title: Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population.
abstract: Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates.
  
  
  
  Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain.
  
  
  
  The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada. clifford.clark@phac-aspc.gc.ca.
authors.forename: Clifford G
authors.initials: CG
authors.lastname: Clark
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada.
authors.forename: Chrystal
authors.initials: C
authors.lastname: Berry
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Walker
authors.affiliation: Bioinformatics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada.
authors.forename: Aaron
authors.initials: A
authors.lastname: Petkau
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, T1J 3Z4, Canada.|Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.
authors.forename: Dillon O R
authors.initials: DO
authors.lastname: Barker
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada.
authors.forename: Cai
authors.initials: C
authors.lastname: Guan
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3R2, Canada.
authors.forename: Aleisha
authors.initials: A
authors.lastname: Reimer
authors.affiliation: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, T1J 3Z4, Canada.|Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.
authors.forename: Eduardo N
authors.initials: EN
authors.lastname: Taboada
mesh_terms: D002169:Campylobacter Infections / Q000453:epidemiology / Q000382:microbiology*; D016123:Campylobacter jejuni / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000821:virology; D002170:Canada / Q000453:epidemiology; D007446:Chromosome Inversion; D002876:Chromosomes, Bacterial; D004196:Disease Outbreaks; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA
keywords: Campylobacter; Chemotaxis proteins; Core genome MLST; Genomic inversions; Phylogenetic analysis; Transducer-like proteins; Whole genome sequence