OR02

1:Vita-Salute San Raffaele University; 2:San Raffaele Scientific Institute; 3:Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille

The evolutionary origin of the Mycobacterium tuberculosis complex (MTBC) remains unresolved, with prevailing theories proposing emergence from terrestrial reservoirs. Here, we investigated the early ecological history of the MTBC progenitor by analyzing molecular imprints of past microbial interactions preserved in the genomes of M. canettii, extant members of the MTBC, and MTB-associated phylotype (MTBAP) species. We explored CRISPR spacer repertoires and prophage-associated genomic elements to trace past exposures to mobile genetic elements (MGEs).

Comprehensive BLAST analyses of CRISPR spacers revealed targeted sequences matching prophages and mobile elements predominantly from aquatic mycobacteria, including M. marinum and sponge-associated species. Notably, multiple M. canettii strains harbored spacers with high-identity matches to prophages infecting aquatic hosts, and a substantial prophage region in M. canettii STB-I showed remarkable collinearity with a M. marinum phage genome. Parallel analyses of integrated prophage-like regions in MTBAP genomes (M. lacus, M. shinjukuense, M. riyadhense) also highlighted predominant affiliations with aquatic and waterborne bacteria.

The convergence of independent evidence from CRISPR spacer targeting and prophage fossil records strongly suggests that the progenitor of the MTBC evolved within an aquatic environment, with sponges and aquatic microbiomes likely acting as key ecological reservoirs. These findings challenge traditional soil-based hypotheses and offer new perspectives for understanding tuberculosis evolution and potential environmental sources of emerging pathogenic mycobacteria.