Source: WASHINGTON STATE UNIVERSITY submitted to
AN ECOLOGICAL APPROACH TO DISEASE RISK MANAGEMENT ON ORGANIC POULTRY FARMS.
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1013573
Grant No.
2017-51106-27026
Cumulative Award Amt.
$458,145.00
Proposal No.
2017-03409
Multistate No.
(N/A)
Project Start Date
Sep 1, 2017
Project End Date
Aug 31, 2022
Grant Year
2017
Program Code
[112.E]- Organic Transitions
Project Director
Owen, J.
Recipient Organization
WASHINGTON STATE UNIVERSITY
240 FRENCH ADMINISTRATION BLDG
PULLMAN,WA 99164-0001
Performing Department
Entomology
Non Technical Summary
Organic poultry are free to roam in outdoor settings. This encourages normal foraging and integrates poultry with the soil, vegetation and wildlife that are natural parts of farm ecosystems. While bringing benefits for animal welfare and farm ecology, there are also risks. Outdoorpoultry are exposed to parasites and pathogens in the soil (e.g. Coccidia and Salmonella), or vectored by wild birds (e.g., Avian influenza virus and ectoparasites). These infections endanger animal and human health. There have been very few holistic studies of factors that make organic poultry farms susceptible or resistant to parasite/pathogen invasion. Growers' inability to predict and manage these risks forms a major barrier to organic transition. Working on farms with free-range and pastured poultry, we will fill these knowledge gaps by: (1) Measuring frequencies of poultry contact with wild birds and soil; (2) Surveying pathogen and parasite communities withinon-farm wild bird populations, while characterizing transmission routes between wild and domesticated birds; and (3) Characterizing properties of soil that affect persistence of fecal-borne poultry parasites and pathogens. Each research objective leads directly to a specific outreach product, providing poultry producers with practical ways to reduce the risk of harboring parasites and pathogens on their farms. We address USDA-ORG priorities by (1) improving methods to describe and optimize environmental services in organic animal production while (2) reducing barriers to organic transition.
Animal Health Component
70%
Research Effort Categories
Basic
30%
Applied
70%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
7223299111050%
3113999117050%
Knowledge Area
311 - Animal Diseases; 722 - Zoonotic Diseases and Parasites Affecting Humans;

Subject Of Investigation
3299 - Poultry, general/other; 3999 - Animal research, general;

Field Of Science
1110 - Parasitology; 1170 - Epidemiology;
Goals / Objectives
The major goals of this project are to determine (I) the impact of wild bird species on the introduction and/or maintenance of poultry parasites, and (II) the effect of soil properties (biotic and abiotic) on the persistence of fecal-borne poultry parasites in farming systems that allow chickens to contact the ground and wildlife. The purpose of this work is to provide evidence-based guidance for improving biosecurity on organic poultry farms that are encouraged to the place chickens on the ground outdoors.OBJECTIVESObjective 1: Characterize farm landscapes using GIS-based tools, and measure frequency/duration of contact between (i) poultry and wild birds and (ii) poultry and soil.Objective 2: Determine on-farm wild bird diversity, while measuring parasites and pathogens in both wild birds and chickens.Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms.Objective 4: Use data collected from objectives 1-3 to develop a risk model for potential infectious diseases in poultry systems that utilize outdoor access for birds.
