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Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.

Davie JJ, Earl J, de Vries SP, Ahmed A, Hu FZ, Bootsma HJ, Stol K, Hermans PW, Wadowsky RM, Ehrlich GD, Hays JP, Campagnari AA - BMC Genomics (2011)

Bottom Line: These findings are consistent with the distributed genome hypothesis (DGH), which posits that the species genome possesses a far greater number of genes than any single isolate.Multiple and pair-wise whole genome alignments highlight limited chromosomal re-arrangement.M. catarrhalis gene content and chromosomal organization data, although supportive of the DGH, show modest overall genic diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA.

ABSTRACT

Background: M. catarrhalis is a gram-negative, gamma-proteobacterium and an opportunistic human pathogen associated with otitis media (OM) and exacerbations of chronic obstructive pulmonary disease (COPD). With direct and indirect costs for treating these conditions annually exceeding $33 billion in the United States alone, and nearly ubiquitous resistance to beta-lactam antibiotics among M. catarrhalis clinical isolates, a greater understanding of this pathogen's genome and its variability among isolates is needed.

Results: The genomic sequences of ten geographically and phenotypically diverse clinical isolates of M. catarrhalis were determined and analyzed together with two publicly available genomes. These twelve genomes were subjected to detailed comparative and predictive analyses aimed at characterizing the supragenome and understanding the metabolic and pathogenic potential of this species. A total of 2383 gene clusters were identified, of which 1755 are core with the remaining 628 clusters unevenly distributed among the twelve isolates. These findings are consistent with the distributed genome hypothesis (DGH), which posits that the species genome possesses a far greater number of genes than any single isolate. Multiple and pair-wise whole genome alignments highlight limited chromosomal re-arrangement.

Conclusions: M. catarrhalis gene content and chromosomal organization data, although supportive of the DGH, show modest overall genic diversity. These findings are in stark contrast with the reported heterogeneity of the species as a whole, as wells as to other bacterial pathogens mediating OM and COPD, providing important insight into M. catarrhalis pathogenesis that will aid in the development of novel therapeutic regimens.

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Pair-wise comparisons of the gene content of the 12 M. catarrhalis strains used in this study. Strain vs. strain comparisons are characterized as described in the text. Values in which one strain differs from its partner by one or more standard deviations are denoted by color code.
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Figure 4: Pair-wise comparisons of the gene content of the 12 M. catarrhalis strains used in this study. Strain vs. strain comparisons are characterized as described in the text. Values in which one strain differs from its partner by one or more standard deviations are denoted by color code.

Mentions: An exhaustive pair-wise comparison of all possible strain pairs (n = 66) was performed to gauge the mean and range of gene possession variability within the species (Figure 4). This analysis compares the sum of all gene clusters present in both strains (similarity score), the sum of all clusters not present in both strains (difference score) and the remainder of the latter subtracted from the former (comparison score) to provide an objective metric to quantify the relationship between any two strains. These analyses revealed that any two strains differed on average by the possession of 217.7 ± 55.9 gene clusters.


Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates.

Davie JJ, Earl J, de Vries SP, Ahmed A, Hu FZ, Bootsma HJ, Stol K, Hermans PW, Wadowsky RM, Ehrlich GD, Hays JP, Campagnari AA - BMC Genomics (2011)

Pair-wise comparisons of the gene content of the 12 M. catarrhalis strains used in this study. Strain vs. strain comparisons are characterized as described in the text. Values in which one strain differs from its partner by one or more standard deviations are denoted by color code.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045334&req=5

Figure 4: Pair-wise comparisons of the gene content of the 12 M. catarrhalis strains used in this study. Strain vs. strain comparisons are characterized as described in the text. Values in which one strain differs from its partner by one or more standard deviations are denoted by color code.
Mentions: An exhaustive pair-wise comparison of all possible strain pairs (n = 66) was performed to gauge the mean and range of gene possession variability within the species (Figure 4). This analysis compares the sum of all gene clusters present in both strains (similarity score), the sum of all clusters not present in both strains (difference score) and the remainder of the latter subtracted from the former (comparison score) to provide an objective metric to quantify the relationship between any two strains. These analyses revealed that any two strains differed on average by the possession of 217.7 ± 55.9 gene clusters.

Bottom Line: These findings are consistent with the distributed genome hypothesis (DGH), which posits that the species genome possesses a far greater number of genes than any single isolate.Multiple and pair-wise whole genome alignments highlight limited chromosomal re-arrangement.M. catarrhalis gene content and chromosomal organization data, although supportive of the DGH, show modest overall genic diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA.

ABSTRACT

Background: M. catarrhalis is a gram-negative, gamma-proteobacterium and an opportunistic human pathogen associated with otitis media (OM) and exacerbations of chronic obstructive pulmonary disease (COPD). With direct and indirect costs for treating these conditions annually exceeding $33 billion in the United States alone, and nearly ubiquitous resistance to beta-lactam antibiotics among M. catarrhalis clinical isolates, a greater understanding of this pathogen's genome and its variability among isolates is needed.

Results: The genomic sequences of ten geographically and phenotypically diverse clinical isolates of M. catarrhalis were determined and analyzed together with two publicly available genomes. These twelve genomes were subjected to detailed comparative and predictive analyses aimed at characterizing the supragenome and understanding the metabolic and pathogenic potential of this species. A total of 2383 gene clusters were identified, of which 1755 are core with the remaining 628 clusters unevenly distributed among the twelve isolates. These findings are consistent with the distributed genome hypothesis (DGH), which posits that the species genome possesses a far greater number of genes than any single isolate. Multiple and pair-wise whole genome alignments highlight limited chromosomal re-arrangement.

Conclusions: M. catarrhalis gene content and chromosomal organization data, although supportive of the DGH, show modest overall genic diversity. These findings are in stark contrast with the reported heterogeneity of the species as a whole, as wells as to other bacterial pathogens mediating OM and COPD, providing important insight into M. catarrhalis pathogenesis that will aid in the development of novel therapeutic regimens.

Show MeSH
Related in: MedlinePlus