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

大肠杆菌病是一种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，我们不知道在鸡群中出现大肠杆菌病是否代表一个农场管理问题，或者是否存在导致疾病的特定的“毒性”大肠杆菌菌株。在抗生素使用受到严格管制的情况下，疾病分离物的潜在来源以及控制疾病的适当方法都在争论中。我们的项目旨在通过使用现代基于测序的方法来追踪SK肉鸡群中的大肠杆菌分离株来调查这些问题。比较健康和病禽的整个基因组，或每个大肠杆菌分离物的完整基因集合，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大肠杆菌病病例的数量至关重要。我们的分析还将揭示大肠杆菌分离株的抗微生物药物耐药性（AMR）谱。萨斯喀彻温省养鸡户与dr。亚伦·怀特、乔-安妮·狄龙和约瑟夫·鲁宾是细菌生态学和抗生素耐药性领域的领军人物，他们将把研究结果反馈给加拿大的生产商和更大的生产商团体。我们的研究结果可以对更好地了解大肠杆菌病、学习控制该疾病的新策略和开发行业向前发展的工具产生广泛影响。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抗菌素耐药性趋势，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.