Direct experimental evidence that early-life farm environment influences regulation of immune responses

Background: In mammals, early-life environmental variations appear to affect microbial colonization and therefore competent immune development, and exposure to farm environments in infants has been inversely correlated with allergy development. Modelling these effects using manipulation of neonatal rodents is difficult due to their dependency on the mother, but the relatively independent piglet is increasingly identified as a valuable translational model for humans. This study was designed to correlate immune regulation in piglets with early-life environment. Methods: Piglets were nursed by their mother on a commercial farm, while isolatorreared siblings were formula fed. Fluorescence immunohistology was used to quantify T-reg and effector T-cell populations in the intestinal lamina propria and the systemic response to food proteins was quantified by capture ELISA. Results: There was more CD4+ and CD4+CD25+ effector T-cell staining in the intestinal mucosa of the isolator-reared piglets compared with their farm-reared counterparts. In contrast, these isolator-reared piglets had a significantly reduced CD4+CD25+Foxp3+ regulatory T-cell population compared to farm-reared littermates, resulting in a significantly higher T-reg-to-effector ratio in the farm animals. Consistent with these findings, isolator-reared piglets had an increased serum IgG anti-soya response to novel dietary soya protein relative to farm-reared piglets. Conclusion: Here, we provide the first direct evidence, derived from intervention, that components of the early-life environment present on farms profoundly affects both local development of regulatory components of the mucosal immune system and immune responses to food proteins at weaning. We propose that neonatal piglets provide a tractable model which allows maternal and treatment effects to be statistically separated.

Sources and spread of thermophilic Campylobacter spp. during partial depopulation of broiler chicken flocks

The practice of partial depopulation or ‘thinning’, i.e. early removal of a proportion of birds from a commercial broiler flock, is a reported risk factor for Campylobacter colonization of residual birds because of the difficulty in maintaining biosecurity during the process. Therefore, the effect of this practice was studied in detail for 51 target flocks, each at a different growing farm belonging to one of seven major poultry companies throughout the United Kingdom. On 21 of these farms, the target flock was already colonized by Campylobacter and at slaughter all cecal samples examined were positive, with a mean of log10 8 cfu / g. A further 27 flocks became positive within 2 – 6 days of the start of thinning and had similarly high levels of cecal carriage at slaughter. Just prior to the thinning process, Campylobacter could be isolated frequently from the farm driveways, transport vehicles, equipment and personnel. Strains from seven such farms on which flocks became colonized after thinning were examined by PFGE typing. The study demonstrated an association between strains occurring at specific sampling sites and those isolated subsequently from the thinned flocks. There were also indications that particular strains had spread from one farm to another, when the farms were jointly company-owned and served by the same bird-catching teams and / or vehicles. The results highlighted the need for better hygiene control in relation to catching equipment and personnel, and more effective cleaning and disinfection of vehicles, and bird-transport crates.

Modelling the economics of farm-based anaerobic digestion in a UK whole-farm context

Anaerobic digestion (AD) technologies convert organic wastes and crops into methane-rich biogas for heating, electricity generation and vehicle fuel. Farm-based AD has proliferated in some EU countries, driven by favourable policies promoting sustainable energy generation and GHG mitigation. Despite increased state support there are still few AD plants on UK farms leading to a lack of normative data on viability of AD in the whole-farm context. Farmers and lenders are therefore reluctant to fund AD projects and policy makers are hampered in their attempts to design policies that adequately support the industry. Existing AD studies and modelling tools do not adequately capture the farm context within which AD interacts. This paper demonstrates a whole-farm, optimisation modelling approach to assess the viability of AD in a more holistic way, accounting for such issues as: AD scale, synergies and conflicts with other farm enterprises, choice of feedstocks, digestate use and impact on farm Net Margin. This modelling approach demonstrates, for example, that: AD is complementary to dairy enterprises, but competes with arable enterprises for farm resources. Reduced nutrient purchases significantly improve Net Margin on arable farms, but AD scale is constrained by the capacity of farmland to absorb nutrients in AD digestate.

