Using genomics to understand Salmonella transmission from farm-to-fork and the environment in the Philippines

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More than 60% of current and emerging human infections have a zoonotic origin, that is, they are transferred between animals and people, and have "One health" impacts. Salmonella bacterial infections have a major one health burden, with up to 183 million cases and 1.4 million deaths each year. Worringly, the rise of resistance to antibiotics is acutely exacerbating the risk of Salmonella infections, with the global spread of strains that are resistant to frontline drugs. Whole genome sequencing (WGS) data can provide insights into the transmission and spread of such infectons, as well as the genetics underlying antibiotic resistance, thereby informing one health infection control decision making. The proposed PhD project will focus initially on generating and analysing WGS data for Salmonella collected from farms, markets and clinics (n>1,000) around the Philippines to understand genomic diversity, circulating strain-types ("serovars") and antibiotic resistance variants, and transmission pathways. These data will be contextualised with globally sourced public sequences, and subsequent sampling across other populations, including within The Philippines. Other important One health pathogens will also be sequenced across study sites using portable platforms (e.g., Oxford Nanopore Technology MinION), with associated capacity strengthening activities. This project is funded by the OneZoo CDT, and is multidisciplinary in nature, spanning the remits of the underlying funders (BBSRC, NERC, and MRC). Namely, the project focuses on "microbes" (BBRSC), "ecology, biodiversity, and systematics" (NERC), and "global health" and "infections and immunity" (MRC). This project covers 3 of the 5 UKRI strategic themes: "Building a secure and resilient world", "securing better health, ageing and wellbeing" and "tackling infections", as well as cross-council interests in "antimicrobial resistance".This project willl leverage off my microbiology and laboratory skillset, and involve the acquistion of other skills, such as genomics, big data analysis and epidemiology thereby providing a trandisciplinary experience involving skills in the laboratory, and data and digital sciences, which are needed to conduct independent genomics-based One health investigations. Training will be provided by the LSHTM, including through hands on field, laboratory and computational work, and directly from OneZoo CDT core capacity strengthening activities.