A CURE for <i>Salmonella</i>: A Laboratory Course in Pathogen Microbiology and Genomics

Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with computational and ‘big data’ methods. Additionally, laboratory experience in the isolation, identification, and characterization of unknown bacteria is a vital part of a microbiology student’s training. This lesson is a course-based undergraduate research experience (CURE) focusing on Salmonella enterica, a common and relatively low-virulence foodborne pathogen. In Module 1, students isolate and identify S. enterica strains from stream sediment, poultry litter, or other sources. They conduct phenotypic evaluation of antimicrobial resistance (AMR) and can search for plasmids. Isolates’ whole genomes may be sequenced by the United States FDA or public health laboratories, typically at no charge. In Module 2, students learn basic methods of genome assembly, analysis, annotation, and comparative genomics. They use easily accessible, primarily web-based tools to assemble their genomes and investigate areas of interest including serotype, AMR genes, and in silico evidence of mobile genetic elements. Either module can be used as a standalone learning experience. After course completion, students will be able to isolate and identify Salmonella from natural sources, and use computational analysis of microbial genomic data, particularly of the Enterobacteriaceae. This lesson offers undergraduate microbiologists a genuine research experience and a real-world microbiology application in genomic epidemiology, as well as a valuable mix of field, laboratory, and computational skills and experiences.基因组学和生物信息学领域的迅速发展，下一代测序产生的海量数据，以及 '-omics' 技术在生物学众多领域的广泛应用，催生了对具备计算和‘大数据’方法实践经验的学生的需求。此外，实验室中关于未知细菌的分离、鉴定和特征描述的经验，对于微生物学学生的培训至关重要。本课程旨在提供一个基于课程的本科研究经验（CURE），聚焦于沙门氏菌属（Salmonella enterica），这是一种常见且相对致病力较低的食源性病原体。在模块1中，学生将从河流沉积物、家禽粪便或其他来源中分离和鉴定 S. enterica 菌株。他们将对抗菌药物耐药性（AMR）进行表型评估，并能够搜索质粒。分离菌株的全基因组测序可能由美国食品药品监督管理局或公共卫生实验室进行，通常无需付费。在模块2中，学生将学习基因组组装、分析、注释和比较基因组学的基本方法。他们使用易于获取的、主要基于网络的工具来组装他们的基因组，并调查包括血清型、AMR 基因和移动遗传元件的计算机模拟证据在内的感兴趣领域。任一模块均可作为独立的学习经历。课程结束后，学生将能够从自然来源中分离和鉴定沙门氏菌，并利用微生物基因组数据的计算分析，尤其是肠杆菌科的基因组数据。本课程为微生物学本科生提供真正的科研经历，以及基因流行病学领域的真实世界应用，同时融合了野外、实验室和计算技能与经验的宝贵组合。