Comparative Genomics Members of the same genus and/or species are often isolated from various environments or exhibit different phenotypic capabilities, indicating that different genes may be present that provide selective advantages between strains. Determining the differences in genetic content between highly related strains often required painstaking mapping or whole genome sequencing methods. Researchers can now use GeneChip arrays to compare the genetic content between multiple isolates on a gene-by-gene basis in a single experiment to reveal the subtle or significant differences in chromosomal content in a rapid and efficient manner.
Staphylococcus aureus, an opportunistic pathogen that causes serious infections in humans, is becoming increasingly refractive to antibiotic intervention. Cassat et al. used GeneChip® S. aureus Genome Arrays to compare the genomic content in two highly virulent clinical musculoskeletal isolates of Staphylococcus aureus with that of a prototypic lab strain (RN6390) and seven fully sequenced S. aureus genomes. Their results demonstrated that the genomes of the two highly virulent strains contained several key differences as compared to the lab strain. The cna (collagen binding adhesion) gene was present in the two virulent strains, but not in the lab strain, while the isaB (immunodominant antigen B) gene was absent, as well as genes in the sar (staphylococcal accessory regulator) regulatory circuit, which is associated with virulence. In addition to the characterization of virulence, the researchers used the GeneChip array results to group the strains into distinct clades. When they compared the seven fully sequenced genomes with those of the two virulent strains, they found that the two virulent strains were most closely related to the dominant oxacillin-resistant European clone, and most distant from a clade comprising the lab strain and three of the sequenced genomes. These results highlight the need to reassess the relevance of studies focusing on strains like the lab strain RN6390 compared with use of clinical isolates.
Pseudomonas aeruginosa causes a variety of life-threatening infections in humans, but the genetic basis for this capability is not well known. To determine whether genomic variation within Pseudomonas aeruginosa can be associated with differences in pathogenicity or type of infection, Wolfgang et al. employed GeneChip® P. aeruginosa Genome Arrays to compare the content of the prototypic lab strain PAO1 to eighteen different P. aeruginosa isolates, ranging from human clinical to environmental sources. These included isolates from pediatric Cystic Fibrosis patients, blood and ocular isolates, urinary tract infection isolates, environmental isolates (soil, water), and laboratory strains. Of the 5,549 genes present in PAO1, more than 93% or 5,183 were present in all eighteen strains tested, regardless of source, representing a “core set” of genes that allows P. aeruginosa to survive in diverse environments. An even higher degree of conservation, 97%, was found among the 267 genes involved in virulence, indicating that P. aeruginosa possesses a basic pathogenesis mechanism that confers an opportunistic infection capability to the organism.
Mycobacterium tuberculosis is the causative agent of tuberculosis, one of the oldest and most common human infectious diseases that results in millions of deaths per year worldwide. BCG (Bacillus Calmette-Geurin), the attenuated strain originally derived from virulent M. bovis, has been used as a tuberculosis vaccine since it was originally isolated in 1921. Mostowy et al. used GeneChip® M. tuberculosis Genome Arrays to compare the genomic structure of the thirteen clonal BCG strains that have been propagated through thousands of passages in different laboratories since BCG was originally isolated. This in vitro selection is thought to be responsible for the over-attenuation of BCG, rendering it no longer able to elicit an adequate immune response in humans for protection against M. tuberculosis . Analysis of GeneChip data indicated that in addition to the 9458 bp deletion (called RD1) that is present in all BCG strains and is the basis for attenuation, an additional eight deletions were observed. These deletions, which are spread throughout the genome, range from being unique to one strain to being shared by several others, and are associated with reduced virulence as compared to M. tuberculosis.
In a subsequent study, Hirsch et al. used GeneChip® M. tuberculosis Genome Arrays to characterize 68 unique deletions found in 100 clinical isolates from M. tuberculosis -infected patients representing both recent transmission of the disease or reactivation of a latent infection in a geographically- and ethnically-diverse population. By comparing the presence or absence of all 68 deletions in each of the 100 isolates to the geographic origin of the patients from which the isolates were derived, they were able to demonstrate a relationship between M. tuberculosis clade and the host?s place of origin. If this relationship is stable, it indicates that M. tuberculosis spreads within, rather than between large geographic regions, and that there may be underlying genetic, cultural, or environmental factors that lead to adaptation of specific M. tuberculosis lineages to specific host populations.
References
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Cassat, J.E., et al. Comparative Genomics of Staphylococcus aureus musculoskeletal isolates. J. Bacteriol.187: 576-592 (2005).
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Wolfgang, M., et al. Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci USA100: 8484-8489 (2003).
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Mostowy, S., et al. The in vitro evolution of BCG strains. Vaccine21: 4270-4274 (2003).
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Hirsh, A., et. al. Stable association between strains of Mycobacterium tuberculosis and their human host populations. ProcNatl Acad Sci USA101: 4871-4876 (2004).
Related Scientific Publications
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Mostowy, S., et al. Genomic interrogation of the Dassie Bacillus reveals it as a unique RD1 mutant with in the Mycobacterium tuberculosis complex. J Bacteriol186: 104-109 (2004).
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Tsolaki, A., et al. Functional and evolutionary genomics of Mycobacterium tuberculosis: Insights from genomic deletions in 100 strains. Proc Natl Acad Sci USA101: 4865-4870 (2004).
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Tsolaki, A., et al. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J Clin Microbiol.43: 3185-3191 (2005).
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Daran-Lapujade, P., et al. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Research4: 259-269 (2003).
Members of the same genus and/or species are often isolated from various environments or exhibit different phenotypic capabilities, indicating that different genes may be present that provide selective advantages between strains. Determining the differences in genetic content between highly related strains often required painstaking mapping or whole genome sequencing methods. Researchers can now use GeneChip arrays to compare the genetic content between multiple isolates on a gene-by-gene basis in a single experiment to reveal the subtle or significant differences in chromosomal content in a rapid and efficient manner.
Mycobacterium tuberculosis is the causative agent of tuberculosis, one of the oldest and most common human infectious diseases that results in millions of deaths per year worldwide. BCG (Bacillus Calmette-Geurin), the attenuated strain originally derived from virulent M. bovis, has been used as a tuberculosis vaccine since it was originally isolated in 1921. Mostowy et al. used GeneChip® M. tuberculosis Genome Arrays to compare the genomic structure of the thirteen clonal BCG strains that have been propagated through thousands of passages in different laboratories since BCG was originally isolated. This in vitro selection is thought to be responsible for the over-attenuation of BCG, rendering it no longer able to elicit an adequate immune response in humans for protection against M. tuberculosis . Analysis of GeneChip data indicated that in addition to the 9458 bp deletion (called RD1) that is present in all BCG strains and is the basis for attenuation, an additional eight deletions were observed. These deletions, which are spread throughout the genome, range from being unique to one strain to being shared by several others, and are associated with reduced virulence as compared to M. tuberculosis.
