title: Genomics of an emerging clone of Salmonella serovar Typhimurium ST313 from Nigeria and the Democratic Republic of Congo.
abstract: BACKGROUND
  Salmonella enterica serovar Typhimurium ST313 is an invasive and phylogenetically distinct lineage present in sub-Saharan Africa. We report the presence of S. Typhimurium ST313 from patients in the Democratic Republic of Congo and Nigeria.
  
  
  METHODS
  Eighteen S. Typhimurium ST313 isolates were characterized by antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Additionally, six of the isolates were characterized by whole genome sequence typing (WGST). The presence of a putative virulence determinant was examined in 177 Salmonella isolates belonging to 57 different serovars.
  
  
  RESULTS
  All S. Typhimurium ST313 isolates harbored resistant genes encoded by blaTEM1b, catA1, strA/B, sul1, and dfrA1. Additionally, aac(6')1aa gene was detected. Phylogenetic analyses revealed close genetic relationships among Congolese and Nigerian isolates from both blood and stool. Comparative genomic analyses identified a putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and S. Dublin.
  
  
  CONCLUSIONS
  We showed in a limited number of isolates that S. Typhimurium ST313 is a prevalent sequence-type causing gastrointestinal diseases and septicemia in patients from Nigeria and DRC. We found three distinct phylogenetic clusters based on the origin of isolation suggesting some spatial evolution. Comparative genomics showed an interesting putative virulence fragment (ST313-TD) unique to S. Typhimurium ST313 and invasive S. Dublin.
authors.affiliation: Division of Bacterial Genomics and Epidemiology, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, National Food Institute and Center for Biological Sequence Analysis, Department of System Biology Technical University of Denmark, Kemitorvet, Building 204, DK-2800 Kgs. Lyngby, Denmark. pile@food.dtu.dk.
authors.forename: Pimlapas
authors.initials: P
authors.lastname: Leekitcharoenphon
authors.forename: Carsten
authors.initials: C
authors.lastname: Friis
authors.forename: Ea
authors.initials: E
authors.lastname: Zankari
authors.forename: Christina Aaby
authors.initials: CA
authors.lastname: Svendsen
authors.forename: Lance B
authors.initials: LB
authors.lastname: Price
authors.forename: Maral
authors.initials: M
authors.lastname: Rahmani
authors.forename: Ana
authors.initials: A
authors.lastname: Herrero-Fresno
authors.forename: Kayode
authors.initials: K
authors.lastname: Fashae
authors.forename: Olivier
authors.initials: O
authors.lastname: Vandenberg
authors.forename: Frank M
authors.initials: FM
authors.lastname: Aarestrup
authors.forename: Rene S
authors.initials: RS
authors.lastname: Hendriksen
mesh_terms: D000349:Africa; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D015023:Democratic Republic of the Congo; D016521:Electrophoresis, Gel, Pulsed-Field; D005260:Female; D016680:Genome, Bacterial; D023281:Genomics; D005838:Genotype; D006801:Humans; D007223:Infant; D008297:Male; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009549:Nigeria; D010802:Phylogeny; D012480:Salmonella Infections / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors