Tracking virulence and AMR in colibacillosis isolates from Saskatchewan broiler farms using whole genome sequencing.

大肠杆菌病是由大肠杆菌引起的家禽急性疾病，是导致萨斯喀彻温省和加拿大肉鸡行业经济损失的头号细菌性疾病。目前，我们还不知道鸡群中大肠杆菌病的存在是否代表了养殖场管理问题，或者是否存在特定的“毒性”大肠杆菌。导致疾病的大肠杆菌菌株。疾病分离物的潜在来源正在争论之中，因为现在抗生素的使用受到如此严格的管制，控制疾病的正确方法也是如此。我们的项目旨在研究这些问题，通过使用现代测序为基础的方法来跟踪E。从SK肉鸡群分离的大肠杆菌。比较整个基因组，或每个E.从健康和患病鸟类中分离的大肠杆菌将使我们能够确定遗传和环境因素对感染的影响。这对于帮助减少萨斯喀彻温省的大肠杆菌病病例数量至关重要。我们的分析还将揭示大肠杆菌的抗菌药物耐药性（AMR）概况。大肠杆菌分离株。萨斯喀彻温省养鸡户与细菌生态学和抗生素耐药性领域的领导者Aaron白色博士、Jo-Anne Dillon博士和Joseph Rubin博士之间的伙伴关系将致力于将研究结果反馈给加拿大境内的生产者和更大的生产者团体。我们的研究结果可以产生广泛的影响，更好地了解大肠杆菌病，学习新的战略来控制疾病和开发工具，为行业向前发展。这些现代工具也被用于跟踪医院内的人类分离株，并将在未来应用于农场诊断和治疗评估。我们的项目还旨在领先于未来的AMR趋势，以填补萨斯喀彻温省存在的知识空白。

Colibacillosis, an acute disease in poultry caused by Escherichia coli, is the #1 bacterial disease leading to economic losses in the Saskatchewan and Canadian broiler industries. Currently, we do not know if the presence of colibacillosis in a flock represents a farm-management issue or if there are specific, "virulent" E. coli strains that cause disease. The potential sources of disease isolates are under debate, as is the proper way to control disease now that antibiotic use is so heavily regulated. Our project is designed to investigate these questions, by using modern sequencing-based methods to track the E. coli isolates from SK broiler flocks. Comparing the whole genomes, or the complete collection of genes in each E. coli isolate, from healthy and diseased birds will allow us to determine the impact of genetic and environmental factors in infection. This will be critical for helping to reduce the number of colibacillosis cases in Saskatchewan. Our analysis will also reveal the antimicrobial resistance (AMR) profiles of the E. coli isolates. The Partnership between the Chicken Farmers of Saskatchewan and Drs. Aaron White, Jo-Anne Dillon and Joseph Rubin, leaders in the field of bacterial ecology and antibiotic resistance, will aim to communicate the findings back to producers and larger producer groups within Canada. Our results can have a wide-ranging impact for better understanding colibacillosis, learning new strategies to control the disease and developing tools for the industry moving forward. These modern tools are also being used to track human isolates within hospitals, and will have future applications for on-farm diagnosis and treatment evaluation. Our project also aims to get ahead of future AMR trends to fill in the knowledge gaps that exist in Saskatchewan.