A national picture of which tuberculosis strains are circulating in the Philippines, which drug-resistance mutations they carry, and where transmission is concentrated.
Reading the figure
The tree in the centre is built from genome-wide variation across all 732 isolates, so two tips sitting close together are two patients carrying nearly identical bacteria. The rings around it carry the metadata for each isolate: lineage, with L1, the Manila strain, dominant and L2, L3 and L4 also present; island group, splitting Luzon, Visayas and Mindanao; drug-resistance type, running from sensitive through MDR to XDR; and year of collection, from 2011 to 2019.
The finding is in the coincidence of the rings rather than in any one of them. Where a red-branch cluster lines up with a solid block in the resistance ring and a single colour in the island ring, that is resistant TB being passed from person to person in one place, rather than resistance arising independently in each patient. Those two situations call for completely different responses, and only the genomes can tell them apart. The clusters that stand out this way are the prison-linked ones, and they are also where the novel bedaquiline resistance mutations were found.
Approach
- Whole-genome sequencing of 732 M. tuberculosis isolates from across the country
- Genome-wide association and phylogenetic analysis to link strain types to resistance
- Time-scaled Bayesian phylogenetics to reconstruct transmission dynamics
Findings
- The L1 Manila strain predominates, alongside emerging drug-resistant L4 lineages
- MDR-TB and XDR-TB clusters trace to transmission within prisons
- Novel bedaquiline resistance mutations found in prison-derived isolates, a direct public health concern in carceral settings