Genetic Diversity of Mycobacterium tuberculosis Isolates from a Rural Community in the Philippines

Background: Despite the high tuberculosis (TB) burden in the Philippines, data on genetic diversity and transmission dynamics of M. tuberculosis remains sparse. This study aims to determine the prevalent genotype of M. tuberculosis isolates obtained from a rural community and the factors associated with genotype and clustering. Methods: 125 culture-positive isolates from symptomatic Filipino patients aged 15 and above from San Juan, Batangas were genotyped using combined spoligotyping and 15-loci MIRU-VNTR. Clustering rate was used as an index for recent transmission. Results: EAI2_Manila was the most prevalent genotype (121/125, 96.8%) followed by Beijing (2/125, 1.6%), EAI5 (1/125, 0.8%), and LAM2 (1/125, 0.8%). Genotype was statistically associated with sex (p = 0.025) and polyresistance to RMP + SM (p = 0.032). The clustering rate was 26.4%. The majority of the clustered isolates were from male patients (40/48, 83.3%), 15–49 yr old (36/48, 75.0%), smear-positive cases (41/48, 85.4%), and with low bacillary load (44/48, 91.7%). Clustered isolates were associated with age groups (p = 0.01) and smear positivity (p = 0.037). No association was observed between clustered isolates and drug resistance. Conclusion: This study provides important baseline data on the predominance of EAI2_Manila strain in a rural community in the Philippines using classical genotyping techniques. The recent transmission was observed among isolates obtained from younger patients and smear-positive samples. Larger community-based prospective studies in the Philippines are recommended using techniques with higher discriminatory power like whole-genome sequencing to further evaluate the EAI2_Manila genotype.