Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents.

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

doi:10.3390/pathogens10091183

Nusrat A Jahan, Bradley J Heins + Show 5 more

Open Access

https://doi.org/10.3390/pathogens10091183

Copy DOI

Abstract

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.

Highlights

Rodents are the largest group of mammals in the world, and they are well known for harboring a plethora of zoonotic pathogens of concern for human and animal health [1].Both native and invasive species of mice and rats benefit from human activities, especially agricultural systems
We identified five rodent species across our study sites, including three native (Peromyscus maniculatus, P. leucopus, and Microtus pennsylvanicus) and two invasive species (Mus musculus and Rattus norvegicus)
We used MinION nanopore sequencing to metabarcode fecal microbial communities in peridomestic small mammals

Summary

Introduction

Rodents are the largest group of mammals in the world, and they are well known for harboring a plethora of zoonotic pathogens of concern for human and animal health [1].Both native and invasive species of mice and rats benefit from human activities, especially agricultural systems. Rodents are the largest group of mammals in the world, and they are well known for harboring a plethora of zoonotic pathogens of concern for human and animal health [1]. Rodents are a common hindrance of food production systems globally and they are known to transmit zoonotic pathogens to food animals and raw produce by contaminating the overall farm environment [2,3,4,5]. This transmission is largely due to the amplification of foodborne pathogens through the daily deposition of urine and fecal pellets into the production environment. Clear links have been identified between rodent pests and outbreaks of zoonotic diseases throughout Europe and Asia [8,9,10,11,12]; yet, little research has been devoted to studying this relationship in the United States [4,13]

Methods

Results

Conclusion