Chicken gut microbiota and antibiotic-resistant bacteria

Background

The world faces multiple health threats, and antimicrobial resistance (AMR) tops this list in humans and animals. From all antibiotic resistance mechanisms, extended spectrum beta-lactamases (ESBLs) are specifically relevant due to their ability to inactivate a large group of critically important antibiotics known as beta-lactams. ESBLs have emerged globally in livestock and have been observed primarily in the Enterobacteriaceae family, especially in Escherichia coli strains.  

Numerous studies suggest foodborne transmission of ESBLs from chicken meat to humans. However, the attribution of chickens or chicken meat as a source of ESBL E. coli to humans remains unclear.  

E. coli is a ubiquitous early coloniser of the chicken’s gastrointestinal tract (GIT) and plays a crucial role as a reservoir of ESBLs. The chicken caeca are two small organs in the chicken’s GIT in which fermentation of nutrients occurs, for which they harbour complex and dynamic microbial communities. The caeca are located between the small and large intestines and have unique characteristics that make it a rich and favourable environment for bacteria to transfer multidrug resistance plasmids to each other. 

Developing successful strategies to reduce the transfer of ESBL genes in broiler production is only possible by understanding the successional dynamics of the chicken caecal microbiota and the role of ESBL-producing bacteria therein. Although the successional dynamics of the caecal chicken microbiome have previously been investigated, no studies accounted for the effect of ESBL-E. coli colonisation on the chicken caecal microbiota development or vice versa. Moreover, no research is available yet on the effect of in vitro microbiota interventions (e.g. synbiotics) on the horizontal transmission of ESBL genes to the caecal microbiota. 

Therefore, the aims of this research project are: to better understand the interactions between the chicken caecal microbiota and ESBL-E.coli during the broiler chicken lifespan and to establish a chicken caecal in vitro model to assess the effect of microbiota interventions such as probiotics, prebiotics and synbiotics on the horizontal transmission of ESBL plasmids.

Project description

The PhD project is divided in two components: In vivo and in vitro studies of the chicken caecal microbiota. 

The main objective of the in vivo component is to study the dynamic processes of the developing caecal microbiota of commercial broiler-chickens in relation to ESBL-E. coli colonisation.

The specific objectives of the in vivo studies are: 

• To identify key differences in caecal microbial community composition of ESBL-colonised and ESBL non-colonised broiler chickens.
• To determine whether there is a critical time window in the developing chicken caecal microbiome to implement suitable intervention strategies such as probiotics and prebiotics against ESBL-producing E. coli.

On the other hand, the main objective of the in vitro component is to study horizontal gene transfer dynamics in the in vitro chicken caecal microbiota after the inoculation of an ESBL E. coli and other microbiota interventions. 

The specific objectives of the in vitro studies are: 

• To establish a reproducible in vitro chicken gut model able to maintain the main members of the caecal microbial community.
• To assess the effect of introducing ESBL-E. coli on the in vitro cultured chicken caecal microbiome composition.
• To evaluate the effect of interventions (e.g. probiotics, prebiotics, and synbiotics) on the horizontal transmission of ESBL plasmids.

Results in vivo component

In our first study, we assessed the role of ESBL-E.coli in the successional dynamics of the caecal microbiota in developing broilers. Our findings suggest that ESBL-E.coli is associated with mild but consistent alpha diversity reductions and transient bacterial compositional differences. We also documented the prevalence trend and clonal spread of ESBL-E. coli in a broiler farm and pointed to the farm environment as a potential source for ESBLs. Additional information about this study can be found in the publication.