Project Methods
Determination of wild bird communityTo characterize the communities of wild birds found on poultry farms, we will use visual observations (point counts). For each census a survey team (one Ph.D. student and one undergraduate researcher) will observe birds at 4 locations on a farm, twice in a day (morning and mid-day). At each selected location, one observer will identify and count birds within a 50-meter radius of the location over an 8-minute period. The second observer will identify and count birds beyond 50 meters using binoculars. The selected locations will include (i) occupied pastures/pens and (ii) farm infrastructure (e.g. barns), with adjustments made for different farm types and layouts. In addition, wild birds will be captured using mist nets and potter traps.Measurement of poultry contact with wild birds and soilContact between wild birds and poultry, or poultry and the soil will be measured using visual observations of birds. This will involve observing flight-paths that carry wild birds over poultry such that feces from the wild birds would land in the foraging area of chickens. These "fly-overs" will be counted over set time-periods in the morning and evening. In addition, the contact of wild birds with infrastructure and feed will be quantified (e.g. # of birds contacting location X over 10 minutes). Poultry will be observed to determine the foraging patterns of flocks, and farmers will be interviewed to determine larger-scale management of flock locations (e.g. pasture rotation).Landscape dataWe will collect Geographical Information Systems ('GIS') data at two scales. At broad scales, USDA-NASS crop maps (http://www.nass.usda.gov/research/Cropland/SARS1a.htm ), available for free, can be used to identify the nature and extent of habitats surrounding each farm. However, these data are too coarse to reliably reveal the finer-scale hedgerows, outbuildings, small ponds, etc., that we know will also strongly impact bird populations. Therefore, the coarse USDA data will be supplemented with finer-scale GIS data at 30m or lower resolution. Data at this scale are often available from county agencies, or, in some cases, through regional Nature Conservancy offices. These GIS data will allow us to search for correlations between the densities of particular wild bird species (and/or wild-bird biodiversity) and small- and large-scale landscape features. To determine the scale over which landscape features impact wild bird populations, we will consider increasingly-broad concentric rings around each of the study sites looking for statistical consistency of landscape effects across ranges of distances. A consistent challenge with bird surveys of this type is that the failure to record a particular bird species during a farm visit reflects either (1) the bird truly is absent, or (2) the bird is present but was not seen that day. We will use "occupancy modeling" to estimate and account for these sampling errors; this is made possible by our repeated re-surveying of wild birds at our study sites several times per year over each year of the study.Parasite identificationParasites and pathogens will be identified in tracheal swabs, cloacal swabs, and fecal and blood samples collected from both poultry and wild birds on each farm. Samples will be sent to the Washington Animal Disease Diagnostic Laboratory (WADDL), located at Washington State University. This diagnostic laboratory will screen and identify enteric parasites (e.g. helminths, Coccidia, Salmonella and Campylobacter). Blood and swabs will be screened for viral pathogens (e.g. Avian Influenza and Marek's Disease virus). The diagnostic lab uses standard methods, such as microscope identification, bacteria culture and PCR.Soil characterizationSoils will be sampled from the surface to a 10-cm depth. All samples will be a composite of 10 subsamples taken from within each pasture(or yard) at locations with high poultry activity or low poultry activity respectively (20 samples total). Spatial separation of the subsamples will be based on the size of the yard or pasture. The sampling locations will also be used as sites for pitfall traps and degradation studies are completed (see below). Samples will be shipped for chemical and physical analyses to Soiltest Farm Consultants (www.soiltestlab.com). Potentially mineralizable nitrogen, microbial biomass, and C:N ratio will be determined. We will measure biodiversity among soil microbes, to determine whether this impacts the parasite/pathogen degradation in farms' soils. Our approach will be to sequence DNA in our soil samples using a metagenomic approach, which allows determination of both taxa and their functional genetic diversity.Parasite persistence testTo determine the duration of time that parasites/pathogens survive in soil, we will conduct an experimental test of survival times of two parasites important to poultry health- Campylobacter and Eimeria. Soil samples will be collected from areas with high and low foraging activity on each farm. Samples will be pooled for each type of foraging area. We will collect feces from pathogen-free poultry (see below) and add fixed concentrations of Campylobacter bacteria and Coccidia oocysts (Eimeria sp.) to the feces. The Campylobacter will be obtained from a microbiology supplier (Microbiologics) and will be added to the feces to match a concentration reported for poultry feces (7 log CFU/ml). Coccidia oocysts (Eimeria sp.) will be obtained from Merck Animal Health as a suspension of attenuated, live vaccine (Coccivac-D), and added to the feces at a concentration of 20 x 103 oocyts/gram, to match a concentration shed from chickens. Replicates of inoculated soil samples will be held for 8 weeks and subsampled weekly to test for infectivity. Infectivity of pathogens will be tested by allowing pathogen-free chicks to contact the soil. Chicks will be euthanized and screened for infection 1-week after contact with the soil.Infection risk modelingTo assess risks posed by parasites and pathogens carried by birds on farms, we will develop statistical and spatial models thatcharacterize the potential input of infectious organisms into (i) poultry on the farm and (ii) the human food supply. We are not measuring these transmission events directly. Instead, we are measuring properties of the birds and the soil, which serve as the reservoirs for these parasites and pathogens. These properties include bird species, abundances, spatial locations, frequency of contact with chickens, types of contact with the farming landscape, soil composition and weather. We will apply a Bayesian network approach to model the landscape and farming factors that influence the presence/absence of each infectious organism. In addition, we will utilize those models to determine what factors influence the diversity of infectious organisms represented in the bird community. Finally, we will use a logistic regression approach with GIS data to evaluate and map the spatial relationships among landscape features and infection risks. Overall, risk will be represented as a relative level of exposure to infectious organisms at the levels of the flock and local human population.Efforts to disseminate information to stakeholders will include development of online instructive videos and development of infographics ("Intercept Infection Cards") that can be delivered to producers. These infographics will explain the impacts of infectious diseases on poultry and the risk factors on farms that contribute to these infections.

