Whole-Genome Comparison ofMycobacterium tuberculosisClinical and Laboratory Strains

Abstract

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

Genomic Comparison of PE and PPE Genes in the Mycobacterium avium Complex

“…These SNPs can be used for subspecies differentiation. SNPs are frequently used in epidemiological and evolutionary studies to differentiate between closely related species, subspecies, and strains of bacteria without knowledge of what effect the SNP may have on gene function or protein activity (1,19,24,27,47). …”

Unmatched Sequences in Public Databases – Exemplified by Tuberculin‐Active Protein

“…Since Kuwabara's experiments in the 1970 s, the complete nucleotide sequences of M. tuberculosis H37Rv [6], M. tuberculosis CDC1551 [7] and M. bovis [8] have become known. Kuwabara purified the tuberculin-active protein from M. tuberculosis cells as well as from M. bovis bacillus Calmette-Guérin vaccine (BCG) cells, and its 89-aminoacid sequence should therefore be encoded within these genomes.…”

Pulmonary Tuberculosis and Mycobacterium Tuberculosis: Modern Molecular Epidemiology and Perspectives

“…In addition, a sequencing project for M. bovis BCG is ongoing (http://www.sanger.ac.uk/ Projects/Microbes). The comparison of the complete sequences of the two strains (H37Rv, which is the classical reference strain, and one recent MTB strain CDC1551) confirms a much higher degree of polymorphism than previously thought [63,82]. These latter studies made it possible to identify large-sequence polymorphisms (LSPs) and singlenucleotide polymorphisms (SNPs), whereas the molecular basis of variability in virulence and transmissibility remains undefined.Tsolaki et al [199] have developed a complementary approach to comparative genomics involving the analysis of unsequenced genomes by DNA microarray.…”

“…Nevertheless, the only way to detect the real genetic diversity of an organism is the whole sequencing of several genomes from different clinical isolates. For MTB, the complete genome sequences of three strains, but also of one M. bovis strain, are now available (www.tigr.org) [63,70]. In addition, a sequencing project for M. bovis BCG is ongoing (http://www.sanger.ac.uk/ Projects/Microbes).…”