Elucidation of Strain Variation in Clinical Mycobacterium tuberculosis isolates using a Proteogenomic Approach

Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand the biology and pathogenicity of M. tuberculosis. In this study we integrated whole-genome sequencing and GeLC-MS/MS proteomics to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach we identified 62 peptides containing single amino acid variants, which covered ~9% of all total coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we also identified 29 unique peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome and provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e. large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation. Our results contribute to the nascent field of M. tuberculosis proteogenomics and facilitate elucidation of strain differences in clinical M. tuberculosis isolates at the proteome level.