Details of 18 whole genome sequence isolates used for <i>in silico</i> comparative gene analysis.

<p>Each analysed genome sequence is listed along with its lineage number <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Comas2" target="_blank">[78]</a>, Principal Genetic Group (PGG) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Sreevatsan1" target="_blank">[2]</a> and family group.</p

Details of the <i>pe</i> and <i>ppe</i> genes examined by whole gene sequencing.

*<p> <b>As defined in reference </b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-GeyvanPittius1" target="_blank">[<b>8</b>]</a><b>.</b></p><p>Each gene sequenced in this study is listed along with its phylogenetic position within its family and any additional information regarding its protein's function available in the literature.</p

Details of clinical isolates used in this study.

<p>Each clinical isolate along with its lineage number <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Comas2" target="_blank">[78]</a>, PGG group <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Sreevatsan1" target="_blank">[2]</a>, spoligotype family group status <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Brudey1" target="_blank">[88]</a> and South African IS<i>6110</i> lineage <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-Streicher1" target="_blank">[84]</a> is listed.</p

Phylogenetic reconstruction of the evolutionary relationships between the members of the pe and ppe protein families.

<p>A. Phylogeny of the ppe protein family. The phylogenetic tree was constructed from the phylogenetic analysis done on the 180 aa N-terminal domains of the ppe proteins. The tree was rooted to the outgroup Rv3873 (ppe68), shown to be the first ppe insertion into the ESAT-6 (esx) gene clusters <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-GeyvanPittius1" target="_blank">[8]</a>. Figure reproduced from reference 8 with permission of the authors. B. Phylogeny of the pe protein family. The phylogenetic tree was constructed from the phylogenetic analysis done on the 110 aa N-terminal domains of the pe proteins. The tree was rooted to the outgroup Rv3872 (pe35), shown to be the first pe insertion into the ESAT-6 (esx) gene clusters <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030593#pone.0030593-GeyvanPittius1" target="_blank">[8]</a>. Figure reproduced from reference 8 with permission of the authors.</p

Proteogenomic Investigation of Strain Variation in Clinical <i>Mycobacterium tuberculosis</i> Isolates

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 the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC–MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we 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 at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates

Frequency of strain genotype combinations cultured on MGIT or LJ media.

<p>Frequency of strain genotype combinations cultured on MGIT or LJ media.</p

Strain genotypes cultured on MGIT and LJ media classified according to PCR amplification.

a<p>strain genotypes other than the strains tested with the 5 primer sets.</p>b<p>isolates did not amplify or amplified with an unknown product.</p>c<p>more than 1 strain genotype was present in the primary culture.</p>d<p>in combination, mixed infection was observed in 15% of cases.</p

Strain genotypes present in single and mixed infections.

<p>Strain genotypes present in single and mixed infections.</p

Primer sequences used to identify strains of the Beijing, LAM, S-family, LCC and Haarlem genotype, respectively.

a<p>according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070178#pone.0070178-Marais1" target="_blank">[20]</a>.</p>b<p>RD105 region according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070178#pone.0070178-Tsolaki1" target="_blank">[22]</a>.</p>c<p>internal primer used for primer set 2 to 4.</p

The population structure of mixed infections cultured on MGIT media and their corresponding LJ media.

*<p>discrepant PCR amplification results of strain genotypes cultured on MGIT or LJ media, respectively.</p