Wildlife Services

Protecting People 

Protecting Agriculture 

Protecting Wildlife

National Wildlife Research Center

FY 2017

Reducing Impacts of Wildlife-Associated

Pathogens to Agriculture and Food Safety

Contact Information:

Dr. Alan B. Franklin, 

Supervisory Research Biologist 

NWRC Headquarters 

4101 LaPorte Avenue 

Fort Collins, CO 80521 

Phone: (970) 266-6137 

FAX: (970) 266-6138 

Email: alan.b.franklin@aphis.usda.gov 

Website: www.aphis.usda.gov/

wildlifedamage/nwrc/ 

Groups Affected:

Consumers

Farmers

Livestock and poultry producers

Federal, State and local

governments

Public health organizations and

hospitals

U.S. citizens

U.S. military

Wildlife and natural resource

managers

Major Cooperators:

Center for Produce Safety

Private feedlot owners

Private farmers

Colorado School of Public Health

Colorado State University

DOI/USGS/Biological Resources

Division

DOI/USGS/National Wildlife Health

Center

High Plains Intermountain Center

for Agricultural Health & Safety

State Departments of Public Health

The Ohio State University

University of Wyoming

USDA/APHIS/Wildlife Services

Operations

USDA/APHIS/Wildlife Services

National Disease Program

USDA/APHIS/Veterinary Services

National Wildlife Research Center Scientists Examine the Roles of Wildlife in the Transmission

and Spread of Emerging Pathogens

Wildlife Services' (WS) National Wildlife Research Center (NWRC) is the only Federal research

organization devoted exclusively to resolving conflicts between people and wildlife through the

development of effective, selective, and socially responsible methods, tools, and techniques. 

Considerable concern exists around the world about emerging infectious diseases, of which 75 percent

are zoonotic, meaning the pathogens causing the disease can be transmitted between animals and

people. Wildlife plays a critical role in both the emergence and increased incidence of pathogens in

livestock and people. For example, highly pathogenic H5 subtypes of avian influenza virus that

originated in Asia, subsequently entered North America in 2014 via migratory waterfowl. In addition,

wildlife has increasingly been implicated in the spread of re-emerging pathogens, such as antibioticresistant bacteria, that are causing significant problems to agricultural, animal, and human health.

NWRC is at the forefront of research and surveillance for many of these pathogens. Much of this effort

has focused on pathogenic bacteria, including antibiotic-resistant strains, and avian influenza viruses.

Applying Science and Expertise to Wildlife Challenges

Role of Wildlife in the Contamination of Produce with Foodborne Pathogens. — Wildlife have

been occasionally linked to outbreaks of foodborne diseases in people that have cost millions of dollars

in health costs and product recalls. Regulations on the contamination of produce in the field by wildlife

feces, which may or may not contain harmful foodborne pathogens, also presents an economic burden

to farmers as all or portions of crops surrounding wildlife feces must be eliminated. However, the extent

to which wildlife contaminate produce fields is poorly understood. With support from the Center for

Produce Safety and Southern Colorado Farms, NWRC scientists examined whether wildlife

contaminated lettuce and spinach fields in the San Luis Valley of Colorado with three major foodborne

pathogens (Salmonella, Shiga-toxin producing E. coli, and noroviruses). Although a variety of wildlife

were found to visit crop fields, none of the three pathogens were found either in wildlife feces or in the

produce from the fields. One possible explanation was that the San Luis Valley lacks potential sources

of these pathogens, such as large urban areas and concentrated livestock facilities. The San Luis

Valley may also have a more sterile environment in terms of high solar radiation in contrast to other

produce areas where foodborne pathogen outbreaks have occurred. In previous research conducted

by NWRC scientists, urban areas have been found to be sources of foodborne pathogens carried by

wildlife, such as elk. Thus, risk from wildlife contamination to agriculture may vary regionally and

depend on the availability of sources of foodborne pathogens and the growing environment.

Reducing Wildlife-Related Risks of Foodborne Pathogens. — Wildlife threatens food safety

because of its ability to spread pathogens to agricultural crops and livestock, mainly through

contaminated feces. To help farmers and ranchers reduce wildlife contamination, NWRC researchers

developed a framework for creating strategic programs to lower and manage these risks at agricultural

operations. This adaptive approach was originally developed for use in natural resource management.

The multi-step framework helps producers 1) identify the potential risks, the species involved, and the

extent and nature of their impact; 2) take effective action to address the problems; and then 3)

continually review and adapt their methods. NWRC researchers also recommend that producers form

local coalitions to share resources; partner with universities, State, and Federal agencies to develop

strategies; and consider an integrated damage management approach to reduce wildlife intrusion in

agriculture fields and facilities.

Antimicrobial-resistant Bacteria in Raccoons at Feedlots. — Antimicrobial-resistant (AMR) bacteria

are becoming a global and national issue in human and agricultural health because excessive use of

antibiotics has rendered many existing drugs useless when fighting off bacterial infections. NWRC

researchers investigated whether wild mammals maintain and move AMR bacteria in livestock facilities.

Findings showed raccoons had a higher prevalence (36-87%) of AMR bacteria relative to other wildlife

species and most (72%) were infected with multiple strains of AMR bacteria. Tagged raccoons

United States Department of Agriculture 

Animal and Plant Health Inspection Service
The U.S. Department of Agriculture is an equal opportunity employment provider and employer

frequently moved from surrounding areas into feed troughs used

by cattle. Although livestock facilities are often assumed to be

sources of AMR bacteria, NWRC scientists note other areas, such

as waste-water treatment plants that allow antibiotic residues and

antibiotic-resistant genes to pass through their systems, may also

be a potential source. Samples from raccoons captured

downstream of waste-water treatment plants had a higher

prevalence of AMR, such as erythromycin-resistance, suggesting

that wildlife may be infected with AMR bacteria from these

sources. Because raccoons are strongly associated with aquatic

habitats, they may act as important traffickers of AMR bacteria to

and from livestock facilities and urban areas.

