National Reference Laboratory for Foodborne and Gastrointestinal Bacteria

Approximately 5,000 people in Denmark are diagnosed each year with a gastrointestinal infection caused by Campylobacter bacterium, making it one of the most common causes of diarrhea. The National Reference Laboratory (NRL) for Campylobacter is responsible for national typing, surveillance and outbreak investigation. It also organizes external quality assessments (EQAs), engages in national and international research activities, and provides expertise in typing of Campylobacter.
The NRL receives Campylobacter isolates from 10-15% of registered human cases through departments of clinical microbiology in the Danish hospitals. The NRL performs whole genome sequencing (WGS)-based typing using a One Health approach, allowing real-time comparisons with isolates collected by national food authorities (Danish Veterinary and Food Administration).

• Surveillance
  • Campylobacter surveillance in numbers
• External Quality Assessments (EQAs)

Clostridioides difficile infection (CDI) causes gastrointestinal infection ranging from self-limiting diarrhea to fulminant colitis. Severe morbidity and mortality are most often associated with patients being elderly, hospitalized and undergoing antibiotic treatment. Approximately 5,000 people in Denmark are diagnosed each year with CDI, making it one of the most common causes of gastrointestinal infection. The National Reference Laboratory (NRL) for C. difficile receives samples from all ten Departments of Clinical Microbiology (DCM) in two different programs: i) ‘all-year’-surveillance where selection criteria are suspicion of outbreak or severe clinical manifestations and ii) sentinel-surveillance where all ten DCMs send in all toxigenic samples in one month in the spring and one month in the fall. Hereby, the NRL receives C. difficile positive samples from approximately 20% of all registered human cases and all of those are analyzed by WGS. WGS is used to identify hypervirulent, MDR types and clonal clusters that may be part of patient-to-patient transmission, and this information is readily communicated to the DCMs to assist local infection control. Overall national surveillance is performed by monitoring major and emerging types together with antimicrobial resistance and this information is shared with the DCMs in two biannual reports.

• Healthcare-Associated Infections Database - HAIBA

E. coli strains isolated from intestinal diseases have been grouped into at least six different categories based on epidemiological evidence, phenotypic traits, clinical features of the disease they produce, and specific virulence factors. The currently recognised categories of diarrhoeagenic E. coli include: Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC), which are also referred to as Vero cytotoxin-producing E. coli (VTEC) enterotoxigenic E. coli (ETEC), Enteroinvasive E. coli (EIEC), and Enteroaggregative E. coli (EAEC).

The NRL receives isolates of registered human cases of STEC infections through the departments of clinical microbiology in the Danish hospitals. The NRL performs whole genome sequencing (WGS)-based typing using a One Health approach, allowing real-time comparisons with isolates collected by the national food authorities (Danish Veterinary and Food Administration).

Pathotypes EPEC, ETEC, EIEC and EAEC are investigated and WGS’ed upon suspicion of an outbreak.

• Surveillance
• STEC surveillance in numbers
• External Quality Assessments (EQAs)
• The International Centre for Reference and Research on Escherichia, Shigella and Klebsiella

Listeriosis is a rare but serious infection usually caused by eating food contaminated with the bacterium Listeria monocytogenes. The infection affects people with weakened immune systems due to illness, old age or pregnant women and their newborns. In Denmark between 40 and 90 patients are diagnosed every year. The National Reference Laboratory (NRL) for Listeria monocytogenes is responsible for national typing, surveillance, and outbreak investigation. It also organizes external quality assessments (EQAs), engages in national and international research activities, and provides expertise in typing of Listeria.
The NRL receives close to a 100% of the registered human cases through hospital clinical microbiology departments. The NRL performs whole genome sequencing (WGS)-based typing using a One Health approach, allowing for real-time comparisons with isolates collected by national food authorities (Danish Veterinary and Food Administration).

• Surveillance
  • Listeria surveillance in numbers 
• External Quality Assessments (EQA)
  • Since 2012, SSI has performed EQA schemes for typing of Listeria monocytogenes organised in collaboration with the European Centre for Disease Prevention and Control (ECDC). Over the years the method assessed in the EQAs has evolved from Pulse-field Gel electrophoresis to WGS-based typing. Read more about EQAs FWD-net 

Salmonellosis is a common gastrointestinal infection caused by the zoonotic bacteria Salmonella. Infection is mostly related to consumption of contaminated food and approximately 1.000 human infections are registered every year. The National Reference Laboratory (NRL) for Salmonella is responsible for national typing, surveillance and outbreak investigation. It also organizes external quality assessments (EQAs), engages in national and international research activities, and provides expertise in typing of Salmonella.
The NRL receives close to all isolates of registered human cases of Salmonella infections through the departments of clinical microbiology in the Danish hospitals. The NRL performs whole genome sequencing (WGS)-based typing using a One Health approach, allowing real-time comparisons with isolates collected by the national food authorities (Danish Veterinary and Food Administration).

• Surveillance
  • Salmonella surveillance in numbers 
• External Quality Assessments (EQAs)

Yersiniosis is a common gastrointestinal infection caused by Yersinia, mainly Yersinia enterocolitica and in rare cases Yersinia pseudotuberculosis. In addition to the gastrointestinal symptoms, 10-30% of adults may get immunological reactions in the form of reactive arthritis or erythema nodosum. Y. enterocolitica is mainly found in pigs, cattle and certain rodents. Insufficiently heat-treated pork and contaminated ready-to-eat vegetables are frequent sources of human infections.
In recent years, approx. 1000 laboratory-confirmed cases of Y. enterocolitica infection have been recorded in Denmark. The NRL receives isolates from approx. 40% of the registered cases through departments of clinical microbiology (DCM) in the Danish hospitals, where the primary diagnostics is done. The NRL performs species confirmation and bio-/serotyping on all received isolates. Whole genome sequencing (WGS)-based typing is carried out in outbreak situations and for research purposes.

• Surveillance
  • Yersinia surveillance in numbers
  • Also reported in the national Zoonosis - annual reports (DTU National Food Institute) and at the EU level in the Annual Epidemiological Reports (ECDC)