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Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants.

Power PM, Bentley SD, Parkhill J, Moxon ER, Hood DW - BMC Microbiol. (2012)

Bottom Line: Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease.When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages.For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, Oxford, UK. .

ABSTRACT

Background: Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species.

Results: Genomic DNA sequence was obtained from 85 strains of H. influenzae and from other related species, selected based on geographical site of isolation, disease association and documented genotypic and phenotypic differences. When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages. For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain. Evidence that this naturally occurring pattern of inter-strain variation in H. influenzae can be mediated by transformation was obtained through sequencing DNA obtained from a pool of 200 independent transformants of a recipient (strain Rd) using donor DNA from a heterologous Hib strain (Eagan).

Conclusion: Much of the inter-strain variation in genome sequence in H. influenzae is likely the result of inter-strain exchanges of DNA, most plausibly through transformation.

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Related in: MedlinePlus

Whole genome heat map, constructed by Mauve, to achieve pairwise percentage of genome sequence alignment. Pair-wise Mauve alignments were conducted with 60 H. influenzae and H. haemolyticus genome sequences from strains included on a single sequencing flow cell. For each pair-wise comparison the length of the alignment achieved, expressed as the percentage of the total sequence length, was calculated and a distance matrix created. The heat map was created using the R statistical package and shows the clustered genomes determined by the default R heatmap function clustering methods (http://www.r-project.org/). At the top of the figure, an indication of the relatedness between genomes is given. Mauve achieved pairwise genome sequence alignments of between 69.8 and 94.4% across our range of genomes. Strains are listed in the same order on the x and y axes; groupings discussed in the text are indicated along the top axis and the relevant strains are indicated by brackets on the right hand side axis, labelled with a Greek letter.
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Figure 1: Whole genome heat map, constructed by Mauve, to achieve pairwise percentage of genome sequence alignment. Pair-wise Mauve alignments were conducted with 60 H. influenzae and H. haemolyticus genome sequences from strains included on a single sequencing flow cell. For each pair-wise comparison the length of the alignment achieved, expressed as the percentage of the total sequence length, was calculated and a distance matrix created. The heat map was created using the R statistical package and shows the clustered genomes determined by the default R heatmap function clustering methods (http://www.r-project.org/). At the top of the figure, an indication of the relatedness between genomes is given. Mauve achieved pairwise genome sequence alignments of between 69.8 and 94.4% across our range of genomes. Strains are listed in the same order on the x and y axes; groupings discussed in the text are indicated along the top axis and the relevant strains are indicated by brackets on the right hand side axis, labelled with a Greek letter.

Mentions: The genome assemblies were aligned in a pair-wise fashion using Mauve[16]. The length of the aligned portion of genomes achieved between any pair of strains, expressed as a percentage of the genome sequence length, was used as a measure of the relatedness of the strains. These pair-wise relationships were displayed as a heatmap using the R statistical package included within the analysis software (Figure‚ÄČ1). This method of ordering of strains is dependent on each having a similar degree of sequence coverage, and hence assembly length, thus the analysis was confined to data for the 60 genomes of H. influenzae and H. haemolyticus sequenced in the same flow cell (see Methods). A tree obtained following a simpler SNP-based analysis of the genome sequences (Additional file1: Figure S1) gave an overall similar grouping of strains, validating the output from the Mauve analysis.


Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants.

Power PM, Bentley SD, Parkhill J, Moxon ER, Hood DW - BMC Microbiol. (2012)

Whole genome heat map, constructed by Mauve, to achieve pairwise percentage of genome sequence alignment. Pair-wise Mauve alignments were conducted with 60 H. influenzae and H. haemolyticus genome sequences from strains included on a single sequencing flow cell. For each pair-wise comparison the length of the alignment achieved, expressed as the percentage of the total sequence length, was calculated and a distance matrix created. The heat map was created using the R statistical package and shows the clustered genomes determined by the default R heatmap function clustering methods (http://www.r-project.org/). At the top of the figure, an indication of the relatedness between genomes is given. Mauve achieved pairwise genome sequence alignments of between 69.8 and 94.4% across our range of genomes. Strains are listed in the same order on the x and y axes; groupings discussed in the text are indicated along the top axis and the relevant strains are indicated by brackets on the right hand side axis, labelled with a Greek letter.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539920&req=5

Figure 1: Whole genome heat map, constructed by Mauve, to achieve pairwise percentage of genome sequence alignment. Pair-wise Mauve alignments were conducted with 60 H. influenzae and H. haemolyticus genome sequences from strains included on a single sequencing flow cell. For each pair-wise comparison the length of the alignment achieved, expressed as the percentage of the total sequence length, was calculated and a distance matrix created. The heat map was created using the R statistical package and shows the clustered genomes determined by the default R heatmap function clustering methods (http://www.r-project.org/). At the top of the figure, an indication of the relatedness between genomes is given. Mauve achieved pairwise genome sequence alignments of between 69.8 and 94.4% across our range of genomes. Strains are listed in the same order on the x and y axes; groupings discussed in the text are indicated along the top axis and the relevant strains are indicated by brackets on the right hand side axis, labelled with a Greek letter.
Mentions: The genome assemblies were aligned in a pair-wise fashion using Mauve[16]. The length of the aligned portion of genomes achieved between any pair of strains, expressed as a percentage of the genome sequence length, was used as a measure of the relatedness of the strains. These pair-wise relationships were displayed as a heatmap using the R statistical package included within the analysis software (Figure‚ÄČ1). This method of ordering of strains is dependent on each having a similar degree of sequence coverage, and hence assembly length, thus the analysis was confined to data for the 60 genomes of H. influenzae and H. haemolyticus sequenced in the same flow cell (see Methods). A tree obtained following a simpler SNP-based analysis of the genome sequences (Additional file1: Figure S1) gave an overall similar grouping of strains, validating the output from the Mauve analysis.

Bottom Line: Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease.When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages.For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, Oxford, UK. .

ABSTRACT

Background: Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species.

Results: Genomic DNA sequence was obtained from 85 strains of H. influenzae and from other related species, selected based on geographical site of isolation, disease association and documented genotypic and phenotypic differences. When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages. For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain. Evidence that this naturally occurring pattern of inter-strain variation in H. influenzae can be mediated by transformation was obtained through sequencing DNA obtained from a pool of 200 independent transformants of a recipient (strain Rd) using donor DNA from a heterologous Hib strain (Eagan).

Conclusion: Much of the inter-strain variation in genome sequence in H. influenzae is likely the result of inter-strain exchanges of DNA, most plausibly through transformation.

Show MeSH
Related in: MedlinePlus