Nanopore-based surveillance of zoonotic bacterial pathogens in farm-dwelling peridomestic rodents

Nusrat A. Jahan, Laramie L. Lindsey, Evan J. Kipp, Adam Reinschmidt, Bradley J. Heins, Amy M. Runck, Peter A. Larsen

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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 Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) 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.

Original languageEnglish (US)
Article number1183
Issue number9
StatePublished - Sep 2021

Bibliographical note

Funding Information:
Funding: This study was supported by start-up research funds awarded to PAL through the Agricultural Research, Education, Extension and Technology Transfer (AGREETT) program at the University of Minnesota.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • 16S amplicon sequencing
  • Agriculture
  • Blarina brevicauda
  • Dairy cattle
  • Metabarcoding
  • Mus musculus
  • Nanopore sequencing
  • One Health
  • Peromyscus leucopus
  • Rattus norvegicus

PubMed: MeSH publication types

  • Journal Article


Dive into the research topics of 'Nanopore-based surveillance of zoonotic bacterial pathogens in farm-dwelling peridomestic rodents'. Together they form a unique fingerprint.

Cite this