Abstract
We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, and perform whole genome assembly and analysis of Salmonella enterica from stream sediments and poultry litter. In the development of the course and over three semesters, successive teams of undergraduate students collected field samples and performed enrichment and isolation techniques specific for the detection of S. enterica. Eighty-eight strains were confirmed using standard microbiological methods and PCR of the invA gene. The isolates’ genomes were Illumina-sequenced by the Center for Food Safety and Applied Nutrition at the FDA and the Virginia state Division of Consolidated Laboratory Services as part of the GenomeTrakr program. Students used GalaxyTrakr and other web- and non-web-based platforms and tools to perform quality control on raw and assembled sequence data, assemble, and annotate genomes, identify antimicrobial resistance and virulence genes, putative plasmids, and other mobile genetic elements. Strains with putative plasmid-borne antimicrobial resistance genes were further sequenced by students in our research lab using the Oxford Nanopore MinIONTM platform. Strains of Salmonella that were isolated include human infectious serotypes such as Typhimurium and Infantis. Over 31 of the isolates possessed antibiotic resistance genes, some of which were located on large, multidrug resistance plasmids. Plasmid pHJ-38, identified in a Typhimurium isolate, is an apparently self-transmissible 183 kb IncA/C2 plasmid that possesses multiple antimicrobial resistance and heavy-metal resistance genes. Plasmid pFHS-02, identified in an Infantis isolate, is an apparently self-transmissible 303 kb IncF1B plasmid that also possesses numerous heavy-metal and antimicrobial resistance genes. Using direct and indirect measures to assess student outcomes, results indicate that course participation contributed to cognitive gains in relevant content knowledge and research skills such as field sampling, molecular techniques, and computational analysis. Furthermore, participants self-reported a deeper interest in scientific research and careers as well as psychosocial outcomes (e.g., sense of belonging and self-efficacy) commonly associated with student success and persistence in STEM. Overall, this course provided a powerful combination of field, wet lab, and computational biology experiences for students, while also providing data potentially useful in pathogen surveillance, epidemiological tracking, and for the further study of environmental reservoirs of S. enterica.
Highlights
Bacterial genomic epidemiology – the use of genomicsbased methods to aid in the epidemiological investigation of communicable diseases – has become an important new tool in the hands of public health laboratories tasked with tracking pathogen outbreaks (Deng et al, 2016; Armstrong et al, 2019)
Due to the large amount of poultry and cattle farming in the central Shenandoah Valley of Virginia, we hypothesized that Salmonella could be isolated from area streams that drain these farms
Approximately 20% of students indicated that they became less interested in research over the term in the respective areas of microbial ecology, bioinformatics, and genomics. These results suggest that the research course refined student interest by the opportunity to test the proverbial waters of different fields through authentic practice, which may guide their later academic and career intentions in a means comparable to that of a traditional undergraduate research experience (Hunter et al, 2007; Maltese and Harsh, 2015)
Summary
Bacterial genomic epidemiology – the use of genomicsbased methods to aid in the epidemiological investigation of communicable diseases – has become an important new tool in the hands of public health laboratories tasked with tracking pathogen outbreaks (Deng et al, 2016; Armstrong et al, 2019). Non-typhoidal Salmonella enterica (NTS) are the leading cause of foodborne illness in the United States, and one of the main causes of gastrointestinal disease globally. Effective real-time tracking of new outbreaks requires a large database of Salmonella from clinical, food, animal, and environmental sources. As of this writing, over 286,000 draft and complete genomes of Salmonella have been sequenced.
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