Colibacillosis in poultry – Aetiology, pathogenesis, diagnosis, and control

PhD Student: Sofie Kromann
Thesis defended: 7 October 2022


Infections with Escherichia coli, collectively referred to as colibacillosis, constitute a major health challenge in poultry. Even during time periods considered low in colibacillosis prevalence, E. coli bacteria have been determined as the causative agent behind approximately 30% of all disease cases. Furthermore, devastating outbreak-situations periodically occur with vast increases in mortality, condemnations, and use of antibiotics. Consequently, insight into the pathogenesis, detailed characterization of pathogenic strains and efficient preventive measurements are highly warranted to alleviate animal suffering, economic losses, and antimicrobial use.


  1. To develop a discriminative and reproducible in vivo model of avian colibacillosis
  2. To evaluate the efficacy of the Danish autogenous vaccine designed to protect against E. coli infections:
  • In a predictive model of avian colibacillosis
  • Expose potential alterations in the prevalent disease-causing E. coli types in Denmark, possibly attributed to the implementation of the autogenous vaccine
  • To establish a surveillance program based on whole-genome sequencing
  • To expose E. coli types involved in sporadic cases of colibacillosis
  • To identify potential outbreak strains
  • Characterise the disease-causing E. coli strains genomically


A discriminative and reproducible model of aerogenous E. coli infection was successfully developed in broiler breeders exhibiting close resemblance to spontaneous avian colibacillosis in multiple organs both histologically and grossly. Subsequently, the model was applied in a controlled intervention study challenging the Danish autogenous vaccine, which was shown to confer protection against a homologous challenge. Thus, the use of autogenous vaccines is expected to improve animal health and reduce the use of antibiotics. The established model holds great potential as a valuable tool for future investigations, especially on prophylactic interventions and disease mechanisms.

 The project provided a comprehensive insight into the occurrence of lesions in broiler breeders and broilers from farms without general disease problems. Moreover, it presented an in-depth genomic characterisation of isolates involved in background colibacillosis. This revealed a diverse collection of E. coli, including several sequence types previously described as APEC, which could even be isolated from extraintestinal sites in birds lacking colibacillosis-like lesions. The study emphasises the elusive nature of the APEC pathotype and the great diversity of E. coli isolated from poultry during non-outbreak situations.

In addition to the extensive insight into “background” colibacillosis, a comprehensive characterisation of a major Danish E. coli outbreak was provided through post-mortem examination, bacteriological sampling, productivity data and thorough genomic analysis. This resulted in an update of the autogenous vaccine used in Denmark.

 Detailed information on the results and studies conducted during the PhD-project is available through six research articles encompassed by the thesis.