
Additionally, no significant association was found between drug resistance patterns and
patient age. However, lineage distribution showed a significant correlation with patient
nationality and ethnicity, as well as TB outcomes, whereas drug resistance patterns were
only associated with nationality.
Clustering and phylogenetic analyses indicate that TB outbreaks in Chiang Rai are linked to
outbreaks in other Thai provinces. Notably, different drug-resistant strains were sometimes
found within the same WGS cluster. Further analysis suggests that drug-resistant strains,
particularly RR-TB and Pre-XDR-TB, tend to be able to sustain transmission more effectively
compared to non-resistant strains, with transmission potential varying by drug resistance
type and lineage. Specific lineages of interest include L2.2.M3MDR-TB, L2.2.M3Pre-XDR-TB,
L2.2.AA3.2RR-TB, L4.4.2MDR-TB, L2.1Pre-XDR-TB, L2.2.M2.3MDR-TB, L2.2.M2.3Pre-XDR-TB, L2.2.M4.2HR-TB,
L2.2.M4.2
Other DR type, and L2.2.M4.2Pre-XDR-TB, all of which exhibited an average of more than
five WGS lineages at an SNP cut-off of 20. These findings have been shared with public
health authorities to support targeted TB investigations in Chiang Rai and have been
presented at multiple scientific conferences organised or attended by the project team.
Currently, the project is developing a WGS data analysis pipeline for M. tuberculosis, which is
expected to be completed in year 2. Once finalised, the tool will be publicly released for
broader application and impact.
