Phylogenetic inconsistency of pairwise SNP clustering for inferring tuberculosis transmission in a high-burden, endemic setting: a case study from Thailand.

Pairwise SNP clustering with low thresholds often produces non-monophyletic tuberculosis clusters in high-burden, endemic settings like Thailand, challenging its reliability.

• Why it matters: Accurate identification of transmission clusters is vital for controlling tuberculosis spread, but current methods may lack robustness in complex, persistent transmission environments.
• What they did: The study compared pwSNP-distance clustering thresholds between 1 and 25 SNPs using datasets from the UK (N=390) and Thailand (N=3,341), assessing phylogenetic consistency with tree-based methods.
• The result: Findings show that pwSNP-distance clustering aligns with monophyly only at thresholds ≥12 SNPs for the UK and ≥22 SNPs for Thailand, indicating low thresholds may produce unreliable, non-monophyletic clusters in persistent transmission settings.