Progress 09/01/17 to 08/31/22

Outputs
Target Audience:The target audience consisted of poultry farmers and producers, as well as poultry breeders. The efforts to reach the target audience included presentation of research seminars to peer scientists, as well as preparation and delivery of research reports to participating farmers. PI-Owen and graduate students presented research findings to farmers and producers at state and national poultry meetings . Research findings were also presented to avian disease researchers at Hy-Line International, which is a poultry breeding company that supplies some of the most commonly used breeds of chickens on poultry farms. These efforts directly communicated important research findings to stakeholders at the production level and the research level. For participating farmers, we reported summary statistics on the parasites and pathogens found on each farm. In addition, we described the basic biology and associated health risks (poultry or human) associated with the parasites detected. These reports provided cooperating farmers with essential information to use in developing mitigation strategies. Changes/Problems:Field work for this project was severely impaired by the COVID-19 epidemic. The project team was unable to visit field sites as planned due to a combination of farmer hesitancy, University policies, and COVID infections among team members. In the last two years of the study, these problems were complicated further by nationwide outbreaks of avian influenza. Without full access to field sites, we shifted our research questions to utilize samples that we had already collected. Our early data collections revealed diverse chicken breeds used on organic farms that are not observed in conventional poultry production. We were able to explore the immunological characteristics of these breeds using laboratory based assays. This information has provided insights into what breeds may be used to prevent infectious diseases on organic poultry farms. What opportunities for training and professional development has the project provided?This project involved training of 2 M.S. students and one Ph.D. student. How have the results been disseminated to communities of interest?Data from this work has been disseminated through publication of manuscripts in peer reviewed journals, presentations to professional societies, and creation of extension publications. Over the lifetime of this project there have been 10 published manuscripts. At the time of the final REEport, there are 3 additional manuscripts in review and 3 more manuscripts in preparation. Presentations were made to poultry breeders and the Poultry Science Association. Finalized extension publications are in preparation with eOrganic (Oregon State Univeristy) to communicate results directly to stakeholders. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Project Impact: Organic production of chicken eggs and meat is a rapidly growing practice nationwide. Organic chicken egg sales more than doubled from 2014 (~166 million dozen sold) to 2017 (~399 million dozen sold). These sales reflect an increase in market value from ~$419 million to ~$887 million. Sales of chicken meat (broilers) from organic farms increased from ~$372 million in 2014 to ~$1.1 billion in 2017 (USDA National Agricultural Statistics Service). These statistics reveal that organic poultry production has grown to become a high value component of the poultry market. Importantly, many farmers are producing chickens under pastured and outdoor conditions, even though they lack USDA organic certification. A key motivation to produce chickens in these kinds of "open environments" is the appeal to consumers that believe it is healthier and more humane to raise chickens with access to foraging opportunities outdoors. An important barrier to the growth of the organic poultry market is the potential for parasites and pathogens to negatively affect production. Many parasites and pathogens that affect chickens are transmitted via feces or wildlife. These infectious organisms are controlled in conventional production systems by keeping chickens indoors where the farmer can limit chicken contact with the ground, remove feces, and block out wildlife. Under organic production, chickens can roam outdoors where they encounter soil, feces, insects, worms, and wild birds that are all potential sources of parasites and pathogens. This poses a serious risk to organic poultry production that has not been well characterized. As a result, it remains unclear what disease burdens may affect the organic poultry market and there is a lack of essential information to anticipate those risks and develop strategies to minimize disease impacts. The central objective of this research project has been to determine what parasites and pathogens may affect organic poultry production and limit the growth of the industry. The following summarizes activities and accomplishments within each of the project's main objectives over the