The International Centre for Reference and Research on Escherichia, Shigella and Klebsiella

The Laboratory is the National Reference Laboratory (NRL) for typing of E. coli, Shigella and Klebsiella. The Centre collects surveillance data for national and international authorities. The Centre coordinates typing and participates in research projects in Denmark and abroad. It provides advice and counselling on detection and typing.

As of 2008, the Centre functions as microbiological support for surveillance at the EU level for the European Centre for Disease Prevention and Control (ECDC) in Stockholm. This is done in collaboration with the European Union Reference Laboratory (EU-CRL) for Escherichia coli, including Shiga toxin-producing E. coli (STEC), Instituto Superiore di Sanità (ISS) in Rome. The Centre organises annual external quality programmes (EQA) for ECDC and internationally for national reference laboratories on a self-funded basis.


  • Serotyping of Escherichia coli: Complete characterisation of bacterial somatic (O-), flagella- (H-) and capsular- (K-) antigens
  • Virulence characterisation: Detection of relevant virulence factors (adhesins, toxins etc.) using DNA techniques and inoculation of cell cultures. Production of Shiga toxin
  • Whole genome sequencing – especially on STEC. in silico analyses provide information on both the O:H serotype and the virulence profile of an E. coli isolate.

The majority of routine analyses are accredited by DANAK according to ISO 17025.

Characterisation provides information on which of the following groups an E. coli isolate belongs to:
STEC Shiga toksin-producing E. coli (synonymous with Vero cytotoksin-producing E. coli (VTEC)
AEEC Attaching and Effacing E. coli (eae positive, non-classical EPEC)
EPEC Enteropatogenic E. coli. (Classical and new O:H serotypes); an updated list can be obtained from Flemming Scheutz
Enteroinvasive E. coli
Enterotoxigenic E. coli including isolates, that are positive for astA
Enteroaggregative E. coli
Diffusely Adherent Ecoli
Extraintestinal Pathogenic Ecoli
Uropathogenic Ecoli


1. Non-accredited analyses

Subtyping of the genes for Shiga toxin (stx1 and stx2). Sero- and virulence typing of isolates from urinary tract infections, blood and meningitis. Whole genome sequencing.

Reference functions

2. Technical expertise

Evaluation of bacterial virulence, of contamination in production facilities, eg. by ongoing surveillance as part of quality control and specifically in situations where unwanted transmission has occurred.

3. Advice and counselling

The Centre can assist in evaluations of possible transmission routes and risk assessments if relevant (HACCP).



  • Denmark
    • The Danish E. coli network comprises all the Clinical Microbiological departments at 10 regional hospitals.
  • International
    • The International Centre for Reference and Research on Escherichia and Klebsiella
    • Food and Waterborne Diseases (FWD)-ECDC: Flemming Scheutz is the Danish contact point for STEC (and E. coli)
    • Flemming Scheutz is a member of The International VTEC Symposium Steering Committee (IVSSC). 11th International Symposium on Shiga Toxin (Verocytotoxin) - Producing Escherichia coli Infections. These symposiums are held every third year and the next physical conference is scheduled as VTEC2023 in Canada
    • Consultant for Community Reference Laboratories (CRL) network, EU’s network for Food and Feed funded by DG SANCO.
  • External expert for European Food Safety Authority (EFSA) BIOHAZ Working Group on “Pathogenicity assessment of Shiga toxin-producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC (EFSA-Q-2018-00293)”.


  • New O antigens
  • Standardisation of serotyping techniques
  • Nomenclature of Shiga toxins and intimin genes (eae)
  • Molecular methods for typing of virulent E. coli isolates

Quality programmes

The Centre functions as ECDC’s microbiological support and organises an annual EQA on sero- and virulence typing of 10-12 STEC strains
In Denmark, the Centre organises an annual EQA programme. As of 2011, this has included 15 different types of DEC, reflecting Danish epidemiology.

The results for 2014-2015 and 2015-2016 for the self-funded participants outside Denmark are found in these reports EQA self-funded report 2014-2015 (pdf) and EQA self-funded report 2015-2016 (pdf)