Assessing the role of colostrum microbiome properties and early life nutrition management in the acquisition of antimicrobial resistance (AMR) in dairy stock

This project aims to study the relationship between colostrum microbiome properties, early life nutrition management and antimicrobial resistance (AMR) development in pre-weaned calves. 

Perinatal mortality (up to 48 h after birth) accounts for large scale losses of calves worldwide. A quarter of on-farm calf deaths occur within the first 3 months of age, with dairy calf mortality rates of between 6-12% in this timeframe. Colostrum management is the single most important management factor in underpinning the health and survival of neonate calves as colostrum initiates growth, morphological changes and functional maturation of the gastrointestinal tracts of neonates and plays a vital role in the long-term health and productivity of calves. However, poor colostrum quality and quantity can result in limited passive systemic immunity, which increases the risk of disease for the neonate.  

This risk of disease is further compounded by increasing antimicrobial resistant (AMR) pathogens. Furthermore, the emergence of livestock as a reservoir for AMR mainly due to the use of antimicrobials for disease prevention in livestock farming to meet high demand is a critical challenge facing the UK dairy industry. From a public health perspective, AMR in dairy cattle can also jeopardize human health, due to the potential dissemination of AMR pathogens to humans via consumption of infected dairy products or direct contact with the animals.  

Research has shown that antimicrobial resistance genes (ARGs) load and ARG clusters are associated with low gut maturity of the gut microbiome and that post-weaning diet have important effects on the complement of AMR genes and resistotypes in the rumen microbial community. Additionally, ARGs have been detected early in neonate calves (2-5 days) and older lactating cows. However, the nature of AMR in the calf gut microbiome and how AMR is acquired during early life remain largely unknown. 

This project will robustly investigate the relationship between early-life nutrition influences on the development of the GI tract microbiome of calves, their resistome and animal health over time, with an emphasis on elucidating the role of colostrum.  

To achieve this, we will i) investigate how colostrum microbiome properties may benefit gut development and health of pre-weaned calves, ii) assess the resistome of colostrum and milk microbiome reservoirs in early nutrition and how these contribute to shaping the resistome in dairy calves, iii) determine whether improving colostrum through prepartum feed intervention impacts colostrum microbiome and resistome, and iv) develop insights into the interplay that exists between colostrum properties, its microbiome properties and the role this plays in AMR acquisition in dairy stock and the implications for One Health. 

Specific skills/experience required: Willingness, curiosity, and a keen interest in AMR research. Attention to detail. 

This project will be supervised by Dr Linda Oyama and Professor Sharon Huws (Queen's University School of Biological Sciences) and Dr Gillian Scoley (AFBI).

Start Date: 1 October 2023

Duration: 3 years full-time

How to apply: Applicants must be submitted via: https://dap.qub.ac.uk/portal/user/u_login.php