Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak.

Joana Revez,Marja-Liisa Hänninen,Markku Kuusi,Rauni Kivistö,Ann-Katrin Llarena,Thomas Schott,Marjaana Hakkinen,Mirko Rossi

doi:10.1186/1471-2164-15-768

Abstract

BackgroundWaterborne 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.ResultsOne 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-768) contains supplementary material, which is available to authorized users.

Highlights

Waterborne Campylobacter jejuni outbreaks are common in the Nordic countries, and PFGE remains the genotyping method of choice in outbreak investigations
This prophage showed 85.6% global nucleotide identity with the integrated element CJIE2 identified in C. jejuni RM1221 and it is integrated in the same region of the chromosome
The analysis revealed that the human isolate IHV116292 contained several genome rearrangements inside and immediately downstream the CJIE2 element compared to the water isolate, and these were responsible for the observed differences in PFGE profiles

Summary

Introduction

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. PFGE cannot assess the clonal relationship between isolates, leading to difficulties in molecular epidemiological investigations. Infrequently reported compared with sporadic cases, outbreaks of campylobacteriosis do occur and are often associated with the consumption of raw milk and PFGE (pulsed-field gel electrophoresis) typing of isolates has been widely used in outbreak investigations. PFGE profiles cannot conclusively establish the clonal relationship between isolates, affecting the epidemiological investigations. The genomic differences between epidemiologically linked isolates sharing PFGE profiles are expected to be minor since the strains are considered to be the recent expansion of a single clone [14]. Since alterations in the PFGE patterns can result from a single genetic event due to a single-nucleotide polymorphism in a restriction site [9], bacteriophage acquisition or loss or transposition [17,18], a clonal relationship may exist even between strains with different PFGE profiles [9]

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