RVC PhD: Quantifying the use and impact of antimicrobial drugs on chicken gut microbiome and the presence of resistance genes

- Background -
As intensification of chicken production dramatically increases to meet the rising demand for meat and eggs, there is a strong concern about the over and misuse of antimicrobial drugs (AMD) in poultry. Indeed, such practices may promote the emergence and amplification of antimicrobial resistance in the chicken gut microbiome, and pose a significant threat for global health security. In order to design sustainable modes of production and reduce its impact of zoonotic disease risk, it is essential to develop a better understanding of the impact of AMD administration on the evolution of antimicrobial resistance in the gut microbiome of chickens.

- The Project -
The RVC-led UKRI GCRF One Health Poultry hub is a project conducted in Bangladesh, India, Sri Lanka and Viet Nam, focusing on the impact of the intensification of chicken production on zoonotic disease risk. As part of the Poultry Hub project, data will be generated about (i) AMD usage reported by farmers in their flock, (ii) AMD residues in chicken meat and feathers as detected by mass spectrometry and (iii) the composition of chicken gut microbial populations (16S rDNA) and their composition in antimicrobial resistance genes.
The PhD student will integrate these data generated by the Poultry Hub to assess the level, dose and timing of administration of AMD administered to chickens in a range of farming systems and different contexts, along the spectrum of production intensification. The fate of these AMDs, their resulting concentration in the gut and environment will also be estimated. A mathematical model simulating the dynamics of gut microbial communities within a chicken, and the presence of resistance genes will be developed in order to assess the impact of different regimes of AMD administration on these dynamics. This will lead to recommendations about safer and more sustainable use of AMDs in the context of chicken production in Asia.

- Training -
This PhD integrates aspects of pharmacology, molecular biology, epidemiology and computational modelling within a multidisciplinary team (Oxford – RVC). The student will be trained to the principles of pharmacology, pharmacokinetics / pharmacodynamics modelling and drug residue detection technologies (L. Pelligand). We have planned a short placement in an analytical laboratory, to expose the student to mass spectrometry analytical methods. The epidemiological input will be provided by G. Fournie and J. Lourenco (Oxford), with a particular focus on mechanistic dynamical models for the interpretation of the effect of certain practices on antimicrobial resistance in poultry microbiome. D. Blake will provide support for the interpretation of 16s RNA and AMR gene analysis. At the RVC, the student will be an active member of the VEEPH group, and benefit from the group expertise on epidemiology and food production systems.


- Essential Requirements -
Applicants must hold, or expected to achieve a first or upper second-class undergraduate honours degree or equivalent, or an MSci or Masters in molecular biology/biochemistry (or related discipline) or veterinary medicine/medicine
Computer literacy will be important, and this PhD would appeal to those minded to working with computer programs, mathematical modelling and managing large volumes of data.


- Desirable Requirements -
A background in veterinary medicine or allied work is desirable but not essential
A strong interest in epidemiology and/or pharmacology would certainly be an advantage
An interest in bioanalytical sciences (mass spectrometry and drug residue) would also be welcomed