Using genomics to trace Salmonella transmission and antimicrobial resistance (AMR) in the poultry and swine food chains in the Philippines

Salmonellosis, caused by Salmonella spp., is among the most commonly reported foodborne diseases globally, and has a high health and economic burden in both animals and humans. Salmonella enterica is a primary cause of cases and outbreaks of diarrhoea worldwide, including in the Philippines. While numerous potential methods of transmission exist, commercial chicken and pig meat have been recognised as crucial food vehicles for S. enterica. The forecasted increase in consumption and utilisation of swine and poultry products in the Philippines in the next 10 years to over 3 million metric tonnes per annum, increases the likelihood for exposure to the bacterium.

Previous studies from our Philippine team have shown that S. enterica is circulating in the chicken and pig food chains in Metropolitan Manila, and is a likely major and increasing cause of food poisoning. Notably, treatment options for salmonellosis are decreasing as the bacteria increase in their resistance to antimicrobial drugs. Due to frequent use of antibiotics, chickens and pigs are now realized as potential risks in disseminating drug-resistant S. enterica, with multi-drug resistant (MDR) strains now reported to be present in the Philippines.

For this study, we propose to compare at the genetic level of past and present samples of S. enterica across live animal and processed meat domains in the chicken and pig food chains in Metropolitan Manilla. We will perform whole genome sequencing (WGS) of historical and prospectively collected S. enterica bacteria isolated from these samples. WGS technology has become a rapid and affordable tool that is revolutionising the fields of genetics, microbiology, and ecology, as well as public health surveillance and response, including animal health. WGS analysis has enabled new and often unpredicted routes to disease by defining resistance genotypes and their historical generation, predicting resistance phenotypes and identifying similar isolate genomes that are part of a transmission chains. The resulting genomic variation will increase our understanding of transmission and drug resistance to permit more effective interventions. These genomic data will be correlated with laboratory determined virulence and drug resistance outcomes and other collected meta data to enable an important contribution in disease control and prevention, particularly in the design of diagnostics and interventions for Salmonellosis across the food domains (e.g. farms, markets).

The economy:
Advances in sequencing technology now allow the genomic characterization of bacteria on an unprecedented scale. These have the potential to greatly accelerate research aimed at understanding the biology of S. enterica and their interaction with animal/human immunity and meat products, the underlying causes of AMR, and the disease transmission and epidemiology. The knowledge generated in this project and its application could ultimately benefit those developing foodborne disease control measures, such as identifying transmission hotspots (e.g. markets) and molecular diagnostic tools for monitoring the development of AMR and presence of virulent strains. Ultimately, the knowledge gained in this study could improve the health & wealth of the Philippines, where >2 million tonnes of pig/chicken meat are consumed per year, but also globally where Salmonellosis is a major public health issue. The methods used in this project could have application beyond bacterial studies, to help more widely in the control & prevention of infectious diseases in humans/animals, with associated economic benefits.

The general public:
Salmonellosis is among the most frequently reported foodborne diseases worldwide, and has a high animal and human health and economic burden. Knowledge generated in the project could lead to better access to safer and more effective disease control measurements (e.g. diagnostics) and improved methods for preventing transmission. Genomics insights into transmission and AMR could lead ultimately to improved control measures adopted globally. The project therefore specifically addresses the BBSRC strategic aim to impact positively on agriculture & food security, and to assist with bringing the health impacts of fundamental research to animals and people more quickly. Similarly, we address the BBSRC aim of driving advances in fundamental bioscience, establishing and using biobanks, and developing and applying new tools in 'omics.

Academic and industrial organisations:
New sequencing technologies have the ability to generate vast amounts of data, but there is a need to translate this information into knowledge useable by other research scientists and industry. Our work will provide tools useful for genomic data analysis, which can be utilized across diseases and in different settings. Scientific developments arising would enhance the commercial private sector for the production of safer food, more effective disease control measures and AMR monitoring across the food chain. We have links with companies (e.g. GSK) and will work through the technology transfer offices to ensure pipelines to translation tool production and exploitation are in place. Developing a basic understanding of the S. enterica genetic diversity across the food domains will be important for understanding the impact of control measurements such as diagnostics and transmission mechanisms, and can have practical applications for other foodborne diseases. Also, any important findings and technology developed may have enormous implications for policy makers. We will work with the Philippines Dept. of Agriculture to improve current diagnostics for routine monitoring.

Training:
The proposal will employ, train and develop scientists in the Philippines and UK with an 'omic mentality that can be applied in academia, the public sector and industry. The multidisciplinary project team will have an important and economically vital research area. The researchers working on the project will develop team working and project management skills, which they can apply in all employment sectors. Importantly, the scope for multidisciplinary interactions in this proposal should not be underestimated. The Philippine-based researchers employed to carry out the planned activities will have unique opportunities for engagement with experts across project in microbiology, biotechnology, veterinary care, genomics and genomic epidemiology, and public health.