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

Abstract

C ampylobacter 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 notification rates, Campylobacter infections are believed to be highly underdiagnosed (4,5). Denmark's national surveillance system for Campylobacter is based on observation of the number of notified human cases (3); a substantial number of Campylobacter outbreaks may be overlooked because of a lack of routine microbiological typing of isolates. This hypothesis is supported by evidence from a recent study, in which whole-genome sequencing (WGS)-based typing of selected clinical Campylobacter isolates from patients in Denmark identified numerous small outbreak-like clusters (6). This finding suggests that more outbreaks occur in Denmark than the few typically large outbreaks associated with a single event that are detected by the current surveillance system (7-10). To achieve a national surveillance system that will detect ongoing Campylobacter outbreaks in real time, highly discriminatory subtyping of isolates is needed. Thus, we more comprehensively evaluated the frequency of Campylobacter outbreaks among humans in Denmark by using WGS-based typing. To match the clinical isolates with their sources, we compared them with isolates from food and animals, covering the main putative sources of human Campylobacter infections (i.e., contact with or consumption of animals or animal products, primarily contaminated poultry meat). Although Campylobacter infections are primarily foodborne, a recent case-control study in Denmark found that contact with animals and the environment might account for a substantial proportion of domestic infections (11). Several other reported sources of infection include unpasteurized milk, drinking water, bathing water, vegetables, and fruits (1,12-14). WGS offers high-resolution discriminatory subtyping and has been successfully implemented for

Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

“…Many of the more common STs found in Australia, such as ST825, ST827 and ST50, have been isolated from various sources globally. C. jejuni isolates were dominated by ST50 which has been found in poultry in Israel [54], Poland [55], Denmark [56] and South Korea [57], among other countries. To date, ST50 has over 3,500 submissions on the PubMLST database.…”

“…C . jejuni isolates were dominated by ST50 which has been found in poultry in Israel [ 54 ], Poland [ 55 ], Denmark [ 56 ] and South Korea [ 57 ], among other countries. To date, ST50 has over 3,500 submissions on the PubMLST database.…”

Establishment of sentinel surveillance of human clinical campylobacteriosis in Ireland

“…Cluster analysis was carried out within BioNumerics® using a minimum‐spanning tree algorithm based on categorical differences of core genome MLST (cgMLST) loci ( n = 1,343) (Cody et al., 2017). A difference of five cgMLST locus alleles or fewer was used as an alert threshold for public health to consider cluster investigation (Joensen et al., 2020). Detection of AMR‐associated and virulence factor genes in assembled genomes was performed using a BLAST‐based approach with reference gene sequences within BioNumerics®.…”

“…Campylobacteriosis has a seasonal distribution with case notifications in most European countries peaking between May and July though some countries can experience a secondary winter peak (Bless et al., 2017; Lake et al., 2019). Outbreaks related to Campylobacter are uncommon, however they are also, like individual cases, likely to be underreported or undetected (Joensen et al., 2020). Outbreaks are most commonly related to animal‐contact, drinking water and unpasteurized milk (Health Protection Surveillance Centre, 2019).…”

Host-Dependent Clustering of Campylobacter Strains From Small Mammals in Finland

“…Campylobacter spp., especially C. jejuni and C. coli , are common causes of gastroenteritis in humans globally, campylobacteriosis being the most frequently reported zoonosis in the EU area ( EFSA and ECDC, 2019 ). Many food-producing animal species are known to be asymptomatic carriers of campylobacters, and undercooked chicken is considered to be the main source for human disease, but also other livestock such as bovines have been associated with human cases ( Cody et al, 2019 ; Joensen et al, 2020 ). However, the original reservoir and mechanisms of spread of these pathogens on livestock farms are not well understood.…”