Mapping resistance to Campylobacter in the chicken

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute


Food security is an increasing priority for the UK Government and food safety is a key component of this. Campylobacter is the most common cause of food poisoning in the UK and is responsible for an estimated 321,000 estimated cases in England and Wales in 2008, with over 15,000 hospitalisations and 76 deaths. Campylobacter accounts for a third of the cost of food-borne illness in England and Wales, estimated at £583 million in 2008. It is found mainly in poultry and control of the organism in this reservoir is expected to lower the inclidence of human infection.

"Campylobacter is a highly complex organism and we will only be able to understand it more fully and to overcome the threat it poses by deploying world-class research across microbiology, immunology and molecular biology... Addressing the Campylobacter challenge involves two of the three BBSRC strategic priorities of food security and basic bioscience underpinning health, in addition to exploiting systems approaches and new research tools." Professor Douglas Kell, BBSRC CEO.

The UK Research and Innovation Strategy for Campylobacter, 2010-2015, is joint funded by the FSA, BBSRC, DEFRA, DARDNI and the Scottish Government. The overarching aim for the funders is to reduce the incidence of Campylobacter infections in humans, through reduction of the level of the bacterium in its farm animal hosts and the potential for cross-contamination in the food chain. Two of the main research priorities are understanding colonisation in the chicken and the chicken's immune response, and development of greater resistance to Campylobacter colonisation in the chicken. However, research in either of these areas was not included in a recent joint call for research into control of Campylobacter.

The availability of chickens with significant innate resistance to Campylobacter colonisation would represent a safe, cost-effective solution. We have shown that genetic variation influences resistance to Campylobacter colonisation inchickens, with one line able to reduce levels of the bacterium in the gut by up 10,000-fold relative to another line. Complex genetic analysis in these inbred chicken lines has indicated that some of the regions, or loci, associated with resistance overlie known bacterial resistance genes. In this proposal we will investigate these loci further to locate the beneficial genes or mutations.

We will carry out further work to map resistance genes, coupled with using the latest methods that allow selection of genes throughout the whole genome. Using tools such as new generations of high density panels to detect single nucleotide polymorphisms (changes in a single base of DNA between two different individuals at the same site) (~750k can be analysed at once), we can identify animals with candidate resistance genes that can be used to select future generations of chickens with robust resistance and greatly reduced levels of Campylobacter colonisation. As recommended by the Strategy, we will carry out this genetic research in collaboration with industry (Aviagen, a UK-based company that produces the pedigree chickens from which are generated over 50% of the world's 50 billion chickens every year), since gene association studies must be implemented in poultry breeding programmes. It is likely that resistance to Campylobacter depends on multiple genes and the selection of resistant lines will depend on the identification of specific traits and candidate animals. Though potential also exists to control Campylobacter on farm via improvements to hygiene and biosecurity, dietary modification, novel antimicrobial agents and vaccination, we believe that the proposed project would allow a targeted and rapid approach to breeding lines of poultry more resistant to Campylobacter colonisation.

Technical Summary

Campylobacter has long been considered to be a commensal in the chicken, and therefore at first consideration it would seem unlikely that there could be resistance to colonisation. However, we believe that rather than being a commensal, Campylobacter is actually an accomplished pathogen. It can induce typical innate immune responses (albeit that these are time- and magnitude-limited), it can be partially controlled by vaccine-induced adaptive immunity, and genetic resistance to colonisation exists in chickens. We have identified four Campylobacter resistance QTL in inbred lines 61 and N.

Our overarching hypothesis is that QTL controlling resistance to Campylobacter are also circulating in commercial chickens, and that some of these will be in common with those identified in the inbred lines. For example, of the 4 QTL we identified for resistance to colonisation with Salmonella, two are circulating in commercial chickens.

We will refine the Campylobacter resistance QTL in the inbred lines, identify candidate genes and nucleotide changes and analyse the functional consequences of this sequence variation. We will also perform whole genome association/genomic selection (WGA/GS) for Campylobacter resistance in commercial lines and then independently validate the WGA/GS results. This dual approach is required as we cannot apply a simple candidate SNP polymorphism approach in the commercial lines, based on the inbred line data, as we have no evidence that there is the same underlying linkage disequilibrium (LD) between the causal mutation and the SNP in the commercial lines.

