Detection of the Mycobacterium tuberculosis S-Genotype and Clarification of the Position of Controversial Spoligotypes of the Euro-American Lineage

— The S genotype (first described in Sicily, hence the name) is a part of the Euro-American lineage of Mycobacterium tuberculosis . Here, we report a method for its detection based on PCR-RFLP of the Rv0557 gene. The method was optimized on strains with known whole genome sequences and further applied to screening the DNA collections from Russia, Bulgaria, China, Japan, and Vietnam. PCR-RFLP analysis confirmed the S genotype in strains with the spoligotypes SIT34 (ancestral to S) and SIT1253 (Yakutia strains). Strains from Bulgaria with abridged spoligoprofiles SIT4 and SIT125 were also assigned to the S genotype. The developed method provides for rapid detection of the M. tuberculosis S genotype and reliably resolves phylogenetic ambiguity of the disputed spoligotypes.