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

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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.

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.