Research – Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019


CDC Campy

Human campylobacteriosis is the most commonly reported zoonotic disease in Europe, with 246,571 reported cases in the European Union (EU) in 2018 [1].  infections are predominantly food-borne, with poultry as the primary source. However, other transmission routes are known, such as bathing, drinking contaminated water or direct contact with animals. In food samples, the highest occurrence of  was detected in fresh chicken meat (37.5% of samples tested) [1]. In Denmark, we had 5,389 registered human cases in 2019 (incidence: 93/100,000 inhabitants) and 33% of conventional chicken meat samples were positive for  at slaughter [2]. Of note, one third of the human infections diagnosed in Denmark are estimated to be travel-related [3].

Efforts to identify the specific source of  infection in humans are rarely made in Denmark or other countries. Therefore, relevant information for targeted public health actions to prevent  infections often does not exist. For decades, surveillance of other food-borne pathogens, especially  and  with high-discriminatory typing methods has proved to be a powerful tool for outbreak detection and investigations as well as for following trends and emergence of epidemic strains. Similar typing-based surveillance for  has not been widely used and generally has not been very useful for the decision-making process on mitigating efforts by the public health and food safety authorities. The high diversity of  isolates and the general assumption that most  infections are sporadic are plausible explanations.

We have previously shown that, based on whole genome sequencing (WGS) data of  isolates in 2015–17, we could identify numerous small outbreak-like clusters and, in many instances, genetically link them to concurrent animal and food isolates [4]. A large fraction of all 774 clinical isolates (27%) could be genetically linked to broilers or chicken meat, whereas only a few clinical isolates (2%) could be genetically linked to cattle isolates. A Danish case–control study conducted in the same period pointed at several food sources of campylobacteriosis among children and young adults, including consumption of chicken meat, minced beef, and fresh strawberries [5]. Therefore, in addition to sampling of chicken meat, the Danish Veterinary and Food Administration (DVFA) initiated sampling and analysis for  in several other food sources that were identified by the case–control study to obtain knowledge on the impact of these sources.

In our 2015–17 study, a comparison of human isolates to food and animal isolates was done retrospectively and therefore no specific public health actions were taken. To evaluate the value of a prospective and continuous WGS-based surveillance system for  in Denmark, we initiated WGS of isolates from human cases and retail food samples as well as the concurrent analysis of these cross-sector data. Here, we report the first year of surveillance (2019) and show that integrated WGS-based surveillance of  in humans and food sources can identify correlations between the occurrence of specific strains in chicken meat and in human infections. The surveillance was also able to detect prolonged or reappearing outbreaks, which allows for specific interventions to control  in the food production chain and thereby prevent human infections.

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