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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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Relatedness among strains. Each strain was assayed for its relatedness to every other strain by several methods. A) The MLST type of each isolate was identified as described in the Methods; the scale bar indicates topological distance in relative distance units (RDU) between strains. Isolate O35E was excluded from A) as it contained two sequence variants (adk and fumC alleles) that were not present in the M. catarrhalis MLST database at the time of submission. In addition, * denotes strains whose MLST types were taken from the M. catarrhalis MLST database [16]; all other data presented here are taken from pyrosequencing efforts. Neighbor-Joining analysis of was performed for both point mutations in the core genome (B) or genic differences in the distributed (C) genome. Branches in the same neighbor group are identically color-coded and length bars indicate the topological distance measured in 1-average nucleotide identity between each genome.
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Figure 3: Relatedness among strains. Each strain was assayed for its relatedness to every other strain by several methods. A) The MLST type of each isolate was identified as described in the Methods; the scale bar indicates topological distance in relative distance units (RDU) between strains. Isolate O35E was excluded from A) as it contained two sequence variants (adk and fumC alleles) that were not present in the M. catarrhalis MLST database at the time of submission. In addition, * denotes strains whose MLST types were taken from the M. catarrhalis MLST database [16]; all other data presented here are taken from pyrosequencing efforts. Neighbor-Joining analysis of was performed for both point mutations in the core genome (B) or genic differences in the distributed (C) genome. Branches in the same neighbor group are identically color-coded and length bars indicate the topological distance measured in 1-average nucleotide identity between each genome.

Mentions: MLST analyses demonstrated that each of the twelve genomes represented a different sequence type, including four novel sequence types and novel sequence variants for the fumC and adk alleles present in O35E (Table 3 and Figure 3A), indicating success in selecting a diverse group of strains for sequence analysis. Because of the expected high degree of genomic mosaicism resulting from extensive horizontal gene transfer, relationship dendrograms were constructed by employing a non-phylogenetic identity-by-state, whole-genome clustering method [14,22]. In one case, sequence polymorphisms present in the core genes were used to construct the relationships, and in a second analysis gene possession data were used (Figures 3B and 3C, respectively). These analyses revealed intriguing differences depending upon the analytical method; no clear clade structure could be determined using allelic differences within the core genome, however, the use of the distributed genome data produced a dendrogram that was broadly similar to that generated from the MLST data, albeit with several exceptions. Interestingly, all three methods consistently formed two clusters; one cluster consisting of strains ATCC 43617, 7169, and BC1, and a second group comprised of 101P30B1, CO72, and 103P14B1. Notably, the consistent clustering of these two groups of strains does not correlate with patient age group, geographic origin, COPD exacerbation or OM. These data suggest that using any of these methods alone is insufficient for correctly inferring the relationships among M. catarrhalis isolates.


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)

Relatedness among strains. Each strain was assayed for its relatedness to every other strain by several methods. A) The MLST type of each isolate was identified as described in the Methods; the scale bar indicates topological distance in relative distance units (RDU) between strains. Isolate O35E was excluded from A) as it contained two sequence variants (adk and fumC alleles) that were not present in the M. catarrhalis MLST database at the time of submission. In addition, * denotes strains whose MLST types were taken from the M. catarrhalis MLST database [16]; all other data presented here are taken from pyrosequencing efforts. Neighbor-Joining analysis of was performed for both point mutations in the core genome (B) or genic differences in the distributed (C) genome. Branches in the same neighbor group are identically color-coded and length bars indicate the topological distance measured in 1-average nucleotide identity between each genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Relatedness among strains. Each strain was assayed for its relatedness to every other strain by several methods. A) The MLST type of each isolate was identified as described in the Methods; the scale bar indicates topological distance in relative distance units (RDU) between strains. Isolate O35E was excluded from A) as it contained two sequence variants (adk and fumC alleles) that were not present in the M. catarrhalis MLST database at the time of submission. In addition, * denotes strains whose MLST types were taken from the M. catarrhalis MLST database [16]; all other data presented here are taken from pyrosequencing efforts. Neighbor-Joining analysis of was performed for both point mutations in the core genome (B) or genic differences in the distributed (C) genome. Branches in the same neighbor group are identically color-coded and length bars indicate the topological distance measured in 1-average nucleotide identity between each genome.
Mentions: MLST analyses demonstrated that each of the twelve genomes represented a different sequence type, including four novel sequence types and novel sequence variants for the fumC and adk alleles present in O35E (Table 3 and Figure 3A), indicating success in selecting a diverse group of strains for sequence analysis. Because of the expected high degree of genomic mosaicism resulting from extensive horizontal gene transfer, relationship dendrograms were constructed by employing a non-phylogenetic identity-by-state, whole-genome clustering method [14,22]. In one case, sequence polymorphisms present in the core genes were used to construct the relationships, and in a second analysis gene possession data were used (Figures 3B and 3C, respectively). These analyses revealed intriguing differences depending upon the analytical method; no clear clade structure could be determined using allelic differences within the core genome, however, the use of the distributed genome data produced a dendrogram that was broadly similar to that generated from the MLST data, albeit with several exceptions. Interestingly, all three methods consistently formed two clusters; one cluster consisting of strains ATCC 43617, 7169, and BC1, and a second group comprised of 101P30B1, CO72, and 103P14B1. Notably, the consistent clustering of these two groups of strains does not correlate with patient age group, geographic origin, COPD exacerbation or OM. These data suggest that using any of these methods alone is insufficient for correctly inferring the relationships among M. catarrhalis isolates.

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