Tools for Detecting Pathogens and Antimicrobial-resistant

Bacteria in Wildlife. — A cornerstone of infectious disease

mitigation is the availability of diagnostics which allow for the

identification and characterization of virulence traits associated

with the offending pathogens. Accordingly, NWRC researchers

have developed multiple diagnostic systems for pathogens

affecting wildlife, humans, and livestock. 

Among the most advanced of the diagnostic systems developed

at NWRC is a mass spectrometry-based method that predicts

different types of AMR found within a bacterium. Specifically, this

system has demonstrated the ability to rapidly detect AMR to 10

different antibiotics. The applicability of this system is multifaceted and will serve diagnostic needs in human and

veterinary medicine, food safety, and for monitoring AMR in

wildlife. 

Aerosol sampling is increasingly recognized as a tool to help

reduce the transmission of influenza viruses, as well as other

airborne pathogens. NWRC scientists, in collaboration with the

High Plains Intermountain Center for Agricultural Health & Safety,

developed a bioaerosol sampling system that is 6.5 times more

effective at detecting influenza compared to previous systems. 

Yersinia pestis, the causative agent of plague, is classified as a

category A priority pathogen due to its potential to be used in

bioterrorism. Y. pestis is found in wildlife within the Western U.S.,

but relatively little is known about the extent to which wildlife are

exposed to this pathogen. NWRC scientists have developed a

system capable of detecting prior Y. pestis exposure in multiple

wildlife species. Using an archive of more than 10,000 wildlife

samples from potentially impacted regions, NWRC researchers

are gaining new insights into the dynamics of plague across the

U.S. landscape.

Developing an Early-warning System for Avian Influenza. —

In 2014, highly pathogenic avian influenza viruses were detected

for the first time in wild birds in the United States. These viruses

were eventually detected in domestic poultry facilities, where the

subsequent outbreaks and response efforts cost the U.S.

government more than $3 billion. Highly pathogenic avian

influenza strains continue to emerge in Asia and are actively

circulating in Europe. In order to better understand what viruses

are circulating in the U.S. and provide an early warning system for

poultry producers, NWRC scientists developed a targeted wild

bird avian influenza surveillance system. The surveillance system

has detected two highly pathogenic viruses in wild birds since

2014, highlighting the importance of continued biosecurity in

domestic poultry facilities, even in the absence of active epidemic

outbreaks. Genetic sequencing of these viruses and other low

pathogenic viruses has offered insights into domestic poultry

outbreaks and virus transmission in wild birds.

Selected Publications:

Bevins S.N., K. Pedersen, M.W. Lutman, J.A. Baroch, B.S.

Schmit, D. Kohler, T. Gidlewski, D.L. Nolte, S.R. Swafford, and

T.J. DeLiberto. 2014. Large-scale avian influenza surveillance in

wild birds throughout the United States of America. PLoS ONE 8:

e104360. 

Bevins, S.N., R.J. Dusek, C.L. White, T. Gidlewski, B. Bodenstein,

K.G. Mansfield, P. Debruyn, D. Kraege, E. Rowan, C. Gillin, B.

Thomas, S. Chandler, J. Baroch, B. Schmit, M.J. Grady, R.S.

Miller, M.L. Drew, S. Stopak, B. Zscheile, J. Bennett, J. Sengl, C.

Brady, H.S. Ip, E. Spackman, M.L. Killian, M.K. Torchetti, J.M.

Sleeman, and T.J. DeLiberto. 2016. Widespread detection of

highly pathogenic H5 influenza viruses in wild birds from the

Pacific Flyway of the United States. Scientific Reports 6:28980. 

Chandler J.C., A. Perez-Mendez, J.R. Paar, M.M. Doolittle, B.

Bisha, and L.D. Goodridge. 2017. Field-based evaluation of a

male-specific (F+) RNA coliphage concentration method. Journal

of Virological Methods 239:9-16. 

Franklin, A.B., K.C. VerCauteren, H. Maguire, M.K. Cichon, J.W.

Fischer, M.J. Lavelle, A. Powell, J.J. Root, and E. Scallan. 2013.

Wild ungulates as disseminators of Shiga toxin-producing

Escherichia coli in urban areas. PLoS ONE 8(12):e81512. 

Franklin, A. B., and K.C. VerCauteren. 2016. Keeping wildlife out

of your food: Mitigation and control strategies to reduce the

transmission risk of food-borne pathogens. In M. Jay-Russell and

M. P. Doyle, editors. Food Safety Risks from Wildlife. Springer

International Publishing. Pgs.183-199. doi: 10.1007/978-3-319-

24442-6_8.

Major Research Accomplishments:

WS researchers found there may be regional and

environmental differences in risks associated with crop

contamination from wildlife feces.

WS researchers developed a multi-step framework to help

farmers and ranchers identify and address the potential risks of

wildlife contamination on their farms.

WS research found a high prevalence of anti-microbial

resistant bacteria in raccoons captured near livestock feedlots

and downstream from waste-water treatment plants.

WS research developed novel systems to enhance the

detection and surveillance of wildlife-associated microorganisms

that impact agricultural and human health.

WS and partners developed a nationwide early detection

system for highly pathogenic avian influenza viruses in wild birds.

This system samples 35,000 to 45,000 wild birds each year and

has already detected highly pathogenic viruses that were believed

to be gone, but continue to pose a threat to the domestic poultry

industry.