The overall aim is to identify markers (SNPs), candidate genes and ultimately causative mutations for resistance/susceptibility to colonisation with Campylobacter in chickens. The resistance-associated genotypes will inform commercial breeding programmes to reduce the incidence of Campylobacter contamination of poultry carcasses and thereby levels of this food-borne zoonosis in humans.

Planned Impact

The UK poultry industry faces numerous challenges in order to remain sustainable. These include the imminent move to more extensive rearing systems; the withdrawal of prophylactic and many therapeutic antibiotics, and other drugs such as anti-coccidials; resistance and residue problems with anti-helminthics. These challenges will all have an impact on poultry health, but also have the potential to impact on human health. For example, with an increased incidence of zoonotic pathogens in chickens, there is the potential to lead to an increase in these diseases in humans.

It is important that poultry breeders are able to select for genetic improvement in performance when birds are reared in such environments. New and effective disease control requires detailed understanding of host-pathogen interactions.
We have recently shown that, far from being a commensal of the chicken, Campylobacter is actually a very accomplished pathogen. Campylobacter can induce typical innate immune responses (albeit that these are time- and magnitude-limited), it can be partially controlled by vaccine-induced adaptive immunity in chickens, and genetic resistance to Campylobacter colonisation exists (we recently identified four resistance QTL in inbred lines).

However, we still need to identify the genes and mutations that are responsible for the resistance phenotype and if these, or others, segregate in modern commercial pedigree chicken lines, as these lines form the basis of selection for the broiler birds we eat.
The proposal is supported by Aviagen Ltd, the UK-based world's premier poultry breeding company that produces the pedigree chickens from which are generated over 50% of the world's 50 billion chickens every year. Aviagen is committed to improving the health status of their commercial broiler stock through selection for resistance to disease challenges, pathogens associated with food-safety and general fitness. Improving our understanding of the genetic basis of resistance to Campylobacter will complement current research in this area. Their motivation for supporting this research is to better understand these important food security pathogens with the ultimate objective of informing their ongoing breeding programme. If successful, the results from this project will allow a targeted and rapid approach to breeding lines of poultry more resistant to Campylobacter colonisation and infection.

Beneficiaries from this research therefore include academics interested in the genetics of disease resistance, host-pathogen interactions and disease control. The support of Aviagen will ensure this transfer of knowledge from the academic environment to industry. Results will be published, when appropriate, in peer-reviewed scientific journals and will be presented at various conferences (e.g. the XIIIth Avian Immunology Research Group meeting, Edinburgh 2012 and the 7th International Chick Meeting in Japan, 2013).

Effective uptake of the outcomes of our research are also facilitated by close links with the Biosciences KTN, who identified disease resistance and animal health as the top priorities for UK breeding industries. This work has the potential to impact on the sustainability of the poultry industry in the UK, and also to inform FSA and DEFRA policy. It also therefore falls within the remit of the BBSRC Sustainable Agriculture Strategy Board and priority for research on Global Food Security. Most importantly, this proposal falls squarely into the research priorities of the UK Research and Innovation Strategy for Campylobacter, 2010-2015, jointly funded by the FSA, BBSRC, DEFRA, DARDNI and the Scottish Government, the remit of the BBSRC 'Animal Disease, Health and Welfare' Committee and matches the BBSRC scientific priority of 'Animal Health'. Policy priorities of 'economic and social impact' and 'welfare of managed animals' will also be addressed by this research.


