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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.

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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

Size of SNP blocks found in the β1 group of Hib strains. This histogram represents the frequency of different sizes of SNP blocks (as defined in the text) in the genomes of β1 H. influenzae type b strains.
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Figure 3: Size of SNP blocks found in the β1 group of Hib strains. This histogram represents the frequency of different sizes of SNP blocks (as defined in the text) in the genomes of β1 H. influenzae type b strains.

Mentions: We hypothesised that “blocks” of DNA sequence with a high frequency of SNPs, separated by regions of the genome with low SNP density, could each represent an individual transformation event (Figure 2). To investigate this, we analysed two strains (RM7578 and RM7122) that have the same multi-locus sequence type. RM7578, the strain most closely related to the reference strain 10810, has five blocks of SNPs. For this analysis, blocks were defined as contiguous regions containing at least 30 SNPs, with each SNP separated by no more than 300 bp. 91% of 694 SNPs between strains RM7578 and 10810 were found within these five blocks, amounting in total to 23.5 kbp of DNA, or 1.2% of the genome. Strain RM7122 had 15 blocks of SNPs when compared to strain 10810, equivalent to 2.4% of the genome. In the β1 strains, the size of these blocks ranged from less than 0.5 to more than 25 kbp, with a median size of 4.8 kbp (Figure 3), findings within the range recently reported experimentally for H. influenzae strains[17]. We concluded that the blocks of SNPs identified between the closely related Hib strains represented recombination events, resulting in allelic exchanges that could delete or insert novel DNA, including whole genes.


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)

Size of SNP blocks found in the β1 group of Hib strains. This histogram represents the frequency of different sizes of SNP blocks (as defined in the text) in the genomes of β1 H. influenzae type b strains.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Size of SNP blocks found in the β1 group of Hib strains. This histogram represents the frequency of different sizes of SNP blocks (as defined in the text) in the genomes of β1 H. influenzae type b strains.
Mentions: We hypothesised that “blocks” of DNA sequence with a high frequency of SNPs, separated by regions of the genome with low SNP density, could each represent an individual transformation event (Figure 2). To investigate this, we analysed two strains (RM7578 and RM7122) that have the same multi-locus sequence type. RM7578, the strain most closely related to the reference strain 10810, has five blocks of SNPs. For this analysis, blocks were defined as contiguous regions containing at least 30 SNPs, with each SNP separated by no more than 300 bp. 91% of 694 SNPs between strains RM7578 and 10810 were found within these five blocks, amounting in total to 23.5 kbp of DNA, or 1.2% of the genome. Strain RM7122 had 15 blocks of SNPs when compared to strain 10810, equivalent to 2.4% of the genome. In the β1 strains, the size of these blocks ranged from less than 0.5 to more than 25 kbp, with a median size of 4.8 kbp (Figure 3), findings within the range recently reported experimentally for H. influenzae strains[17]. We concluded that the blocks of SNPs identified between the closely related Hib strains represented recombination events, resulting in allelic exchanges that could delete or insert novel DNA, including whole genes.

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