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

沙门氏菌病，由沙门氏菌属引起，是全球最常报告的食源性疾病之一，对动物和人类都有很高的健康和经济负担。肠道沙门氏菌是全世界腹泻病例和暴发的主要原因，包括在菲律宾。虽然存在许多潜在的传播途径，但商业鸡肉和猪肉已被认为是S。肠预计未来10年菲律宾猪和家禽产品的消费和使用量将增加到每年超过300万公吨，这增加了接触这种细菌的可能性。肠杆菌在马尼拉大都会的鸡和猪食物链中传播，可能是食物中毒的主要和日益增加的原因。值得注意的是，沙门氏菌病的治疗选择正在减少，因为细菌对抗菌药物的耐药性增加。由于抗生素的频繁使用，鸡和猪是传播耐药沙门氏菌的潜在危险。在本研究中，我们建议在遗传水平上比较过去和现在的沙门氏菌样本。在马尼拉大都市的鸡和猪食物链中，活动物和加工肉类领域的肠毒素。我们将进行全基因组测序（WGS）的历史和前瞻性收集S。肠道细菌分离自这些样品。WGS技术已成为一种快速且经济实惠的工具，正在彻底改变遗传学，微生物学和生态学领域，以及公共卫生监测和响应，包括动物健康。WGS分析通过定义耐药基因型及其历史世代、预测耐药表型和鉴定作为传播链一部分的相似分离株基因组，实现了新的且通常不可预测的疾病途径。由此产生的基因组变异将增加我们对传播和耐药性的理解，从而允许更有效的干预。这些基因组数据将与实验室确定的毒力和耐药性结果以及其他收集的Meta数据相关联，以便为疾病控制和预防做出重要贡献，特别是在食品领域（例如农场，市场）的沙门氏菌病诊断和干预措施的设计中。

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).