A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics

Abstract

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. Citation: Jurgensen SK, Harsh J, Herrick JB. 2021. A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics. CourseSource. https://doi.org/10.24918/cs.2021.24 Editor: William Morgan, College of Wooster Received: 5/19/2020; Accepted: 2/24/2021; Published: 9/15/2021 Copyright: © 2021 Jurgensen, Harsh, and Herrick. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: None of the authors has a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. CURE for Salmonella – Laboratory safety contract; S2. CURE for Salmonella – Pre-enrichment and enrichment media preparation; S3. CURE for Salmonella – Field sampling protocol; S4. CURE for Salmonella – Lab notebook grading rubric; S5. CURE for Salmonella – Pre-enrichment and enrichment inoculation protocol; S6. CURE for Salmonella – Plate media preparation; S7. CURE for Salmonella – Plating and purification protocol; S8. CURE for Salmonella – Miscellaneous test protocols oxidase, catalase, KOH; S9. CURE for Salmonella – invA PCR and gel visualization protocol; S10. CURE for Salmonella – Preparing isolates for shipping and freezing; S11. CURE for Salmonella – Bioinformatics Lab Guide Navigating and using GalaxyTrakr and Galaxy; S12. CURE for Salmonella – Bioinformatics lab notebook grading rubric; S13. CURE for Salmonella – Bioinformatics Lab Guide Salmonella serotyping; S14. CURE for Salmonella – Bioinformatics Lab Guide Assessing & filtering illumina data using FastQC and Trimmomatic; S15. CURE for Salmonella – Bioinformatics Lab Guide File naming conventions; S16. CURE for Salmonella – Bioinformatics Lab Guide Genome assembly using SPAdes and Shovill; S17. CURE for Salmonella – Bioinformatics Lab Guide Assessing assembly quality Using QUAST and Bandage; S18. CURE for Salmonella – Bioinformatics Lab Guide Selecting reference genomes/Ordering and viewing assembled contigs using Mauve; S19. CURE for Salmonella – Bioinformatics Lab Guide Gene annotation; S20. CURE for Salmonella – Bioinformatics Lab Guide Antibiotic resistance gene detection; S21. CURE for Salmonella – Bioinformatics Lab Guide Miscellaneous gene and genetic feature detection; S22. CURE for Salmonella – Presentation evaluation rubric; S23. CURE for Salmonella – Poster evaluation rubric; S24. CURE for Salmonella – Sources and description of preexisting survey instruments; S25. CURE for Salmonella – Course Overview; S26. CURE for Salmonella – Media, Isolation, Sampling; S27. CURE for Salmonella – Intro to GalaxyTrakr mini-lecture; S28. CURE for Salmonella – Overview of Next-Gen Sequencing and Assembly; and S29. CURE for Salmonella – FastQC & Trimmomatic. *Correspondence to: Dept. of Biology, MSC 7801, James Madison University, Harrisonburg, VA USA 22807. Email: herricjb@jmu.edu. CourseSource | www.coursesource.org 2021 | Volume 08 1 Lesson