DNA polymorphisms in the pepA and PPE18 genes among clinical strains of Mycobacterium tuberculosis: implications for vaccine efficacy

Abstract

Tuberculosis continues to be a leading cause of death worldwide. Development of an effective vaccine against Mycobacterium tuberculosis is necessary to reduce the global burden of this disease. Mtb72F, consisting of the protein products of the pepA and PPE18 genes, is the first subunit tuberculosis vaccine to undergo phase I clinical trials. To obtain insight into the ability of Mtb72F to induce an immune response capable of recognizing different strains of M. tuberculosis, we investigated the genomic diversity of the pepA and PPE18 genes among 225 clinical strains of M. tuberculosis from two different geographical locations, Arkansas and Turkey, representing a broad range of genotypes of M. tuberculosis. A combination of single nucleotide polymorphisms (SNPs) and insertion/deletions resulting in amino acid changes in the PPE18 protein occurred in 47 (20.9%) of the 225 study strains, whereas SNPs resulted in amino acid changes in the PepA protein in 14 (6.2%) of the 225 study strains. Of the 122 Arkansas study strains and the 103 Turkey study strains, 32 (26.2%) and 15 (14.6%), respectively, had at least one genetic change leading to an alteration of the amino acid sequence of the PPE18 protein, and many of the changes occurred in regions previously reported to be potential T-cell epitopes. Thus, immunity induced by Mtb72F may not recognize a proportion of M. tuberculosis clinical strains.

FIG. 1.

Mapping of the amino acid changes in the PPE18 protein that were found among the 122 study strains of M. tuberculosis from Arkansas (a) and the 103 study strains of M. tuberculosis from Turkey (b) in relation to the PPE18 protein sequence of reference strain H37Rv and the T-cell epitope likelihood scale of PPE18 generated using the data reported by Dillon et al. (11). (Panels A) T-cell epitope likelihood score distributions for 38 overlapping peptides of PPE18 described by Dillon et al. (11). The top graph shows the T-cell epitope likelihood score distribution for the overlapping peptide fragments having odd numbers of amino acids (amino acids 11 to 30, 31 to 50, etc.), and the bottom graph shows the T-cell epitope likelihood score distribution for the overlapping peptide fragments having even numbers of amino acids (amino acids 1 to 21, 21 to 40, etc.). The scale on the right ranges from 0 to 100; 0 is equivalent to a stimulatory index of ≤5 for all four donors, and 100 is equivalent to a stimulatory index of >5 for all four donors. (Panels B) Maps of locations of the different amino acid variations among the study strains in relation to the PPE18 protein of H37Rv. Vertical lines extending from the PPE18 amino acid map represent amino acid changes resulting from nsSNPs (B-1). Squares represent amino acid changes caused by nucleotide deletions (panel a, B-2), triangles represent amino acid changes resulting from nucleotide insertions (panel a, B-3; panel b, B-2), the horizontal line represents early termination of transcription (B-4), and the diamond represents two consecutive frameshifts, resulting in three amino acid changes (B-5). Each vertical line represents one amino acid change. The length of a vertical line indicates the proportion of the study strains having the specific change. Percentage scales are shown on the right.