last reporting period: Objective 1: Characterize farm landscapes using GIS-based tools, and measure frequency/duration of contact between (i) poultry and wild birds and (ii) poultry and soil. We used statistical models to evaluate the wild bird species most observed contacting chickens in open environments. Of 91 wild bird species observed near poultry flocks, only 15 species exhibited regular contact with chickens. These data suggest it may be possible for farmers to develop targeted mitigation strategies to discourage wild bird contact with chickens, while also supporting bird diversity that is an important ecosystem service that many organic farmers seek to strengthen. These accomplishments represent a change in knowledge for farmers that previously lacked information about (i) the diversity and abundance of parasites that may affect flocks in open environments and (ii) the wild bird species that most frequently interact with chickens on the farm to create avenues for parasite introduction. With this change in knowledge, farmers and researchers will be better equipped to develop mitigation strategies to limit the impacts of these parasitic diseases and lower the barriers to growth of the organic poultry market. This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). We determined that chicken contact with the soil was strongly influenced by farm management practices (e.g. flock rotation frequency), flock size, and chicken breed (meat versus layer). Importantly, we found that chicken-soil contact was highly varied among farms and that no single factor among the farms was a determinant of the duration of chicken-soil contact. This is important, because it indicates the reduction of parasite risk cannot not be accomplished through modification of any single farming practice. Instead, management of parasitic disease on open environment poultry farms will have to be accomplished by consideration of the farming system. These results represent a change in knowledge for farmers that previously lacked information about the multiple ways that on-farm practices could affect risk of parasite exposure. This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). Objective 2: Determine on-farm wild bird diversity, while measuring parasites and pathogens in both wild birds and chickens. Data collected for the project revealed 91 species of wild birds that live and forage on open environment poultry farms. Among poultry samples, 10 different groups of parasites and pathogens were detected. These data represent a change in knowledge for farmers that previously lacked information about the diversity of wild birds on the farm and the diversity of parasites infecting their flocks. This information will be essential to farmers that want to more closely monitor flock health and maximize wild bird diversity for their ecosystem services to other farm assets (e.g. removal of insect prey on crops). This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms. We have characterized soil biochemistry on farms and evaluated the potential effects of weather on the occurrence of chicken parasites. Our data suggest that chicken contact with soil affects levels of parasitism (see below), but there is not strong evidence that soil biochemistry is a contributing factor. Our data also indicate that wind is a strong predictor of flock infection with Campylobacter jejuni bacteria that cause foodborne illness. The frequency of Campylobacter infections is also related to the percentage of agriculture in the surrounding landscape. Poultry farms surrounded by other farms had higher frequencies of infections. These data suggest complex relationships between poultry pathogens, weather, and the surrounding landscape. We will continue to collect more data this next year using measurements of micro-habitats on the farm. Objective 4: Use data collected from objectives 1-3 to develop a risk model for potential infectious diseases in poultry systems that utilize outdoor access for birds. We have used statistical models (mixed effects linear regression) to evaluate relationships between the occurrence of parasites, wild bird contact with chickens, farm management practices, soil, and weather. These analyses reveal a very complex system of factors that affect the frequency of parasite infections. Important factors include: contact between chickens and soil, the breeds of chickens in a flock, chicken age, flock density, wind, and surrounding farms. Our models represent a change in knowledge for farmers that did not previously have information about what factor(s) influenced risk of parasitic disease for their poultry. These models will ultimately help to form "best practices" for poultry farming in open environments that will maximize chicken health and minimize the need for chemical interventions (e.g. antibiotics and parasiticides). We have prepared some of these model results in manuscripts that are currently under peerreview. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University).

