title: Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.
abstract: BACKGROUND
  Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay.
  
  
  RESULTS
  266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators.Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour.
  
  
  CONCLUSIONS
  The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics.
authors.affiliation: Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay. laurabet@higiene.edu.uy
authors.forename: Laura
authors.initials: L
authors.lastname: Betancor
authors.forename: Lucia
authors.initials: L
authors.lastname: Yim
authors.forename: Maria
authors.initials: M
authors.lastname: Fookes
authors.forename: Araci
authors.initials: A
authors.lastname: Martinez
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Alasdair
authors.initials: A
authors.lastname: Ivens
authors.forename: Sarah
authors.initials: S
authors.lastname: Peters
authors.forename: Clare
authors.initials: C
authors.lastname: Bryant
authors.forename: Gabriela
authors.initials: G
authors.lastname: Algorta
authors.forename: Samuel
authors.initials: S
authors.lastname: Kariuki
authors.forename: Felipe
authors.initials: F
authors.lastname: Schelotto
authors.forename: Duncan
authors.initials: D
authors.lastname: Maskell
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Jose A
authors.initials: JA
authors.lastname: Chabalgoity
mesh_terms: D018938:Caco-2 Cells; D004196:Disease Outbreaks; D014644:Genetic Variation; D044404:Genomic Islands / Q000235:genetics; D023281:Genomics; D006801:Humans; D010641:Phenotype; D010957:Plasmids / Q000235:genetics; D039002:Prophages / Q000235:genetics; D012480:Salmonella Infections / Q000453:epidemiology / Q000382:microbiology*; D012477:Salmonella enteritidis / Q000235:genetics* / Q000378:metabolism; D014583:Uruguay / Q000453:epidemiology