A nonsynonymous SNP catalog of mycobacterium tuberculosis virulence genes and its use for detecting new potentially virulent sublineages

Abstract

Mycobacterium tuberculosis is divided into several distinct lineages, and various geneticmarkers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin-antitoxin systems. Another catalog of 1,573 M. tuberculosis isolates of different lineages has been developed. The developed SNP-calling program has identified 3,563 nonsynonymous SNPs. The constructed SNP-based phylogeny reflected the evolutionary relationship between lineages and detected new sublineages. SNP analysis of sublineage F15/LAM4/KZN revealed four lineage-specificmutations in cyp125, mce3B, vapC25, and vapB34. The Ural lineage has been divided into two geographical clusters based on different SNPs in virulence genes.Anewsublineage, B0/N-90, was detected inside the Beijing- B0/W-148 by SNPs in irtB,mce3F and vapC46.We have found 27members of B0/N-90 among the 227 available genomes of the Beijing-B0/W-148 sublineage. Whole-genome sequencing of strain B9741, isolated from an HIV-positive patient, was demonstrated to belong to the new B0/N-90 group.Aprimer set for PCR detection of B0/N-90 lineage-specificmutations has been developed. The prospective use of mce3 mutant genes as genetically engineered vaccine is discussed.