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

Abstract

Background Campylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied. Aim Typing-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks. Methods We performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat. Results Seventy-two clusters were detected, 58 small clusters (2–4 cases) and 14 large clusters (5–91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak. Conclusion Our WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.

Global epidemiology of campylobacteriosis and the impact of COVID-19

“…Another two smaller outbreaks involving 20 and 18 cases due to the consumption of Danish-produced chicken and unknown causes were also reported ( National Food Institute, 2021 ). In 2019, a total of 5,389 cases were notified, which was the highest number ever recorded ( Statens Serum Institut, 2019 ; Joensen et al., 2021 ). Among those cases, 701 human clinical isolates were analysed, of which 93% (652/701) were C. jejuni and 7% were C. coli ( Joensen et al., 2021 ).…”

Search term “One Health” remains of limited use to identify relevant scientific publications: Denmark as a case study

“…The publications included in this analysis reported various applications of One Health. Three of the 13 publications had focus on antimicrobial resistance ( 13 , 14 , 18 ), three on disease surveillance and/or control ( 19 , 22 , 24 ), one on developing One Health research projects in a clinical context ( 12 ), one on the One Health evaluation of a research center ( 15 ), one on the education of veterinary parasitology in Denmark ( 16 ), one on risk factors for obesity in dogs ( 17 ), one on outbreak investigation and management ( 21 ), one on the role of animals in the transmission of SARS-CoV-2 ( 20 ), and one on the environmental pillar of the One Health approach ( 23 ). None of the publications had evident focus on food.…”

“…None of the publications had evident focus on food. Five of the 13 publications were assessments or evaluations ( 13 – 15 , 22 , 23 ), three were descriptive reviews ( 16 , 19 , 20 ), two were observational studies ( 17 , 18 ), two were descriptions of outbreaks ( 21 , 24 ) and one was a study protocol ( 12 ).…”

Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study

“…Machine learning prediction based on MALDI-TOF mass spectra may be a frontline tool to make a preliminary screening of these recurring genotypes and identify related MALDI-TOF profiles. Nevertheless, WGS may still follow to further elucidate molecular details in case of an outbreak as it has been recently described in Denmark [5].…”

“…The genomic surveillance of C. jejuni infections is only applied in few European countries [5], despite the proven applicability of advanced molecular methods (e.g., next generation sequencing (NGS)) in routine surveillance [6] and following standard protocols (cf. ISO/DIS 23418 standard under development [7]).…”