PhD defence by Meiyao Che

Principal supervisor

• Professor Lisbeth Truelstrup Hansen, DTU National Food Institute

Co-supervisors

• Senior Researcher Ana Fresno Herrero, Universidad de Santiago de Compostela (USC)
• Senior Scientist Henrik Hasman, Statens Serum Institut
• Assistant Professor Tina Birk, Københavns Professionshøjskole

Examiners

• Senior Researcher Annette Nygaard Jensen, DTU National Food Institute
• Professor John Elmerdahl Oleseen, University of Copenhagen
• Professor Emerita Maria Del Rosario Rodicio  Rodicio,Oviedo University

Chairperson at defence

• Senior Scientist Tina Beck Hansen, DTU National Food Institute

Resume
Use of 3rd generation beta-lactam antibiotics, e.g., cephalosporins, in food production systems lead to the selection of resistant bacteria in animals reared for human consumption. Intake of bacteria, e.g., Escherichia coli, with resistance to these antibiotics can lead to serious infections and failed treatments. Resistant E. coli can spread through growth and survival in the food production chain but can potentially also pass mobile resistance genes to other pathogenic bacteria, which threaten human health. However, there is currently limited knowledge of the prevalence of resistant E. coli and their transmissible resistance genes in the poultry production system in Denmark.

To address this knowledge gap, this study conducted a survey of the prevalence of different resistance genes among E. coli in poultry farms and slaughterhouses in Denmark using whole genome sequencing analysis. E. coli with resistance to cephalosporins were found throughout the system with the highest prevalence in slaughterhouses. The most common resistance gene, blaCMY-2 occurred in both slaughterhouses and in one of two production systems. This resistance gene was carried in different sequence type (STs) E. coli on highly similar plasmids, which are small circular pieces of DNA that can be transmitted to other E. coli bacteria to spread this unwanted characteristic. Highly similar plasmids were also identified in human clinical E. coli strains from Denmark and in poultry strains isolated in other countries. Finally, this study performed a series of phenotypic analysis and genotypic analysis of resistant E. coli bacteria to assess the potential risk to human health and ability to survive and persist in the processing environment.

Results from this study provided novel information on the prevalence and characteristics of resistance to cephalosporins among E. coli in the Danish poultry system. Links to clinical cases and international prevalence were shown, pointing to the need for an international One Health approach to limiting the further spread of these antibiotic resistant bacteria.