Antimicrobial resistance in Brazilian pig and poultry production and its contribution to the success of Salmonella serotypes

Antimicrobial resistance (AMR) of bacteria found in livestock represent a grave threat to the health of both animals and humans; resistant infections in livestock also have a significant economic impact. Salmonella enterica is one of the most important bacterial pathogens in pigs and poultry, which are thought to be two of the major reservoirs for human infections. Brazil is one of the world's largest producers and exporters of pig and chicken meat, and these industries are significant contributors to the country's economy. Change in these production systems over the last 10 years, including massive intensification and introduction of a Salmonella Enteritidis vaccine in poultry, have led to dramatic shifts in the Salmonella serotype prevalence observed from pigs and poultry in Brazil. These shifts are probably driven by antimicrobial use and resistance, but this issue has not been fully investigated.

The research outlined in our proposal will investigate the diversity and evolution of AMR determinants in Salmonella isolated from Brazilian pigs and poultry over the last 10 years. We will use whole genome sequencing, and state-of-the-art long read sequencing, combined with molecular biology and epidemiology to explore the role of AMR in the success of different Salmonella serotypes in these populations. This proposal represents a new collaboration between Dr Mather at Quadram Institute Bioscience (QIB) in the UK, and Dr Moreno at the University of São Paulo (USP), along with collaborators Dr Terezinha Knöbl and Dr Luisa Moreno at USP. This research will tackle the huge health and economic threat posed by AMR to Brazilian livestock species, which will help identify where suitable control strategies could be applied most effectively.

Food security and AMR are strategic priorities for BBSRC and FAPESP. The proposed research in this proposal will address those priorities by identifying the trends and diversity of Salmonella and AMR in swine and poultry populations and the role of AMR in the success of Salmonella serotypes in these systems. These data are particularly relevant, given the importance of pigs and poultry to the Brazilian economy and the projected doubling of antimicrobial usage in these systems by 2030 - identifying the role of AMR will allow suitable control strategies to be applied most effectively. Beneficiaries will include policy makers, industry, and the public. The work proposed here will also develop further bioinformatics capacity within Brazil by providing additional training in these skills.

Policy makers: AMR and Salmonella in the food chain is a concern for many governmental agencies, including the Food Standards Agency (FSA) in the UK and the Department of Agriculture in Brazil. We will have strong engagement with these agencies throughout the project; Dr Mather is an FSA Fellow and meets regularly with the organisation. The Quadram Institute also has long-standing collaborative links with the Animal and Plant Health Agency and Public Health England, which will ensure dissemination of our results to relevant agencies. Drs Moreno and Knöbl have links with the Department of Agriculture in Brazil and state government official laboratories as such as the Biological Institute and Butanta Institute.

Industry: Drs Moreno and Knöbl have worked with the pig and poultry industries, respectively, in Brazil for many years. Their close collaborations will facilitate communication of our results to the relevant stakeholders. The Quadram Institute also has many links with the pig and poultry industries in the UK, and these contacts will be utilised to ensure dissemination of results.

Public: Accessible summaries of our research in lay terms will be published on the websites of our respective institutions, University of São Paulo and the Quadram Institute, and shared via social media. We will also participate in various public engagement events, such as the Norwich Science Festival.

Training and knowledge exchange: Throughout the course of this work, training and up-skilling in bioinformatics will be provided for both the Brazilian and UK postdoctoral researchers associated with this project, particularly developing further the bioinformatics capacity in Brazil.