Senior Honors Projects, 2010-current

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Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Date of Award

Spring 2018

Document Type

Thesis

Degree Name

Bachelor of Science (BS)

Department

Department of Biology

Advisor(s)

James B. Herrick

Steven G. Cresawn

Patrice M. Ludwig

Abstract

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also conduct phenotypic detection of antimicrobial resistance and large plasmids. Isolate genomes may be sequenced by the FDA or public health laboratories (ours were sequenced by the Virginia Department of Consolidated Laboratory Services at no charge). The second half of the lesson (Module 2) involves the bioinformatic analysis of this sequence data. Students use easily accessible, primarily web-based tools such as GalaxyTrakr and Enterobase to assemble their genomes and investigate areas of interest including serotyping, identification of antibiotic resistance genes and genomic islands, and evidence of plasmids. After completion of this course, students should be able to demonstrate skills in the isolation and identification of Salmonella from natural sources, as well as skills necessary for computational analysis of microbial genomic data, particularly of members of the Enterobactericaeae. While this course consists of two modules, one focusing on laboratory skills and the other bioinformatics, either could be used as a standalone module.

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