A group of investigators from the Research Institute for Tropical Medicine (RITM), London School of Hygiene and Tropical Medicine (LSHTM), Research Institute of Tuberculosis-Japan Anti Tuberculosis Association (RIT-JATA), and Genome Institute of Singapore (GIS)have led the first nationwide study looking at the genetic diversity of circulatingMycobacterium tuberculosis strains, which cause tuberculosis (TB) disease.
“Up to now, only a handful of NGS studies were done on the M. tuberculosis Manila strain. By far, this is the largest genomic study that involved the WGS of the Manila strain (n=143). We have sequenced a total number of 178 M. tuberculosis isolates sourced from various geographical regions in the Philippines that looked into its genetic diversity, transmission, and drug resistance. We now have an understanding of the genetics of the Manila strain” says National Tuberculosis Reference Laboratory Science Research Specialist and study investigator Dodge R. Lim.
In the Philippines, the incidence of TB is considered very high, and an increase in the prevalence of multidrug-resistant TB (MDR-TB) and Human Immunodeficiency Virus (HIV) makes the disease difficult to control. The country ranks 4th in the burden of TB worldwide with an estimated 22,000 deaths in 2017 and particularly drug-resistant (DR) has cost a projected loss of 0.31 billion USD in the country’s Gross Domestic Product (GDP).
Through the study, it was found that majority of the isolates (80.3%) belonged to the lineage 1 Manila clade, and that the minority belonged to lineages 4 (European-American, 18.5%) and 2 (East Asian, 1.1%). In terms of drug-resistance, a high proportion of the isolates (19.1%) were found to be MDR. Moreover, potential evidence of transmission was established as some of the MDR-TB isolates had nearly identical genomic variation.
Overall, the study provided a significant baseline characterization of the M. tuberculosis genetic diversity in the Philippines. Filling a gap in global datasets, the results will facilitate the development of a nationwide database for epidemiology and decision making. More importantly, a molecular barcode for detecting Manila strains will aid in the design of diagnostic tools for disease control initiatives.
Moving forward, the team led by Dr. Ma. Cecilia Ama (NTRL-RITM), Dr. Eva Cutiongco De la Paz (UP Manila) and Prof. Taane Clark (LSHTM) is sequencing an even larger sample size to gain a deeper understanding of the TB bacteria as it shifts through space and time in the country. They are also planning to correlate this with HIV as a risk group to determine its dynamics in terms of transmission particularly in Metro Manila, a DR-TB and HIV hotspot area in the country.