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: McCulloch, J.B., Owen, J.P., Hinkle, N.C., Mullens, B.A., Busch, J.W. (2019) Genetic Structure of Northern Fowl Mite (Mesostigmata: Macronyssidae) Populations Among Layer Chicken Flocks and Local House Sparrows (Passeriformes: Passeridae). Journal of Medical Entomology 57: 122130, https://doi.org/10.1093/jme/tjz136
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Latimer, C., Smith, O., Taylor, J., Edworthy, A., Owen, J.P., Snyder, W.E., Kennedy, C.M. (2020) Landscape context mediates the physiological stress response of birds to farm diversification. Journal of Applied Ecology. doi.org/10.1111/1365-2664.13583
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Smith, O.M., Snyder, W.E., Owen, J.P. (2020) Are we overestimating risk of enteric pathogen spillover from wild birds to humans? Biological Reviews. 10.1111/brv.12581
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Smith, O.M., Edworthy, A., Taylor, J.M., Jones, M.S., Tormanen, A., Kennedy, C.M., Fu, Z., Latimer, C.E., Cornell, K.A., Michelotti, L.A., Sato, C., Northfield, T.D., Snyder, W.E., Owen, J.P. (2020) Agricultural intensification and landscape simplification increase food safety risks imposed by wild birds on produce farms. J. Applied Ecology. doi.org/10.1111/1365-2664.13723
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Smith, O.M., Taylor, J.M., Echeverri, A., Northfield, T., Cornell, K.A., Jones, M.S., Latimer, C.E., Owen, J.P., Snyder, W.E., Kennedy, C.M. (2021). Big wheel keep on turnin: Linking grower attitudes, farm management, and delivery of avian ecosystem services. Biological Conservation. doi.org/10.1016/j.biocon.2021.108970
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Smith, O. M., Kennedy, C.M., Echeverri, A., Karp, D., Latimer, C., Taylor, J., Wilson-Rankin, R., Owen, J.P., Snyder, W. (2021) Complex landscapes stabilize farm bird communities and their expected ecosystem services. J. Applied Ecology. http://doi.org/10.1111/1365-2664.14104
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Cornell, K.A., Smith, O.M., Crespo, R., Jones, M.S., Snyder, W.E., Owen, J.P. (2021) Prevalence patterns for enteric parasites of chickens managed in open environments of the Western United States. Avian Diseases. doi.org/10.1637/21-00079
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Smith, O.M., Olimpi, E., Navarro-Gonzalez, N., Cornell, K., Frishkoff, L., Northfield, T., Bowles, T., Edworthy, A., Eilers, J., Fu, Z., Garcia, K., Gonthier, D., Jones, M., Kennedy, C M., Latimer, C., Owen, J.P., Sato, C., Taylor, J., Wilson-Rankin, E., Snyder, W.E., Karp, D. (2021) A trait-based framework for predicting foodborne pathogen spillover from wild birds. Ecological Applications. doi.org/10.1002/eap.2523
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Chambless, K.N., Cornell, K.A., Crespo, R., Snyder, W.E., Owen, J.P. (2022) Diversity and Prevalence of Ectoparasites on Poultry from Open Environment Farms in the Western United States of Washington, Idaho, Oregon, and California. Journal of Medical Entomology. doi.org/10.1093/jme/tjac093
  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Laura Vang Rasmussen*1, Ingo Grass*2, Zia Mehrabi3, Olivia M. Smith4,5, Jennifer Blesh6, Lucas Alejandro Garibaldi7,8, Marney E. Isaac9, Christina Kennedy10, Rachel Bezner Kerr11, Hannah Wittman 12, P�ter Bat�ry13, Rolando Cerda14, David Crowder15, Kevin Darras16, Kathryn DeMaster17, Karina Garcia18, David Gonthier19, Purnama Hidayat20, Juliana Hip�lito21, Lesli Hoey22, Dana James23, Innocensia John24, Andrew Jones25, Daniel S. Karp26, Martyna Kotowska27, Yodit Kebede28, Carmen Bezner Kerr29, Susanna Klassen30, Holger Kreft31, Ramiro Llanque32, Christian Levers30,33, Diego Lizcano34, Adrian Lu35, Rosebelly Nunes Marques36, Pedro Buss Martins36, America Melo34, Sidney Madsen37, Hanson Nyantakyi-Frimpong38, Elissa M. Olimpi39, Jeb. P. Owen40, Heiber Pantevez34, Matin Qaim41, Sarah Redlich42, Christoph Scherber43, Amber Sciligo44, Sieg Snapp45, William E. Snyder46, Ingolf Steffan-Dewenter42, Anne Elise Stratton33, Joseph M. Taylor47, Vivian Valencia48, Cassandra Vogel42, Claire Kremen49 Agricultural diversification promotes environmental and social synergies. Nature (2022) Agricultural diversification promotes environmental and social synergies. Nature (in review)
  • Type: Journal Articles Status: Under Review Year Published: 2022 Citation: Achyut Adhikari, Aiko Dora Adell Nakashima, Alda Francelina Andrade Pires, Ana Allende, Angela Ferelli Gruber, Austin R. Spence, Claire Murphy, Daniel S Karp, Daniel Weller, Don Stoeckel, Donna Clements, Elissa Olimpi, Faith Critzer, Gretchen Wall, Hyatt Green, Jasna Kovac, Jeb P. Owen, Jeffery McGarvey, Kate Scow, Lisa Gorski, Matthew Jones, Naresh Devarajan, Nicole L. Arnold, Nicole Richard, Nikki W. Shariat, Nora Navarro-Gonzalez, Olivia M. Smith, Patrick Baur, Radomir Schmidt, Sandipan Samaddar, Sarah M. Beno, Sarah I. Murphy, Thao Dang-Hien Tran (2022) Evidence for the efficacy of pre-harvest agricultural practices in mitigating food-safety risks to fresh produce. Frontiers in Sustainable Food Systems (in review)
