Research

Sequence and functional analyses of Haemophilus spp. genomic islands

Mario Juhas¹ , Peter M Power² , Rosalind M Harding³ , David JP Ferguson⁴ , Ioanna D Dimopoulou¹ , Abdel RE Elamin¹ , Zaini Mohd-Zain⁵ , Derek W Hood² , Richard Adegbola⁶ , Alice Erwin⁷ , Arnold Smith⁷ , Robert S Munson⁸ , Alistair Harrison⁸ , Lucielle Mansfield⁹ , Stephen Bentley¹⁰ and Derrick W Crook¹

¹Clinical Microbiology and Infectious Diseases, NDCLS, University of Oxford, Headley Way, Oxford OX3 9DU, UK

²The Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK

³Departments of Zoology and Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK

⁴Department of Pathology, University of Oxford, Headley Way, Oxford OX3 9DU, UK

⁵Faculty of Medicine, University Technology MARA, Shah Alam, 40450, Malaysia

⁶Medical Research Council Laboratories, PO Box 273, Banjul, Gambia

⁷Seattle Biomedical Research Institute, University of Washington, Westlake Avenue North, Seattle, WA 98109, USA

⁸The Center for Microbial Pathogenesis in Nationwide Children's Research Institute and The Center for Microbial Interface Biology, The Ohio State University, Children's Drive, Columbus, OH 43205, USA

⁹OCDEM, Churchill Hospital, Old Road, Oxford OX3 7LJ, UK

¹⁰The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK

author email corresponding author email

Genome Biology 2007, 8:R237doi:10.1186/gb-2007-8-11-r237

Published:	8 November 2007

Subject areas: Genome studies, Microbiology and parasitology, Evolution

Abstract

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.