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

超过60%的当前和新出现的人类感染具有人畜共患起源，即它们在动物和人之间转移，并且具有“一个健康”影响。沙门氏菌感染是一个主要的健康负担，每年有多达1.83亿例病例和140万例死亡。令人担忧的是，随着对一线药物具有耐药性的菌株在全球范围内的传播，抗生素耐药性的上升正在急剧加剧沙门氏菌感染的风险。全基因组测序（WGS）数据可以提供对此类感染的传播和传播以及抗生素耐药性的遗传学的见解，从而为健康感染控制决策提供信息。拟议的博士项目最初将侧重于生成和分析从菲律宾各地的农场，市场和诊所（n> 1，000）收集的沙门氏菌的WGS数据，以了解基因组多样性，循环菌株类型（“血清型”）和抗生素耐药性变体以及传播途径。这些数据将与全球来源的公共序列以及随后在包括菲律宾在内的其他人群中进行的采样相结合。其他重要的One health病原体也将使用便携式平台在研究中心进行测序（例如，Oxford Nanopore Technology MinION），以及相关的能力加强活动。 该项目由OneZoo CDT资助，本质上是多学科的，涵盖了基础资助者（BBSRC，NERC和MRC）的职权范围。即，该项目侧重于“微生物”（BBRSC）、“生态学、生物多样性和系统学”（NERC）以及“全球健康”和“感染和免疫”（MRC）。该项目涵盖UKRI 5个战略主题中的3个：“建立一个安全和有弹性的世界”，“确保更好的健康，老龄化和福祉”和“应对感染”，以及跨理事会的利益“抗菌素耐药性”。这个项目将利用我的微生物学和实验室技能，并涉及收购其他技能，如基因组学，大数据分析和流行病学，从而提供了一个跨学科的经验，涉及在实验室的技能，数据和数字科学，这是需要进行独立的基因组为基础的一个健康调查。培训将由LSHTM提供，包括通过现场，实验室和计算工作，并直接从OneZoo CDT核心能力加强活动。

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.