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Description The project related to the basis of heritable resistance of chickens to Campylobacter. C. jejuni is the leading cause of foodborne diarrhoeal illness in humans in the developed world and poultry are the principal reservoir. Our research aimed to identify regions of the chicken genome associated with resistance to C. jejuni colonisation to inform the design of selective breeding programmes for the poultry industry. We performed genome-wide association studies (GWAS) using the progeny of crosses between inbred lines that differ in C. jejuni resistance and have identified quantitative trait loci (QTL) associated with resistance, including one locus shared in separate backcross and advanced inter-cross populations of lines 6 x N. A manuscript reporting these findings was published in BMC Genomics in 2016. We have also completed a GWAS using ~3000 broilers exposed to Campylobacter in a commercial setting and have defined bird genotypes and C. jejuni burden. This has identified QTL associated with resistance in commercial birds, and two of the regions identified are common to the analysis in the progeny of crosses of inbred lines. With ongoing BBSRC core funding and a new grant from the Scottish Government we seek validate that the predicted QTL are associated with resistance to Campylobacter colonisation (e.g. by challenge of birds of predicted resistant and susceptible genotype) and understand how QTL exert their effect (e.g. by examining the sequence and expression of genes in the QTL intervals) .
Exploitation Route We have received Scottish Government funding to extend the work, including to establish if birds predicted to be resistant or susceptible on the basis of SNP genotype can repel challenge with diverse C. jejuni strains on experimental inoculation, as well as to understand the basis by which QTL exert their effect (e.g. studies of the function and expression of genes within QTL).
Sectors Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology

Description Scottish Government RESAS initiative
Amount £450,000 (GBP)
Organisation Scottish Government 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 10/2016 
End 09/2019
Description Collaboration with Aviagen Ltd 
Organisation Aviagen Group
Country United States of America 
Sector Private 
PI Contribution The project was funded via the BBSRC LINK scheme and involved a close collaboration with Aviagen Ltd, part or the Erich Wesjohann Group and a major global breeder of poultry. In broad terms, the project sought to define the genetic basis of avian resistance to Campylobacter colonisation. This involved genome-wide association studies using the progeny of crosses of inbred lines that differ in heritable resistance to Campylobacter (specifically backcross and advanced inter-cross populations derived from lines 6 and N), and identified quantitative trait loci (QTL) associated with resistance (Psifidi et al. 2016). The project also involved a genome-wide association study using over 3000 Aviagen broilers in a simulated field context. High quality genotypes and Campylobacter colonisation phenotypes were identified for 2750 broilers and QTL associated with resistance were identified, two of which were shared with the study using inbred lines (manuscript in preparation). Studies to validate QTL and understand how they exert their effect are ongoing with core funding from the BBSRC and a grant from the Scottish Government.
Collaborator Contribution As above. Aviagen provided access to its flocks and expertise, as well as costs for genotyping and validation of QTL.
Impact See publications & additional funding sections of this return. By defining the genomic architecture of avian resistance to Campylobacter our studies will inform the scope to breed selectively for birds with improved control of an important zoonotic pathogen. Our studies show that a relatively modest proportion of the variation in the trait (caecal C. jejuni numbers) can be explained by bird genetics and that resistance-associated QTL are already prevalent in the commercial broiler line studied. Work is ongoing to validate the associations between QTL and Campylobacter levels, and understand how they exert their effect. There is scope for long-term societal gain from the research as chicken continues to be the primary reservoir of human campylobacteriosis.
Start Year 2011
Description Feature for BBC2 Food Detectives programme 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Professor Stevens took part in a BBC2 Food Detectives programme which featured Campylobacter in chickens. He helped to design a survey of Campylobacter contamination in a sample of fresh chicken obtained from Scottish retailers and interpret the findings. This were close to Food Standards Agency findings, which were broadcast as part of an interview with Prof. Alice Roberts. The interview took place at The Roslin Institute and included a lay description of Campylobacter, the importance of chickens as a reservoir of infection and strategies by which consumers can protect themselves. It also highlighted BBSRC-funded work at Roslin to mitigate the problem based on genetic selection (this project) and vaccines (other BBSRC projects held by Prof. Stevens).
Year(s) Of Engagement Activity 2016
Description Public lecture on Campylobacter in chickens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Public talk on 'Chickens and the enemy within' at The Roslin Institute Open Doors Day in 2012. This highlighted the problem of Campylobacter infections in people, the role of poultry as a reservoir, and research at Roslin to control the problem via genetic selection and vaccination in poultry and to understand the molecular basis of virulence of the organism.
Year(s) Of Engagement Activity 2012