title: Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak.
abstract: BACKGROUND
  Waterborne Campylobacter jejuni outbreaks are common in the Nordic countries, and PFGE (pulsed field gel electrophoresis) remains the genotyping method of choice in outbreak investigations. However, PFGE cannot assess the clonal relationship between isolates, leading to difficulties in molecular epidemiological investigations. Here, we explored the applicability of whole genome sequencing to outbreak investigation by re-analysing three C. jejuni strains (one isolated from water and two from patients) from an earlier resolved Finnish waterborne outbreak from the year 2000.
  
  
  RESULTS
  One of the patient strains had the same PFGE profile, as well as an identical overall gene synteny and three polymorphisms in comparison with the water strain. However, the other patient isolate, which showed only minor differences in the PFGE pattern relative to the water strain, harboured several polymorphisms as well as rearrangements in the integrated element CJIE2. We reconstructed the genealogy of these strains with ClonalFrame including in the analysis four C. jejuni isolated from chicken in 2012 having the same PFGE profile and sequence type as the outbreak strains. The three outbreak strains exhibited a paraphyletic relationship, implying that the drinking water from 2000 was probably contaminated with at least two different, but related, C. jejuni strains.
  
  
  CONCLUSIONS
  Our results emphasize the capability of whole genome sequencing to unambiguously resolve the clonal relationship between isolates of C. jejuni in an outbreak situation and evaluate the diversity of the C. jejuni population.
authors.forename: Joana
authors.initials: J
authors.lastname: Revez
authors.forename: Ann-Katrin
authors.initials: AK
authors.lastname: Llarena
authors.forename: Thomas
authors.initials: T
authors.lastname: Schott
authors.forename: Markku
authors.initials: M
authors.lastname: Kuusi
authors.forename: Marjaana
authors.initials: M
authors.lastname: Hakkinen
authors.forename: Rauni
authors.initials: R
authors.lastname: Kivistö
authors.forename: Marja-Liisa
authors.initials: ML
authors.lastname: Hänninen
authors.affiliation: Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P,O, Box 66,(Agnes Sjöberginkatu 2), Helsinki FI-00014, Finland. mirko.rossi@helsinki.fi.
authors.forename: Mirko
authors.initials: M
authors.lastname: Rossi
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D002169:Campylobacter Infections / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission; D016123:Campylobacter jejuni / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004196:Disease Outbreaks; D005387:Finland / Q000453:epidemiology; D023061:Gene Order; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D014871:Water Microbiology
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial