Abstract
BackgroundHaemophilus 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.ResultsGenomic 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).ConclusionMuch 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.
Highlights
Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease
Haemophilus influenzae is a frequently isolated member of the commensal microbiota of the human nasopharynx that causes a variety of diseases including invasive infections as well as diseases resulting from contiguous spread within the respiratory tract, such as otitis media, pneumonia, conjunctivitis, epiglottitis, and exacerbations of chronic obstructive pulmonary disease (COPD)
We estimated the average genome coverage to be 83%, based on comparison with extant complete H. influenzae genome sequences; this data represents a ten-fold increase in the amount of genome sequence information available for H. influenzae
Summary
Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. Within naturally occurring populations of transformable bacteria, it has been proposed that each strain in a population contributes to and can acquire genes from the pan-genome (the superset of all genes of the species) [1,2,3] This hypothesis suggests that genetic exchange, especially through transformation-mediated homologous recombination, plays a major role in shaping the diversity of H. influenzae, and that these variations affect commensal and virulence behaviour. Investigations that detail the extent of the genomic diversity of the species and the mechanisms by which this diversity is transferred between strains are important for understanding both the population dynamics and characterising the genetic basis of the differences in severity and spectrum of disease associated with particular strains. Further evidence for the role of transformation in the import of novel sequence flanked by regions of DNA found in both the donor and recipient was obtained through sequencing DNA obtained from a pool of strains each transformed with DNA from a heterologous donor Hib strain
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