Salmonellosis, caused by Salmonella, is among the most frequently reported foodborne diseases worldwide, including in the Philippines. While numerous potential means of transmission exist, commercial chicken and pig meat has been identified as one of the most important food vehicles for these organisms. Treatment options for salmonellosis are decreasing as the underlying bacteria continue to show resistance to antimicrobial drugs. Multi-drug resistant isolates of Salmonella are present in the Philippines. To fully understand transmission dynamics and virulence across the food chains requires the genomic characterisation of isolates. Whole-genome sequencing (WGS) technology has become a fast and affordable tool that is revolutionizing the fields of genetics, microbiology, and ecology, as well as public health surveillance and response. WGS analysis can potentially be a rapid and cost-effective approach to define resistance genotypes, predict resistance phenotypes and identify identical isolate genomes that are part of a transmission chains. Across domains in the food chain in Manilla and Pampanga, including markets and retailers, we propose to test poultry and swine meat for Salmonella, and sequence the pathogens. We will build phylogenies and compare inferred phenotypes to laboratory determined virulence and drug resistance outcomes.
