title: CTAG-containing cleavage site profiling to delineate Salmonella into natural clusters.
abstract: BACKGROUND
  The bacterial genus Salmonella contains thousands of serotypes that infect humans or other hosts, causing mild gastroenteritis to potentially fatal systemic infections in humans. Pathogenically distinct Salmonella serotypes have been classified as individual species or as serological variants of merely one or two species, causing considerable confusion in both research and clinical settings. This situation reflects a long unanswered question regarding whether the Salmonella serotypes exist as discrete genetic clusters (natural species) of organisms or as phenotypic (e.g. pathogenic) variants of a single (or two) natural species with a continuous spectrum of genetic divergence among them. Our recent work, based on genomic sequence divergence analysis, has demonstrated that genetic boundaries exist among Salmonella serotypes, circumscribing them into clear-cut genetic clusters of bacteria.
  
  
  RESULTS
  To further test the genetic boundary concept for delineating Salmonella into clearly defined natural lineages (e.g., species), we sampled a small subset of conserved genomic DNA sequences, i.e., the endonuclease cleavage sites that contain the highly conserved CTAG sequence such as TCTAGA for XbaI. We found that the CTAG-containing cleavage sequence profiles could be used to resolve the genetic boundaries as reliably and efficiently as whole genome sequence comparisons but with enormously reduced requirements for time and resources.
  
  
  CONCLUSIONS
  Profiling of CTAG sequence subsets reflects genetic boundaries among Salmonella lineages and can delineate these bacteria into discrete natural clusters.
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Le
authors.initials: L
authors.lastname: Tang
authors.affiliation: Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada.
authors.forename: Wei-Qiao
authors.initials: WQ
authors.lastname: Liu
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Fang
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Sun
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Song-Ling
authors.initials: SL
authors.lastname: Zhu
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Wang
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Xiao-Yu
authors.initials: XY
authors.lastname: Wang
authors.affiliation: HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Yong-Guo
authors.initials: YG
authors.lastname: Li
authors.affiliation: Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; College of Pharmacy, Daqing Campus, Harbin Medical University, Daqing, China.
authors.forename: Da-Ling
authors.initials: DL
authors.lastname: Zhu
authors.affiliation: Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada.
authors.forename: Kenneth E
authors.initials: KE
authors.lastname: Sanderson
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.
authors.forename: Randal N
authors.initials: RN
authors.lastname: Johnston
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Gui-Rong
authors.initials: GR
authors.lastname: Liu
authors.affiliation: Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada; Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Shu-Lin
authors.initials: SL
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D053837:DNA Cleavage; D004269:DNA, Bacterial / Q000235:genetics*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D005810:Multigene Family; D010802:Phylogeny; D012475:Salmonella / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D012703:Serotyping; D009626:Terminology as Topic
chemical_list: D004269:DNA, Bacterial; C040836:CTAG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific