Rapid diagnostics and control strategies for enteric bacterial pathogens in backyard and commercial poultry production in Thailand and the Philippines

Lead Research Organisation: University of Liverpool
Department Name: Institute of Infection and Global Health


In many Low to Middle Income Countries (LMICs) poultry meat and eggs are produced in small scale flocks using indigenous breeds of birds. This contrasts with countries that produce meat in large commercial units using chicken strains specifically bred for use in highly controlled environmental conditions with maximal meat production in as short a time as possible. Indigenous breeds are cross-bred and produce fewer eggs and less meat than their commercial equivalent but are are an important source of food at the family or local community level. However, due to differences in regulatory practices, the use of antimicrobials (AMs) as growth promoters is prevalent which limits future commercial development and promotes the spread and maintenance of antimicrobial resistance. The use of AMs needs to be reduced by the provision of alternative growth promoters.

Commercial breeding programmes have resulted in broilers that preferentially deposit muscle (ie breast meat) over allocating proteins toward other processes, including, probably, the immune response. Under commercial conditions of good biosecurity, optimised high nutrient diets over short timescales in highly controlled conditions, commercial birds are very productive. In contrast, indigenous birds are smaller, have a lower nutrient demand and are immunologically more robust; they are however, far less productive. This combination of differing bird genetic background and nutritional requirements along with potentially different immunological responses and intestinal microflora means that poultry disease susceptibility and the potential for colonisation by zoonotic pathogens may be different in indigenous birds. We wish to determine if Indigenous breeds of poultry and modern hybrid birds differ in their genetics, gut microbiome and immunological parameters and establish if these differences associated and if they can be exploited for disease control and management.

The major bacterial zoonotic pathogens, Salmonella enterica and Campylobacter jejuni, frequently colonise poultry and consequently present a very significant human health risk due to contamination of meat or eggs. In addition, certain types of S. enterica (the serovars Pullorum and Gallinarum) also present a disease risk to chickens, affecting the health and welfare of the flock. Our aim is to characterise the infection of an indigenous breed of chicken in backyard flocks to determine how infection modulates the composition of the bacterial community living in the chicken gut and the AM resistance genes that are present. In addition, we will characterise how the immune response of the indigenous birds responds to infection. We will use this information to develop a probiotic to competitively exclude Salmonella and/or Campylobacter and also develop a cheap and simple test for the presence of different types of Salmonella in backyard flocks. This project will provide both commercial and backyard producers with a much-needed management tool to reduce the disease burden and health risk associated with poultry products.

Planned Impact

Who may benefit from this research?

The research will directly benefit the Thai and Filipino poultry industries. In the case of Thailand the research benefits a largely commercial industry focussed on export and domestic supply. In the Philippines, the work is more directed towards support of backyard producers of native breeds and eggs for local markets and home consumption

International poultry industries

Public in Thailand and Philippines

Academic and industrial research communities

How will they benefit?
1. Improved control and diagnostics of bacterial infections such as Salmonella and Campylobacter that affect bird and human health
2. Improved skills, capacity and knowledge base around poultry health and food safety
3. Increased food safety for poultry meat and eggs in Thailand and Philippines
4. Improved knowledge of the genetics and biology of SE Asian indigenous chickens
5. Better development of probiotics directly relevant to SE Asian chicken production
6. Reduction in the public health barriers to export of poultry meat from SE Asia
7. Development of training resources
8. Improvements in poultry management, health and welfare
9. Improved understanding of the avian microbiome, its diversity and its role in health


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Description This work has for the first time shown that high levels of the foodborne pathogens Salmonella and Campylobacter are found in small-scale chicken production in Philippines. This is important as these small-scale producers make up close to 50% of the total output. Ongoing work from another project also suggest that there is a high-level of Campylobacter in these chicken at retail in supermarkets and markets.

We have also been able to characterise the microbiome of chickens and importantly we have found significant carriage of genes associated with antimicrobial resistance representing a significant risk.

Partners at Roslin are sequencing the genome of several Filipino chicken breeds. Studies in Africa have shown local adaptations can be utilised in selective breeding suited to the conditions and infection threats in that area. This will form a resource to use in breeding programmes.

Our partners in Thailand have developed systems that can integrate the data from the genome, the microbiome and the infection and health status of the birds. This forms a platform to identify microbiota components associated with health and potentially probiotics that can be used locally

Support and training for young scientists and veterinarians in Philippines
Exploitation Route KMUTT have developed pathway tools that can combine metadata with microbiome and host genomics data to understand the microbiome contribution to health and disease status of chickens.

Ongoing sequencing of Filipino chicken breeds at Roslin will provide a valuable genetic resource for local breeding programmes.

Improved understanding of the carriage of Salmonella and Campylobacter in Filipino production conducted by UPLB with the support of Liverpool and Leicester will inform risk analysis for foodborne pathogens and the development of control strategies in the region.

Microbiome data for indigenous breeds throughout their production life represents a resource for future researcher and the agri sector in SE Asia
Sectors Agriculture, Food and Drink,Education,Environment,Healthcare

Description Wide uptake of the poultry guide (over 1500 distributed and more than 5,000 online reads) and smartphone app (over 2000 downloads) associated with the project to support vets and producers in Philippines and other LMICs. Uptake has continued to be good of the app and book thanks to features in several industry magazines and websites. Local training and support has been provided by Leicester and Liverpool at UPLB to support the training of veterinarians and through MSc projects, including microbiome analysis. As no work has yet been published and Covid has stopped us holding any stakeholder meetings, then other jmpacts including those related to ODA goals are yet to be realised.
First Year Of Impact 2020
Sector Agriculture, Food and Drink,Education
Impact Types Economic,Policy & public services

Title Microbiome and related metadata database 
Description Colleagues at KMUTT, Bangkok, have developed a database that incorporates microbiome sequences with full metadata (bird, health status, location, morphological features) for use across all 7 project partners and will be made freely available once populated 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact None as yet 
Description Shared diagnostic development 
Organisation University of Surrey
Country United Kingdom 
Sector Academic/University 
PI Contribution Discussion between teams of different project in Philippines to share diagnostic tools, samples and impact material
Collaborator Contribution Agreement to share resources for diagnostics of bacterial infections
Impact None as yet
Start Year 2019
Description Android Smartphone Application for Chicken disease 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Together with the University development team we have created a standalone app. which covers the major diseases of chicken along with videos around biosecurity, chicken examination and diagnostics. It was designed around Android as this is the main system used in SE Asia. There have been more than 1500 installations of the app, with the majority in LMICs, though a significant number in the UK though word-of -mouth as a useful diagnostic tool. The app has content on all major diseases, their diagnosis, epidemiology and interventions to treat or control infection. As it can be downloaded it does not require a phone signal so can be utilised in remote villages. Preliminary analysis of the downloads shows more than 70% are from LMICs with a high concentration in SE and South Asia (Philippines, Thailand, Bangladesh, Pakistan and India) but also across Africa, Middle-East and Latin America.
We have been approached by a feed company to link the app to theirs around nutrition and feed quality for use in SE Asia
Year(s) Of Engagement Activity 2019,2020,2021
URL https://play.google.com/store/apps/details?id=uk.ac.liverpool.pocketguideforpoultrydiseases&gl=GB
Description Chicken Infectious Disease Manual 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We have produced a handbook of major chicken diseases with a focus on those diseases most prevalent in SE Asia including basic management advice. Around 2000 print copies have been distributed in Philippines, Thailand and East Africa. Electronic PDF versions have been supplied to several collaborators in UK, Europe and Africa for use in country or with collaborators. The pocket guide allows free access to key information for students, producers/farmers and veterinarian without the need for access to large and expensive textbooks with this information. Under a Creative Commons licence it is free to be reproduced in LMICs without licensing costs.
We have also made the guide available via the University repository and placed in on the open access platform Research Gate where it has received more than 2,000 reads.
Year(s) Of Engagement Activity 2019,2020,2021
Description Gut health Workshop for developing poultry industries at WVPAC Bangkok 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We held a 2 hour workshop based around enteric disease and improved poultry gut health for LMICs at the World Veterinary Poultry Association conference. 130 delegates attended from multiple countries and led to significant interest in the project and our work. Some material was later used by one of the keynote speakers.
Year(s) Of Engagement Activity 2019
Description Science Fair, Ness Gardens 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact October half term science fair-theme of 'Good and Bad Bugs" with Halloween Theme. Pre-booked activity (due to Covid restrictions) with 5 sessions of 10 families.
Year(s) Of Engagement Activity 2021
Description Support and training for MSc and Postgraduate Veterinary Students at University of Philippines Los Banos 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Seminars held at UPLB for veterinarians prior to professional entry exams.
Specific research-related seminars and in-lab support for MSc students undertaking work related to the project
Year(s) Of Engagement Activity 2019