Genomic Diversity of Mycobacterium tuberculosis Complex in Tahiti, French Polynesia

Evolving genomic diversity of Mycobacterium tuberculosis complex pathogens is poorly known in French Polynesia, a remote archipelago in the southern Pacific Ocean. A total of 321 mycobacteria sampled from 321 patients presenting pulmonary tuberculosis between 1998 and 2010 at the microbiology laboratory of the French Polynesia Hospital Centre in Tahiti were whole genome sequenced (WGS), disclosing three major M. tuberculosis sensu stricto sublineages: L4.4.1.1 S-type, L4.1.1.3 X-Type, and L4.1.2.1 Haarlem. Furthermore, 20 isolates were identified as nontuberculous mycobacteria, including Mycobacterium fortuitum, which accounted for 65% of the identified nontuberculous mycobacteria, as well as Mycobacterium paragordonae and Mycobacterium gordonae identified with M. tuberculosis in two samples. Two further isolates were potentially representative of novel species in the Mycobacterium and Actinomadura genera. In total, 43 isolates exhibited in silico predicted antibiotic resistance to first- and second-line antibiotics. Combined with previously published data, the data reported here indicate a 12-year trend of decreasing diversity among the M. tuberculosis population circulating in Tahiti and the seemingly unsuccessful implantation of a recently imported of East African-Indian sublineage (L1.2.1.2.1). These findings contrast with the long-term persistence and predominance of the X-type family with L4.1.1.3; the S-type family with L4.4.1.1 and L4.4.2; the Haarlem family with L4.1.2 and L4.1.2.1, and the LAM family with L4.3.3, L4.3.2, and L4.3.4.2. These observations suggest that in remote territories such as the French Polynesia archipelago M. tuberculosis may rapidly adapt to local ecosystems.