Comparative genomics and evolution of Staphylococcus aureus, epidermidis and haemolyticus

Fumihiko Takeuchi1, Tadashi Baba1,Shinya Watanabe1, Harumi Yuzawa1, Teruyo Ito1, Longzhu Cui1, Yuh Morimoto1, Makoto Kuroda1, Mikio Takahashi2, Akiho Ankai2, Katsumi Isono2, Keiichi Hiramatsu1
1Department of Bacteriology, Juntendo University, Tokyo 2National Institute of Technology and Evaluation, Sendai

S.aureus, S.epidermidis and S.haemolyticus are among the 39 species belonging to staphylococci. S.aureus having virulence and antibiotic resistant genes is a pathogen of nosocomial infection. S.epidermidis has low virulence and is prevalent in human skin. S.haemolyticus has low virulence as well and is known for quick phenotypic conversion. We study the evolution driving their speciation and resulting in the difference of phenotypes in these species. Genomes sequences of S.aureus and S.epidermidis are already determined. We sequenced and annotated S.haemolyticus JCSC1435. For comparative analysis, we defined a 'homologue set' as a group of open reading frames (orfs) having similarity at least 70% in nucleotide sequence. The homologue sets were categorized by the species sharing them. In each category, the proportions of the sets according to biological functions were studied. Local chromosomal regions not having orfs from homologue sets shared across species were extracted as regions of alien origin.
A staphylococci has around 2800 orfs, and 1282 homologue sets were shared across three species. The 821 specific to S.aureus had higher proportion of pathogenic factors compared to other categories. The 112 specific to S.epidermidis and S.haemolyticus had higher proportion of orfs for metabolism of coenzymes and prosthetic groups. In any species, the regions around the origin of replication had low proportion of orfs common across species, and genes indispensable for growth were not included here. Genomic islands including Staphylococcus Cassette Chromosome or phages were found in S.haemolyticus as well. This implies that the mechanism of horizontal transfer using genomic islands is common in staphylococci. However, genomic islands assembling virulence genes were found only in S.aureus. As many as 82 Insertion Sequences (ISs) were scattered in the chromosome of S.haemolyticus, and recombinations mediated by these ISs were observed, which might be realizing the phenotypic plasticity of this species.