title: Comparative genomic analysis between typhoidal and non-typhoidal Salmonella serovars reveals typhoid-specific protein families.
abstract: BACKGROUND
  The genus Salmonella contains more than 2600 serovars. While most cause a self-limiting gastroenteritis, four serovars, S. Typhi, S. Paratyphi A, B and C, elicit typhoid, a potentially fatal systemic infection. Because of the prevalence in certain regions, such as South Asia, and the disease severity of typhoidal Salmonella infections, comprehensive studies are needed to elucidate the pathogenesis of diseases caused by these typhoidal serovars.
  
  
  RESULTS
  We performed comparative genomic analyses on eight human typhoidal strains and 27 non-human typhoidal Salmonella strains to elucidate their evolutionary relationships and identify the genes specific to the four typhoidal serovars. Our results indicate that Salmonella may have an open pan-genome. A core-genome based phylogeny demonstrated that divergence between S. Paratyphi A and S. Typhi took place not long ago and S. Paratyphi B shared a recent common ancestor with S. Paratyphi C. Of great interest, the divergence between S. Paratyphi B and S. Paratyphi C was shown to be more recent than that between S. Paratyphi A and S. Typhi. Alignment and comparisons of the genomes identified unique complements of protein families to each of the typhoidal serovars. Most of these protein families are phage related and some are candidate virulence factors. Importantly, we found 88 protein families specific to two to three of the four typhoidal serovars. All but two of the 88 genes are present in S. Typhi, with a few in the three paratyphoidal serovars but none in the non-human typhoidal serovars. Most of these genes are predicted to encode hypothetical proteins and some are known to code for virulence factors such as Vi polysaccharide related proteins.
  
  
  CONCLUSIONS
  By comprehensive genomic comparisons, we identified protein families specific to the human typhoidal serovars, which will greatly facilitate investigations on typhoid pathogenesis.
authors.affiliation: Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
authors.forename: Qing-Hua
authors.initials: QH
authors.lastname: Zou
authors.affiliation: Institute of Immunology, Beijing Center for Disease Control and Prevention, Beijing, China.
authors.forename: Ren-Qing
authors.initials: RQ
authors.lastname: Li
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China. Electronic address: grliu.natsumi@gmail.com.
authors.forename: Gui-Rong
authors.initials: GR
authors.lastname: Liu
authors.affiliation: Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Faculty of Pharmacy, Harbin Medical University, Harbin, China; Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada. Electronic address: slliu@ucalgary.ca.
authors.forename: Shu-Lin
authors.initials: SL
authors.lastname: Liu
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D005810:Multigene Family; D016366:Open Reading Frames; D010802:Phylogeny; D012475:Salmonella / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012480:Salmonella Infections; D012485:Salmonella typhi / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D065288:Serogroup; D014435:Typhoid Fever
chemical_list: D001426:Bacterial Proteins
keywords: S. Paratyphi A; S. Paratyphi B; S. Paratyphi C; S. Typhi; Salmonella; Specific protein families