Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens
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...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.592422/full |
| _version_ | 1818328780196806656 |
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| author | Noah A. Greenman Sophie K. Jurgensen Charles P. Holmes Curtis J. Kapsak Raechel E. Davis William M. Maza Desiree Edemba Bethany A. Esser Selena M. Hise Tara N. Keen Hunter G. Larson Dominique J. Lockwood Brian Wang Joseph A. Harsh James B. Herrick James B. Herrick |
| author_facet | Noah A. Greenman Sophie K. Jurgensen Charles P. Holmes Curtis J. Kapsak Raechel E. Davis William M. Maza Desiree Edemba Bethany A. Esser Selena M. Hise Tara N. Keen Hunter G. Larson Dominique J. Lockwood Brian Wang Joseph A. Harsh James B. Herrick James B. Herrick |
| author_sort | Noah A. Greenman |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T12:37:36Z |
| format | Article |
| id | doaj.art-1d3f43adf7ae46408398c65a3af0bfc1 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T12:37:36Z |
| publishDate | 2021-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-1d3f43adf7ae46408398c65a3af0bfc12022-12-21T23:45:46ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-04-011210.3389/fmicb.2021.592422592422Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne PathogensNoah A. Greenman0Sophie K. Jurgensen1Charles P. Holmes2Curtis J. Kapsak3Raechel E. Davis4William M. Maza5Desiree Edemba6Bethany A. Esser7Selena M. Hise8Tara N. Keen9Hunter G. Larson10Dominique J. Lockwood11Brian Wang12Joseph A. Harsh13James B. Herrick14James B. Herrick15Department of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesDepartment of Biology, James Madison University, Harrisonburg, VA, United StatesCenter for Genome and Metagenome Studies, James Madison University, Harrisonburg, VA, United StatesWe 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.https://www.frontiersin.org/articles/10.3389/fmicb.2021.592422/fullSalmonellacourse-based undergraduate researchpathogen reservoirsbioinformaticspathogen surveillanceenvironmental pathogens |
| spellingShingle | Noah A. Greenman Sophie K. Jurgensen Charles P. Holmes Curtis J. Kapsak Raechel E. Davis William M. Maza Desiree Edemba Bethany A. Esser Selena M. Hise Tara N. Keen Hunter G. Larson Dominique J. Lockwood Brian Wang Joseph A. Harsh James B. Herrick James B. Herrick Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens Frontiers in Microbiology Salmonella course-based undergraduate research pathogen reservoirs bioinformatics pathogen surveillance environmental pathogens |
| title | Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens |
| title_full | Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens |
| title_fullStr | Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens |
| title_full_unstemmed | Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens |
| title_short | Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens |
| title_sort | genomics of environmental salmonella engaging students in the microbiology and bioinformatics of foodborne pathogens |
| topic | Salmonella course-based undergraduate research pathogen reservoirs bioinformatics pathogen surveillance environmental pathogens |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.592422/full |
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