title: Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua.
abstract: BACKGROUND
  Helicobacter pylori (H. pylori) is one of the most common bacterial infections in humans and this infection can lead to gastric ulcers and gastric cancer. H. pylori is one of the most genetically variable human pathogens and the ability of the bacterium to bind to the host epithelium as well as the presence of different virulence factors and genetic variants within these genes have been associated with disease severity. Nicaragua has particularly high gastric cancer incidence and we therefore studied Nicaraguan clinical H. pylori isolates for factors that could contribute to cancer risk.
  
  
  METHODS
  The complete genomes of fifty-two Nicaraguan H. pylori isolates were sequenced and assembled de novo, and phylogenetic and virulence factor analyses were performed.
  
  
  RESULTS
  The Nicaraguan isolates showed phylogenetic relationship with West African isolates in whole-genome sequence comparisons and with Western and urban South- and Central American isolates using MLSA (Multi-locus sequence analysis). A majority, 77 % of the isolates carried the cancer-associated virulence gene cagA and also the s1/i1/m1 vacuolating cytotoxin, vacA allele combination, which is linked to increased severity of disease. Specifically, we also found that Nicaraguan isolates have a blood group-binding adhesin (BabA) variant highly similar to previously reported BabA sequences from Latin America, including from isolates belonging to other phylogenetic groups. These BabA sequences were found to be under positive selection at several amino acid positions that differed from the global collection of isolates.
  
  
  CONCLUSIONS
  The discovery of a Latin American BabA variant, independent of overall phylogenetic background, suggests hitherto unknown host or environmental factors within the Latin American population giving H. pylori isolates carrying this adhesin variant a selective advantage, which could affect pathogenesis and risk for sequelae through specific adherence properties.
authors.affiliation: Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. kaisa.thorell@ki.se.|Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. kaisa.thorell@ki.se.|Present address: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Box 280, 171 77, Stockholm, Sweden. kaisa.thorell@ki.se.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Thorell
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. shaghayegh.Hosseini@chalmers.se.
authors.forename: Shaghayegh
authors.initials: S
authors.lastname: Hosseini
authors.affiliation: Laboratorio de Patología, Hospital Salud Integral, Managua, Nicaragua. palacios.g.reyna@gmail.com.
authors.forename: Reyna Victoria Palacios
authors.initials: RV
authors.lastname: Palacios Gonzáles
authors.affiliation: Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. cchoatham@gmail.com.
authors.forename: Chatchai
authors.initials: C
authors.lastname: Chaotham
authors.affiliation: Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, TX, USA. dgraham@bcm.edu.
authors.forename: David Y
authors.initials: DY
authors.lastname: Graham
authors.affiliation: Dalla Lana School of Public Health, University of Toronto, Toronto, Canada. lawrence@ices.on.ca.
authors.forename: Lawrence
authors.initials: L
authors.lastname: Paszat
authors.affiliation: Cancer Care Ontario, University of Toronto, Toronto, Canada. Linda.Rabeneck@cancercare.on.ca.
authors.forename: Linda
authors.initials: L
authors.lastname: Rabeneck
authors.affiliation: Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. samuel.lundin@microbiology.gu.se.
authors.forename: Samuel B
authors.initials: SB
authors.lastname: Lundin
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. intawat@chalmers.se.|Present address: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. intawat@chalmers.se.
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
authors.affiliation: Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. asa.sjoling@ki.se.|Present address: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Box 280, 171 77, Stockholm, Sweden. asa.sjoling@ki.se.
authors.forename: Åsa
authors.initials: Å
authors.lastname: Sjöling
mesh_terms: D018829:Adhesins, Bacterial / Q000737:chemistry / Q000235:genetics*; D000293:Adolescent; D000328:Adult; D000368:Aged; D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D016481:Helicobacter Infections / Q000382:microbiology; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009527:Nicaragua; D010802:Phylogeny; D037521:Virulence Factors / Q000737:chemistry / Q000235:genetics; D055815:Young Adult
chemical_list: D018829:Adhesins, Bacterial; D000942:Antigens, Bacterial; C400429:BabA protein, Helicobacter pylori; D037521:Virulence Factors