ArticleScientific reports2024
Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Global mapping of bedaquiline-resistant Mycobacterium tuberculosis: a systematic review.BMC infectious diseases · 2026Pooled it
- Next-generation sequencing: Driving a paradigm shift from pathogen detection to systems-level analysis.Infectious medicine · 2026Article
- Genetic Characterization of First-Line Drug-Resistance Mutations in Multidrug-ResistantPathogens (Basel, Switzerland) · 2026Article
- High efficacy of BPaL among patients infected withIJTLD open · 2026Article
- Drug-Resistant Tuberculosis in Prisons of Latin America and the Caribbean: A Critical Reflection on Structural Challenges and Gaps.Tropical medicine and infectious disease · 2026Review
- Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance.Nature communications · 2025Article
- TOAST: a novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies.BMC genomics · 2025Article
- Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis.PLoS neglected tropical diseases · 2025Review
- Genomic decoding of drug-resistant tuberculosis transmission in Thailand over three decades.Scientific reports · 2025Article
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Authors and funding
24 authors.
Funding
Abstract
The Philippines is a high-incidence country for tuberculosis, with the increasing prevalence of multi- (MDR-TB) and extensively-drug (XDR-TB) resistant Mycobacterium tuberculosis strains posing difficulties to disease control. Understanding the genetic diversity of circulating strains can provide insights into underlying drug resistance mutations and transmission dynamics, thereby assisting the design of diagnostic tools, including those using next generation sequencing (NGS) platforms. By analysing genome sequencing data of 732 isolates from Philippines drug-resistance survey collections spanning from 2011 to 2019, we found that the majority belonged to lineages L1 (531/732; 72.5%) and L4 (European-American; n = 174; 23.8%), with the Manila strain (L1.2.1.2.1) being the most prominent (475/531). Approximately two-thirds of isolates were found to be at least MDR-TB (483/732; 66.0%), and potential XDR-TB genotypic resistance was observed (3/732; 0.4%), highlighting an emerging problem in the country. Genotypic resistance was highly concordant with laboratory drug susceptibility testing. By finding isolates with (near-)identical genomic variation, five major clusters containing a total of 114 isolates were identified: all containing either L1 or L4 isolates with at least MDR-TB resistance and spanning multiple years of collection. Closer inspection of clusters revealed transmission in prisons, some involving isolates with XDR-TB, and mutations linked to third-line drug bedaquiline. We have also identified previously unreported mutations linked to resistance for isoniazid, rifampicin, ethambutol, and fluoroquinolones. Overall, this study provides important insights into the genetic diversity, transmission and circulating drug resistance mutations of M. tuberculosis in the Philippines, thereby informing clinical and surveillance decision-making, which is increasingly using NGS platforms.
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