Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents
The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little rese...
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| Format: | Article |
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MDPI AG
2021-09-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/10/9/1183 |
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| author | Nusrat A. Jahan Laramie L. Lindsey Evan J. Kipp Adam Reinschmidt Bradley J. Heins Amy M. Runck Peter A. Larsen |
| author_facet | Nusrat A. Jahan Laramie L. Lindsey Evan J. Kipp Adam Reinschmidt Bradley J. Heins Amy M. Runck Peter A. Larsen |
| author_sort | Nusrat A. Jahan |
| collection | DOAJ |
| description | The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including <i>Salmonella</i> spp., <i>Campylobacter</i> spp., <i>Staphylococcus aureus</i>, and <i>Clostridium</i> spp., along with many mastitis pathogens circulating within five rodent species (<i>Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus,</i> and <i>Rattus norvegicus</i>) and a shrew (<i>Blarina brevicauda</i>). Interestingly, we observed a higher abundance of enteric pathogens (e.g., <i>Salmonella</i>) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease. |
| first_indexed | 2024-03-10T07:19:19Z |
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| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T07:19:19Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-70ee55a25b5849feb01bd4cdaa02fb822023-11-22T14:43:00ZengMDPI AGPathogens2076-08172021-09-01109118310.3390/pathogens10091183Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic RodentsNusrat A. Jahan0Laramie L. Lindsey1Evan J. Kipp2Adam Reinschmidt3Bradley J. Heins4Amy M. Runck5Peter A. Larsen6Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USADepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USADepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USADepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USADepartment of Animal Science, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USADepartment of Biology, Winona State University, Winona, MN 55987, USADepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USAThe effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including <i>Salmonella</i> spp., <i>Campylobacter</i> spp., <i>Staphylococcus aureus</i>, and <i>Clostridium</i> spp., along with many mastitis pathogens circulating within five rodent species (<i>Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus,</i> and <i>Rattus norvegicus</i>) and a shrew (<i>Blarina brevicauda</i>). Interestingly, we observed a higher abundance of enteric pathogens (e.g., <i>Salmonella</i>) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.https://www.mdpi.com/2076-0817/10/9/1183agriculture16S amplicon sequencingmetabarcodingnanopore sequencingdairy cattleOne Health |
| spellingShingle | Nusrat A. Jahan Laramie L. Lindsey Evan J. Kipp Adam Reinschmidt Bradley J. Heins Amy M. Runck Peter A. Larsen Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents Pathogens agriculture 16S amplicon sequencing metabarcoding nanopore sequencing dairy cattle One Health |
| title | Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents |
| title_full | Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents |
| title_fullStr | Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents |
| title_full_unstemmed | Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents |
| title_short | Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents |
| title_sort | nanopore based surveillance of zoonotic bacterial pathogens in farm dwelling peridomestic rodents |
| topic | agriculture 16S amplicon sequencing metabarcoding nanopore sequencing dairy cattle One Health |
| url | https://www.mdpi.com/2076-0817/10/9/1183 |
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