title: Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model.
abstract: BACKGROUND
  Staphylococcus aureus is associated with a spectrum of symbiotic relationships with its human host from carriage to sepsis and is frequently associated with nosocomial and community-acquired infections, thus the differential gene content among strains is of interest.
  
  
  RESULTS
  We sequenced three clinical strains and combined these data with 13 publically available human isolates and one bovine strain for comparative genomic analyses. All genomes were annotated using RAST, and then their gene similarities and differences were delineated. Gene clustering yielded 3,155 orthologous gene clusters, of which 2,266 were core, 755 were distributed, and 134 were unique. Individual genomes contained between 2,524 and 2,648 genes. Gene-content comparisons among all possible S. aureus strain pairs (n = 136) revealed a mean difference of 296 genes and a maximum difference of 476 genes. We developed a revised version of our finite supragenome model to estimate the size of the S. aureus supragenome (3,221 genes, with 2,245 core genes), and compared it with those of Haemophilus influenzae and Streptococcus pneumoniae. There was excellent agreement between RAST's annotations and our CDS clustering procedure providing for high fidelity metabolomic subsystem analyses to extend our comparative genomic characterization of these strains.
  
  
  CONCLUSIONS
  Using a multi-species comparative supragenomic analysis enabled by an improved version of our finite supragenome model we provide data and an interpretation explaining the relatively larger core genome of S. aureus compared to other opportunistic nasopharyngeal pathogens. In addition, we provide independent validation for the efficiency and effectiveness of our orthologous gene clustering algorithm.
authors.affiliation: Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, PA 15212, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Boissy
authors.forename: Azad
authors.initials: A
authors.lastname: Ahmed
authors.forename: Benjamin
authors.initials: B
authors.lastname: Janto
authors.forename: Josh
authors.initials: J
authors.lastname: Earl
authors.forename: Barry G
authors.initials: BG
authors.lastname: Hall
authors.forename: Justin S
authors.initials: JS
authors.lastname: Hogg
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.forename: Luisa N
authors.initials: LN
authors.lastname: Hiller
authors.forename: Evan
authors.initials: E
authors.lastname: Powell
authors.forename: Jay
authors.initials: J
authors.lastname: Hayes
authors.forename: Susan
authors.initials: S
authors.lastname: Yu
authors.forename: Sandeep
authors.initials: S
authors.lastname: Kathju
authors.forename: Paul
authors.initials: P
authors.lastname: Stoodley
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Post
authors.forename: Garth D
authors.initials: GD
authors.lastname: Ehrlich
authors.forename: Fen Z
authors.initials: FZ
authors.lastname: Hu
mesh_terms: D000465:Algorithms; D000818:Animals; D002417:Cattle; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006193:Haemophilus influenzae / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008957:Models, Genetic; D005810:Multigene Family; D016366:Open Reading Frames; D013203:Staphylococcal Infections / Q000382:microbiology; D013211:Staphylococcus aureus / Q000235:genetics* / Q000302:isolation & purification; D013296:Streptococcus pneumoniae / Q000235:genetics* / Q000302:isolation & purification