Controlling enteric pathogens of poultry: Host/microbiota interactions, risk assessment and effective management interventions

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The global human population is predicted to increase by a third over the next 25 years, with countries of the developing world hosting 97% of this expansion. The ability to 'feed 9Bn people sustainably by 2050' is an urgent priority Indian and UK governments with the 12th Indian Five Year Plan requiring growth of the agricultural sector at 4% per annum to achieve food security. Poultry farming is a highly efficient and cost-effective system for producing animal protein for human consumption, but circulating infectious diseases compromise gut health and impact dramatically on farm economics, animal welfare and occasionally human health through transmission of zoonoses. Poultry gastrointestinal infections of most concern in UK and India are caused by avian pathogenic Escherichia coli (APEC), Campylobacter jejuni, Clostridium perfringens, Eimeria and Salmonella. Susceptibility to gut colonisation and the outcomes of infection are directly influenced by many factors including host genotype, immune status, age at infection, strain of infecting microbe, composition of commensal enteric microbiota and presence of other acute or chronic infections. There are significant interactions between host and microbe biology, genetics, epigenetics, the environment and farm practices. Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as 'thinning', can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.There is rich genetic diversity in India's native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Gaps in current knowledge prompt four fundamental questions around which this proposal is framed: 1. What is the epidemiology of specified gastrointestinal infections, and co-infections, across UK and Indian poultry production systems?2. Does host genotype exert an influence on (a) the prevalence, evolution and transmission of specified microbes and (b) the composition of flock-level enteric microbiota?3. What is the level of genetic variation within specific microbial populations in Indian and UK poultry production?4. What on-farm factors affect the risk of enteric colonisation and carriage of specified microbes and how can changes in poultry husbandry and management practices mitigate this risk?The proposal brings together UK and India experts in poultry genetics, animal health, epidemiology, pathology and pathogen biology. A multidisciplinary approach combining metagenomic sequencing, high density SNP-based QTL mapping, bacteriology, parasitology, molecular epidemiology and mathematical modelling will be used to quantify and predict disease risks at farm and national levels and to inform the development of intervention and management strategies, including future breeding and husbandry planning.