title: Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK.
abstract: BACKGROUND
  Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions.
  
  
  RESULTS
  Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka.
  
  
  CONCLUSIONS
  We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources.
authors.affiliation: Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey, UK. Matthew.Hayward.2009@live.rhul.ac.uk
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Hayward
authors.forename: Vincent  A A
authors.initials: V
authors.lastname: Jansen
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Woodward
mesh_terms: D000818:Animals; D002417:Cattle; D005798:Genes, Bacterial / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics; D023281:Genomics; D058751:Livestock / Q000382:microbiology*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D039002:Prophages / Q000502:physiology; D015203:Reproducibility of Results; D019779:Salmonella enterica / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D057345:Sequence Inversion; D013045:Species Specificity; D006113:United Kingdom