Evaluation of the iSeq platform for E. coli pathotyping

用于大肠杆菌病理分型的 iSeq 平台评估

• 批准号: 9913825
• 负责人: Laura Brunengraber Goodman
• 金额: $ 22.49万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-05 至 2020-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9913825
• 关键词: Evaluation; iSeq; platform; E.; coli

Project Summary/Abstract There is a growing need for veterinary and public health laboratories to perform whole genome sequencing for monitoring antimicrobial resistance and protecting the safety of people and animals. The FDA Vet-LIRN is currently assessing a small benchtop sequencing platform (Illumina iSeq) that could potentially be deployed across their network. Thus far, it has only been tested with Salmonella, and further methods optimization and evaluation is needed to ensure that the platform can be used by other laboratories that have less familiarity with sequencing technologies. E. coli is the most common pathogen tested for antibiotic susceptibility in veterinary diagnostic labs. It is also one of the most concerning for multi-drug resistance; several isolates captured thus far in Vet-LIRN active surveillance are predicted to be pan-resistant to all drugs used in human or animal medicine. Because the methods for susceptibility testing are not standardized, and specific drug panels are used for animal isolates that do not cover all antibiotics used in humans, it was not until these strains were sequenced that the severity was fully appreciated. Having sequencing capacity for this organism in more labs will facilitate rapid surveillance and better equip labs to participate in pet food contamination cases, which are now heavily focused on sequencing results. This directly supports the mission of FDA to ensure the safety of our nation's food supply and protect public health. Since E. coli is commonly found in people and animals, another critical need is the ability to discern the potential virulence of different strains using molecular subtyping. Unfortunately, no bioinformatic tools currently exist that will provide interpretations that are host specific for animals while still conforming to the pathogenic profiles used for humans. The capacity to perform advanced molecular characterization of bacterial isolates in a reliable manner is critical to our ability to respond quickly to suspected microbiological contamination and monitor antimicrobial resistance in animals and feed. The proposed studies will have important impacts for both human and veterinary health and will improve the capabilities of the Vet-LIRN to perform effective surveillance for food-borne pathogens.

项目总结/摘要 越来越需要兽医和公共卫生实验室进行全基因组测序， 监测抗菌素耐药性，保护人和动物的安全。FDA Vet-LIRN 目前正在评估一个小型台式测序平台（Illumina iSeq）， 通过他们的网络。到目前为止，它只与沙门氏菌进行了测试，进一步的方法优化和 需要进行评估，以确保该平台可供不太熟悉的其他实验室使用 测序技术。 E.大肠杆菌是兽医诊断实验室中进行抗生素敏感性测试的最常见病原体。也是 最令人担忧的多药耐药性之一;迄今为止在Vet-LIRN活性中捕获的几种分离株 监测预计对人类或动物医学中使用的所有药物具有泛耐药性。因为 药敏试验的方法没有标准化，对动物分离株使用特定的药物板 这并不包括所有用于人类的抗生素，直到这些菌株被测序， 得到了充分的赞赏。在更多的实验室中拥有这种生物体的测序能力将有助于快速 监督和更好地装备实验室参与宠物食品污染案件，这是现在严重 专注于测序结果。这直接支持FDA的使命，以确保我们国家的安全， 保障食品安全，保护公众健康。 自E.大肠杆菌在人和动物中很常见，另一个关键的需求是能够辨别 使用分子亚型分析不同菌株的潜在毒力。不幸的是，目前没有生物信息学工具， 存在，将提供对动物的宿主特异性的解释，同时仍符合致病性 用于人类的配置文件。对细菌分离株进行先进分子表征的能力， 可靠的方式对我们迅速应对可疑微生物污染的能力至关重要， 监测动物和饲料中的抗菌素耐药性。拟议的研究将对以下方面产生重要影响： 人类和兽医健康，并将提高Vet-LIRN的能力， 监测食源性病原体。