  • Type: Journal Articles Status: Under Review Year Published: 2023 Citation: Smith, O.M., Cornell, K.A., Crossley, M.S., Crespo, R., Jones, M.S., Snyder, W.E., Owen, J.P. (2023) Wind speed and agriculture mediate Campylobacter risk among poultry reared in open environments. Animals (in review)
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Owen, J.P., Eilers, J., Smith, O., Brunner, J. (2023) Estimating contact rates between wild birds and poultry in open environment production systems. Poultry Science (in preparation)
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Chambless, K., Konkel, M., Owen, J.P. (2023) Comparison of antibody responses to Campylobacter vaccination among chicken breeds associated with organic poultry farming. Poultry Science (in preparation)
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Chambless, K., Cornell, K., Owen, J.P. (2023) Health metrics among chickens raised in open environment farming systems. Poultry Science (in preparation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Chambless, K., Pautzke, K., Konkel, M., Niel, K., Fulton, J., Owen, J.P. (2022) Natural Antibody Response to Vaccination in Poultry. Presentation to Poultry Science Association, National Meeting, July 11-14, San Antonio, TX
  • Type: Journal Articles Status: Other Year Published: 2023 Citation: Owen, J.P., Cornell, K., Chambless, K. (2023) Emerging parasite risks during the transition to organic poultry farming. Online article for eOrganic (in preparation)
  • Type: Other Status: Other Year Published: 2023 Citation: Owen, J.P. and Pautzke, K. (2023) Identifying and managing parasite risks in organic poultry farming. PDF education/extension bulletins from eOrganic (in preparation)
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Smith, O.M., Kennedy, C.M., Owen, J.P., Northfield, T.D., Latimer, C.E., Snyder, W.E. (2019) Highly diversified crop-livestock farming systems reshape wild bird communities. Ecological Applications. doi.org/10.1002/eap.2031


Progress 09/01/20 to 08/31/21

Outputs
Target Audience: Nothing Reported Changes/Problems:As described in our last REEport, our field work was effectively stopped by the COVID-19 epidemic. We will be using this final year of the project to collect environmental data that will strengthen our infection risk models. We were unable to collect robust data on parasites/pathogens in wild bird species. We will use data collected on wild bird contact with chickens to model potential for transmission. We observed substantially wider variation in farming practices than we anticipated at the beginning of the project. One factor that varies considerably among farms is the choice of chicken breeds. There is evidence that susceptibility to infection varies among standard commercial chicken breeds. There is very little information about parasite resistance among the "heritage" chicken breeds that we have observed are used on open environment farms. We will use the final year of the project to evaluate variation in immune function and Campylobacter resistance among heritage chicken breeds, which aligns with the aims of project Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms. In that original objective, we proposed to test infectivity of bacteria in chickens. That aim will be carried out with the modification of explicitly comparing infectivity among different chicken breeds. What opportunities for training and professional development has the project provided?This project involves the training of 2 M.S. students in addition to the past training of one Ph.D. student. How have the results been disseminated to communities of interest?Scientific papers have been prepared and submitted. They are currently under peer-review. We are currently working with eOrganic (Oregon State Univeristy) on extension bulletins and web content that will communicate our results directly to stakeholders. What do you plan to do during the next reporting period to accomplish the goals?Over the next reporting period we will collect additional environmental data on farms to better understand the apparent relationships between weather, farms in the surrounding landscape, and the occurrence of Campylobacter infections that may be a source of human foodborne illness. In addition, we will be directly evaluating immune defense and responses to Campylobacter infection among poultry breeds utilized by these farms.