Participatory research approaches in the development of improved management practices in indigenous chickens production systems with smallholder farmers in Kenya

This thesis is concerned with development of improved management practices in indigenous chicken production systems in a research process that includes participatory approaches with smallholder farmers and other stakeholders in Kenya. The research process involved a wide range of activities that included on-station experiments, field surveys, stakeholder consultations in workshops, seminars and visits, and on-farm farmer participatory research to evaluate the effect of some improved management interventions on production performance of indigenous chickens. The participatory research was greatly informed from collective experiences and lessons of the previous activities. The on-station studies focused on hatching, growth and nutritional characteristics of the indigenous chickens. Four research publications from these studies are included in this thesis. Quantitative statistical analyses were applied and they involved use of growth models estimated with non-linear regressions for the growth characteristics, chi-square determinations to investigate differences among different reciprocal crosses of indigenous chickens and general linear models and covariance determination for the nutrition study. The on-station studies brought greater understanding of performance and production characteristics of indigenous chickens and the influence of management practices on these characteristics. The field surveys and stakeholder consultations helped in understanding the overarching issues affecting the productivity of the indigenous chickens systems and their place in the livelihoods of smallholder farmers. These activities created strong networking opportunities with stakeholders from a wide spectrum. The on-farm farmer participatory research involved selection of 200 farmers in five regions followed by training and introduction of interventions on improved management practices which included housing, vaccination, deworming and feed supplementation. Implementation and monitoring was mainly done by individual farmers continuously for close to one and half years. Six quarterly visits to the farms were made by the research team to monitor and provide support for on-going project activities. The data collected has been analysed for 5 consecutive 3-monthly periods. Descriptive and inferential statistics were applied to analyse the data collected involving treatment applications, production characteristics and flock demography characteristics. Out of the 200 farmers initially selected, 173 had records on treatment applications and flock demography characteristics while 127 farmers had records on production characteristics. The demographic analysis with a dissimilarity index of flock size produced 7 distinct farm groups from among the 173 farms. Two of these farm groups were represented in similar numbers in each of the five regions. The research process also involved a number of dissemination and communication strategies that have brought the process and project outcomes into the domain of accessibility by wider readership locally and globally. These include workshops, seminars, field visits and consultations, local and international conferences, electronic conferencing, publications and personal communication via emailing and conventional posting. A number of research and development proposals were also developed based on the knowledge and experiences gained from the research process. The thesis captures the research process activities and outcomes in 8 chapters which include in ascending order – introduction, theoretical concepts underpinning FPR, research methodology and process, on-station research output, FPR descriptive statistical analysis, FPR inferential statistical analysis on production characteristics, FPR demographic analysis and conclusions. Various research approaches both quantitative and qualitative have been applied in the research process indicating the possibilities and importance of combining both systems for greater understanding of issues being studied. In our case, participatory studies of the improved management of indigenous chickens indicates their potential importance as livelihood assets for poor people.

An industry viewpoint on the role of farm assurance in delivering food safety to the consumer: the case of the dairy sector in England and Wales

Food safety, alongside food quality, remains a primary concern of both consumers and those along the whole food supply chain, leading to regulation by government alongside private third party certification. Much has been written about the value of these systems primarily from the perception of the consumer. This paper reports on a study that examined industry perceptions on the regulatory and assurance systems within the dairy sector of England and Wales. It found that the primary producer found value in both systems, although from a food hygiene focus regulation was seen to be more rigorous. Other stakeholders along the dairy food supply chain saw the assurance scheme as more rigorous. All stakeholders recognised the need to reduce duplication in delivering food safety through combining key elements of both systems with the added potential for better communication of both food safety and quality to the final consumer.

Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella enterica 4,5,12,i:-, Escherichia coli and Klebsiella pneumoniae on a single UK pig farm

OBJECTIVES: In 2009, CTX-M Enterobacteriaceae and Salmonella isolates were recovered from a UK pig farm, prompting studies into the dissemination of the resistance and to establish any relationships between the isolates. METHODS: PFGE was used to elucidate clonal relationships between isolates whilst plasmid profiling, restriction analysis, sequencing and PCR were used to characterize the CTX-M-harbouring plasmids. RESULTS: Escherichia coli, Klebsiella pneumoniae and Salmonella 4,5,12:i:- and Bovismorbificans resistant to cefotaxime (n = 65) were recovered and 63 were shown by PCR to harbour a group 1 CTX-M gene. The harbouring hosts were diverse, but the group 1 CTX-M plasmids were common. Three sequenced CTX-M plasmids from E. coli, K. pneumoniae and Salmonella enterica serotype 4,5,12:i:- were identical except for seven mutations and highly similar to IncI1 plasmid ColIb-P9. Two antimicrobial resistance regions were identified: one inserted upstream of yacABC harbouring ISCR2 transposases, sul2 and floR; and the other inserted within shfB of the pilV shufflon harbouring the ISEcp1 transposase followed by blaCTX-M-1. CONCLUSIONS: These data suggest that an ST108 IncI1 plasmid encoding a blaCTX-M-1 gene had disseminated across multiple genera on this farm, an example of horizontal gene transfer of the blaCTX-M-1 gene.