title: Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens.
abstract: BACKGROUND
  Non-typhoidal Salmonella enterica serovars, associated with different foods including poultry products, are important causes of bacterial gastroenteritis worldwide. The colonization of the chicken gut by S. enterica could result in the contamination of the environment and food chain. The aim of this study was to compare the genomes of 25 S. enterica serovars isolated from broiler chicken farms to assess their intra- and inter-genetic variability, with a focus on virulence and antibiotic resistance characteristics.
  
  
  RESULTS
  The genomes of 25 S. enterica isolates covering five serovars (ten Typhimurium including three monophasic 4,[5],12:i:, four Enteritidis, three Hadar, four Heidelberg and four Kentucky) were sequenced. Most serovars were clustered in strongly supported phylogenetic clades, except for isolates of serovar Enteritidis that were scattered throughout the tree. Plasmids of varying sizes were detected in several isolates independently of serovars. Genes associated with the IncF plasmid and the IncI1 plasmid were identified in twelve and four isolates, respectively, while genes associated with the IncQ plasmid were found in one isolate. The presence of numerous genes associated with Salmonella pathogenicity islands (SPIs) was also confirmed. Components of the type III and IV secretion systems (T3SS and T4SS) varied in different isolates, which could explain in part, differences of their pathogenicity in humans and/or persistence in broilers. Conserved clusters of genes in the T3SS were detected that could be used in designing effective strategies (diagnostic, vaccination or treatments) to combat Salmonella. Antibiotic resistance genes (CMY, aadA, ampC, florR, sul1, sulI, tetAB, and srtA) and class I integrons were detected in resistant isolates while all isolates carried multidrug efflux pump systems regardless of their antibiotic susceptibility profile.
  
  
  CONCLUSIONS
  This study showed that the predominant Salmonella serovars in broiler chickens harbor genes encoding adhesins, flagellar proteins, T3SS, iron acquisition systems, and antibiotic and metal resistance genes that may explain their pathogenicity, colonization ability and persistence in chicken. The existence of mobile genetic elements indicates that isolates from a given serovar could acquire and transfer genetic material. Conserved genes in the T3SS and T4SS that we have identified are promising candidates for identification of diagnostic, antimicrobial or vaccine targets for the control of Salmonella in broiler chickens.
authors.affiliation: Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
authors.forename: Akhilesh S
authors.initials: AS
authors.lastname: Dhanani
authors.affiliation: Pacific Agri-Food Research Center, Agriculture and Agri-Food Canada (AAFC), Agassiz, British Columbia, V0M 1A0, Canada.
authors.forename: Glenn
authors.initials: G
authors.lastname: Block
authors.affiliation: McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, H3A 1A4, Canada.
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.affiliation: Lady Davis Institute for Medical Research, Montréal, Québec, H3T 1E2, Canada.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Forgetta
authors.affiliation: Southern Crop Protection and Food Research Centre, AAFC, London, Ontario, N5V 4T3, Canada.
authors.forename: Edward
authors.initials: E
authors.lastname: Topp
authors.affiliation: Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Beiko
authors.affiliation: Pacific Agri-Food Research Center, Agriculture and Agri-Food Canada (AAFC), Agassiz, British Columbia, V0M 1A0, Canada.
authors.forename: Moussa S
authors.initials: MS
authors.lastname: Diarra
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D058947:Bacterial Secretion Systems / Q000235:genetics / Q000378:metabolism; D002645:Chickens / Q000382:microbiology*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D044404:Genomic Islands; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008826:Microbial Sensitivity Tests; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011201:Poultry Diseases / Q000382:microbiology*; D012481:Salmonella Infections, Animal / Q000382:microbiology*; D019779:Salmonella enterica / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D000900:Anti-Bacterial Agents; D058947:Bacterial Secretion Systems