16AGRITECHCAT5: A whole supply chain hurdle approach to control Campylobacter

Campylobacter is responsible for 14% of all human diarrheal cases worldwide, with >280,000 food poisoning cases in the UK per year and c. 100 deaths. It costs the UK economy >£580m per year, much of this imposed on the NHS (Strachan et al 2010, Lancet, 376, 665-7). It is an extremely serious issue and the FSA now regularly monitor Campylobacter levels from retail purchased chickens and publish the results. Given the social impacts, Campylobacter is a primary risk threatening the UK poultry industry. An industry that contributes £3.6bn GVA to the UK economy. Defeating Campylobacter is a clear industry and policy aim, any techniques which reduces the impact of this disease will underpin both the economic and social sustainability of the industry and food security of consumers. Given the impact of Campylobacter on human consumers, the control of the disease has been the subject of considerable research, and a number of key interventions are currently deployed by the industry. These include increased emphasis on the biosecurity of flock, hygiene through the supply chain, novel animal feeds, transportation systems, cold chain systems, handling and processing techniques. However, in nearly all instances the impact of different interventions are typically studied in isolation. We still do not fully understand where Campylobacter enters and exits the supply chain, how interventions may select for the survivability of different strains, the impact of a range of different interventions applied in series through the supply chain and the resilience of these treatments with varying flocks and seasons. Given this lack of understanding it is very difficult to develop an integrated approach to defeat the pathogen through the supply chain. However, modern molecular techniques have also progressed at pace and very recent studies suggest whole genome sequencing (WGS) can be applied to effectively track and trace Campylobacter through a supply chain. This enables a hitherto impossible examination of the organism as it moves through a supply chain. We now have the ability to show where a strain entered and exited a supply chain, the specific impact of interventions and how they might be strain selective. In this project, we will apply modern molecular approaches to track and trace Campylobacter through the supply chain. Furthermore, we will examine how a series of interventions through a supply chain (the hurdle approach) can be optimised to help defeat the organism. The interventions studied will be the effects of changes to animal feeds, 2 thermal interventions applied in the factory and the impact of a novel blast chilling and modified atmosphere packaging system. This is a comprehensive study across an entire supply chain. The highly novel combination of a hurdle technology approach with molecular epidemiology will help underpin the poultry supply chain. We are aware of no other similar and wide ranging approach to control Campylobacter in the global poultry industry. WGS can help optimise a supply chain system, but is not a simple tool to apply in industry post project. Therefore, within the project we will also develop a novel quantitative PCR (qPCR) which can rapidly measure Campylobacter level through the supply chain. qPCR systems are available for Campylobacter but they have not yet been optimised to detect only live, rather than dead, cells.

We will rigorously study a novel holistic hurdle technology approach comprising a consecutive series of interventions, underpinned by the largest molecular study of Campylobacter in a supply chain conducted to date. We will test the effect of region and season on Campylobacter populations, and then the efficacy of four novel interventions, including interactions between them. These are: 1) novel antimicrobial dietary Campylobacter control on farm; 2) a novel thermal intervention system; 3) the synergy of a further thermal invention; and 4) a novel packaging method. We will evaluate the effect of interventions, and their interactions on total bacterial communities and Campylobacter genetic variance and track and trace the fate of individual strains and sub-populations of Campylobacter.

Due to cost, previous studies sequenced genomes of a relatively few individual isolates from samples: this prevents any meaningful insight into populations. It is well described that Campylobacter is very genetically diverse in the UK. Sequencing a sufficient number of individuals from samples is not yet economically viable for large-scale studies such as this, where we will analyse populations from 392 samples. Instead we will use a novel pooled sequencing approach to circumvent this massive cost, but retain power. We will combine together 100 individuals from each sample and extract and then sequence this pooled DNA. The trade-off is we cannot track individual strains. The massive cost saving means we can meaningfully statistically compare populations to objectively evaluate if and how populations are affected by novel interventions. Informed by data from stage 1, we will then use targeted genome sequencing of individual Campylobacter to detail changes at the strain and sub-population level to evaluate if and how Campylobacter populations and specific strains are affected by intervention hurdles, and if populations differ in space and time.

This proposed study has significant social, economic and environmental impact. The social impact is compelling. Campylobacter is responsible for 14% of all human diarrheal cases worldwide, with >280,000 food poisoning cases, and the associated abject misery, in the UK per year and c. 100 deaths. It costs the UK economy >£580m per year, much of this imposed on the NHS (Strachan et al 2010, Lancet, 376, 665-7). It is an extremely serious issue and the FSA now regularly monitor Campylobacter levels from retail purchased chickens and publish the results. They were aiming that by 2015 only 10% of sampled chickens will be contaminated at a high level of 1000cfu/g from a 2008 baseline of 27%. To date a level of only 19% has been achieved, and human reported incidence has not decreased. Campylobacter derived from poultry is thought to be associated with 80% of the human incidence of the disease. There is therefore a compelling public health need to reduce the contamination of poultry by Campylobacter. The economic impact is also considerable. Notwithstanding the economic costs of treating those affected by Campylobacter (£580m p.a.), the poultry industry per se contributes £3.6bn GVA (with a sales value of £6,6bn p.a.) to the UK economy. The industry directly employ 35,000 people, and many fold more within the supply chain. Defeating Campylobacter is a clear industry and policy aim, any techniques which reduces the impact of this disease will undepin both the economic and social sustainability of the industry and food security of consumers. Due to the recent FSA public surveys of Campylobacter levels in retail stores, there is now increased competition between suppliers and retailers to reduce reported incidence. This may well lead to changes in retail buying practices which favour high performing suppliers, including those from overseas who have a good track record with Campylobacter. However, conversely, significant export opportunities may arise for UK producers who can control Campylobacter, it may also help UK farmers increase their share of their own market (currently 84%). The environmental impact is also significant. The primary focus of the industry is currently on resolving the issue of Campylobacter. This therefore limits many initiatives to sustainably intensify the environmental impact of poultry production systems. The ability to resolve the Campylobacter issue will be a key enabling step to further intensification of the industry.