The Latin American-Mediterranean (LAM) lineage of the Mycobacterium tuberculosis complex constitutes a widespread family of strains within the Euro-American phylogeographical lineage. In this study we report the genotypic characterization, based on the large sequence deletion and spoligotype polymorphisms, of a collection of LAM strains isolated in Tuscany, Italy, a region with a low prevalence of tuberculosis (TB), but where the ethnic diversity of TB patients provides an opportunity to study a global sample of LAM strains. Large sequence polymorphism (LSP) analysis of a collection of 137 LAM strains detected three prevalent, mutually exclusive deletions, i.e., RD115, RD174 and RD726, respectively in 27.7%, 28.5% and 13.9% of isolates; 94.9% of strains bearing deletion RD174 also harboured the RDRio deletion. Deletions RD182, RD219 and RD761 were detected in occasional strains; deletions RD122, RD183, RD193 and RD724 were not found; 24.1% of strains showed no deletion. Deletion RD726 was found highly prevalent in the LAM10_CAM spoligotype sublineage that includes the “Cameroon” strains. Of the 42 Spoligotype International Types (SITs) assigned to the study strains, eleven were shared by strains belonging to different deletion-defi ned sublineages. In particular, 9 SITs (SIT20, 33, 61, 93, 161, 177, 209, 737 and 1064) were detected in two RD-defi ned sulineages; 1 SIT (SIT60) in three sublineages; and 1 SIT (SIT42) in as many as six distinct RD sublineages. The general lack of concordance between the phylogenetic sublineages defi ned by large sequence deletions and the spoligotype groupings provides a clear evidence of spoligotype homoplasy due to independent deletion events of the same spacers in strains belonging to different evolutive lineages. These considerations argue against the use of spoligotyping for defi ning deep phylogenetic relationships within the LAM family. With regard to the LAM RDRio strains, recently emerged as an important cause of tuberculosis (TB) associated with a more severe disease, high transmissibility and multidrug resistance, we did not observe any clinically distinctive or more severe form of disease in RDRio TB patients; moreover, 15-loci variable-Number-Tandem- Repeat (vNTR) analysis demonstrated that the very large majority of RDRio strains show unique genotypic profi les, which rules out an increased transmissibility of RDRio strains in our low-incidence setting.
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