Molecular epidemiology of tuberculosis in the general and prison populations in the interior of São Paulo: analysis of MIRU-VNTR and RDRio sublineage.

Tuberculosis (TB) is still a serious global public health problem, affecting mostly vulnerable populations such as the population deprived of liberty (PDL). Brazil has the third-largest prison population in the world, and the state of São Paulo has the largest PDL in the country. This study investigated the molecular epidemiology of TB in individuals from the general population (GP) and the PDL belonging to two Epidemiological Surveillance Groups in the state of São Paulo. A total of 522 Mycobacterium tuberculosis isolates were analyzed using MIRU-VNTR genotyping (15 and 24-loci) and multiplex PCR for detection of RDRio/RD174 deletions. Clustering rates were 14.7% for 15-loci and 12.8% for 24-loci. The RDRio sublineage was identified in 26.8% of isolates, showing an association with alcohol use disorder (OR = 1.84; 95% CI 1.17-2.88) and illiteracy (OR = 3.40; 95% CI 1.09-10.58). Clusters with 100% similarity between GP and PDL isolates were observed, indicating intra- and extramural transmission within prison units. These findings highlight the importance of integrated surveillance and control strategies, with strengthened active case finding in both populations, in order to interrupt transmission chains and reduce the TB burden. In addition, further high-resolution genomic studies involving the PDL are recommended, focusing on complete genome sequencing integrated with epidemiological, spatial, and socio-environmental data, which will contribute to the improvement of TB surveillance and control strategies in highly vulnerable contexts.