Whole-Genome Sequencing to Detect Numerous Campylobacter jejuni Outbreaks and Match Patient Isolates to Sources, Denmark, 2015-2017.

Katrine G Joensen,Kristoffer Kiil,Birgitte Nauerby,Hanne M Holt,Hans L Nielsen,Mette R Gantzhorn,Steen Ethelberg,Gudrun Sandø,Jørgen Engberg,Eva M Nielsen,Andreas M Petersen,Katrin G Kuhn

doi:10.3201/eid2603.190947

Abstract

In industrialized countries, the leading cause of bacterial gastroenteritis is Campylobacter jejuni. However, outbreaks are rarely reported, which may reflect limitations of surveillance, for which molecular typing is not routinely performed. To determine the frequency of genetic clusters among patients and to find links to concurrent isolates from poultry meat, broiler chickens, cattle, pigs, and dogs, we performed whole-genome sequencing on 1,509 C. jejuni isolates from 774 patients and 735 food or animal sources in Denmark during 2015–2017. We found numerous clusters; 366/774 (47.3%) clinical isolates formed 104 clusters of >2 isolates. A total of 41 patient clusters representing 199/366 (54%) patients matched a potential source, primarily domestic chickens/broilers. This study revealed serial outbreaks and numerous matches to concurrent food and animal isolates and highlighted the potential of whole-genome sequencing for improving routine surveillance of C. jejuni by enhancing outbreak detection, source tracing, and potentially prevention of human infections.

Highlights

Campylobacter jejuni is the most frequent cause of bacterial gastroenteritis in industrialized countries worldwide [1,2], including in Denmark, where ≈4,000 Campylobacter infections are reported annually [3]
Despite the high genetic diversity of the dataset in general, we identified a large number of genetic clusters
Genetic Clusters Analysis of core-genome multilocus sequence typing (cgMLST) results for all 1,509 isolates indicated that 732 of the isolates were part of 204 clusters consisting of >2 isolates

Summary

Introduction

Campylobacter jejuni is the most frequent cause of bacterial gastroenteritis in industrialized countries worldwide [1,2], including in Denmark, where ≈4,000 Campylobacter infections are reported annually [3]. Recent studies have proven WGS to be applicable for Campylobacter outbreak investigations [17,18,19,20,21,22], and it has recently been shown that WGS could trace back clinical infections directly to chicken slaughter batches [23]. We performed WGS on a large cohort of 1,509 C. jejuni isolates collected from patients and food/animal samples in Denmark over 2 years. We clustered the isolates by using core-genome multilocus sequence typing (cgMLST) to determine the frequency of genetic clusters among clinical isolates (i.e., possible outbreaks) and how they matched concurrent isolates from potential sources. We detected numerous clusters among the patients and a large number of matches between clinical isolates and potential food/animal sources

Methods

Results

Conclusion