Linfeng Wang: Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines

Approximately 70 Filipinos die daily from TB. Worryingly, increasing HIV prevalence and a high burden of multi-drug resistance (MDR-TB) to isoniazid (INH) and rifampicin (RIF) treatments pose serious challenges for effective control3. These challenges are exacerbated by a serious gap between those expected to have MDR-TB (2% new, 21% re-treatment cases) and those detected and subsequently put on treatment, with detrimental consequences including poorer treatment outcomes and strains progressing to extensively drug-resistance (XDR-TB)2. 

Novel applications of whole genome (WGS) and targeted (candidate) amplicon sequencing (Amp-seq) using next generation (NGS) technologies can provide insights into the underlying drug resistance mutations and profiles for clinical and surveillance decision-making. However, there is a lack of WGS studies of M. tuberculosis from low- and middle-income countries, such as the Philippines, where the prevalence and burden of TB tend to be greatest.

In the Philippines, genomic data for local M. tuberculosis isolates is scarce, but previous work has shown that ‘ancient’ (lineage L1) and ‘modern’ lineages (L2 and L4) are present in the country3. Members of the EA12-Manila clade (L1.2.1.2.1) are known to be highly associated with the Filipino population3, with a molecular barcode established to rapidly identify this strain type4. Here, we present the results of sequencing 732 isolates recently collected between 2011 and 2019, including from prison populations. We analysed the temporal evolution of drug resistance and clustering by geography and found evidence of the transmission of L4 and MDR-TB strains across the islands. More generally, TB transmission in prison poses a challenge to infection control, with the potential spread of infections within and outside the institution, and several studies have used sequencing to understand links between isolates5,6,7,8, and inform a public health response. Within confined correctional spaces, TB thrives, driven by overcrowding and potentially limited ventilation and healthcare access, thereby amplifying the risk of transmission. The flow of individuals into and out of prisons poses a broader public health concern, and the response necessitates targeted screening, rapid diagnosis, and tailored treatments.

Mixed infections in TB introduce complex genetic interactions that impact disease severity, treatment response, and transmission dynamics. The co-existence of diverse clones within a host complicates treatment regimes, and genetic investigation of the bacterial population can inform patient management9. Platforms such as Illumina and the development of portable devices, such as Oxford Nanopore Technology, have ushered in a transformative era, making WGS and Amp-seq a cornerstone in deciphering the genome variation and diversity of M. tuberculosis. WGS is now widely used to identify drug resistance markers to guide treatment, determine phylogenetic relatedness and potential transmission events, inform surveillance and infection control decision-making, and discover new targets for drugs and vaccines. Applying such technologies and assays will have the greatest impact in settings with high TB burden, such as The Philippines. In this study, we utilised WGS data from a convenience dataset to explore the dynamics of drug resistance development, transmission, and the complexities of mixed infections in the Philippines. By conducting an integrated analysis of WGS data, we aimed to establish a baseline characterisation of genomic diversity within the country. This foundational insight will inform future routine applications of NGS, guiding public health decision-making and helping to reduce the high burden of TB.

Read full publication here