Impacts
What was accomplished under these goals? Project Impact: Organic production of chicken eggs and meat is a rapidly growing practice nationwide. Organic chicken egg sales more than doubled from 2014 (~166 million dozen sold) to 2017 (~399 million dozen sold). These sales reflect an increase in market value from ~$419 million to ~$887 million. Sales of chicken meat (broilers) from organic farms increased from ~$372 million in 2014 to ~$1.1 billion in 2017 (USDA National Agricultural Statistics Service). These statistics reveal that organic poultry production has grown to become a high value component of the poultry market. Importantly, many farmers are producing chickens under pastured and outdoor conditions, even though they lack USDA organic certification. A key motivation to produce chickens in these kinds of "open environments" is the appeal to consumers that believe it is healthier and more humane to raise chickens with access to foraging opportunities outdoors. An important barrier to the growth of the organic poultry market is the potential for parasites and pathogens to negatively affect production. Many parasites and pathogens that affect chickens are transmitted via feces or wildlife. These infectious organisms are controlled in conventional production systems by keeping chickens indoors where the farmer can limit chicken contact with the ground, remove feces, and block out wildlife. Under organic production, chickens can roam outdoors where they encounter soil, feces, insects, worms, and wild birds that are all potential sources of parasites and pathogens. This poses a serious risk to organic poultry production that has not been well characterized. As a result, it remains unclear what disease burdens may affect the organic poultry market and there is a lack of essential information to anticipate those risks and develop strategies to minimize disease impacts. The central objective of this research project has been to determine what parasites and pathogens may affect organic poultry production and limit the growth of the industry. The following summarizes activities and accomplishments within each of the project's main objectives over the last reporting period: Objective 1: Characterize farm landscapes using GIS-based tools, and measure frequency/duration of contact between (i) poultry and wild birds and (ii) poultry and soil. We used statistical models to evaluate the wild bird species most observed contacting chickens in open environments. Of 91 wild bird species observed near poultry flocks, only 15 species exhibited regular contact with chickens. These data suggest it may be possible for farmers to develop targeted mitigation strategies to discourage wild bird contact with chickens, while also supporting bird diversity that is an important ecosystem service that many organic farmers seek to strengthen. These accomplishments represent a change in knowledge for farmers that previously lacked information about (i) the diversity and abundance of parasites that may affect flocks in open environments and (ii) the wild bird species that most frequently interact with chickens on the farm to create avenues for parasite introduction. With this change in knowledge, farmers and researchers will be better equipped to develop mitigation strategies to limit the impacts of these parasitic diseases and lower the barriers to growth of the organic poultry market. This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). We determined that chicken contact with the soil was strongly influenced by farm management practices (e.g. flock rotation frequency), flock size, and chicken breed (meat versus layer). Importantly, we found that chicken-soil contact was highly varied among farms and that no single factor among the farms was a determinant of the duration of chicken-soil contact. This is important, because it indicates the reduction of parasite risk cannot not be accomplished through modification of any single farming practice. Instead, management of parasitic disease on open environment poultry farms will have to be accomplished by consideration of the farming system. These results represent a change in knowledge for farmers that previously lacked information about the multiple ways that on-farm practices could affect risk of parasite exposure. This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). Objective 2: Determine on-farm wild bird diversity, while measuring parasites and pathogens in both wild birds and chickens. Data collected for the project revealed 91 species of wild birds that live and forage on open environment poultry farms. Among poultry samples, 10 different groups of parasites and pathogens were detected. These data represent a change in knowledge for farmers that previously lacked information about the diversity of wild birds on the farm and the diversity of parasites infecting their flocks. This information will be essential to farmers that want to more closely monitor flock health and maximize wild bird diversity for their ecosystem services to other farm assets (e.g. removal of insect prey on crops). This information has been prepared in a manuscript that is currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University). Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms. We have characterized soil biochemistry on farms and evaluated the potential effects of weather on the occurrence of chicken parasites. Our data suggest that chicken contact with soil affects levels of parasitism (see below), but there is not strong evidence that soil biochemistry is a contributing factor. Our data also indicate that wind is a strong predictor of flock infection with Campylobacter jejuni bacteria that cause foodborne illness. The frequency of Campylobacter infections is also related to the percentage of agriculture in the surrounding landscape. Poultry farms surrounded by other farms had higher frequencies of infections. These data suggest complex relationships between poultry pathogens, weather, and the surrounding landscape. We will continue to collect more data this next year using measurements of micro-habitats on the farm. Objective 4: Use data collected from objectives 1-3 to develop a risk model for potential infectious diseases in poultry systems that utilize outdoor access for birds. We have used statistical models (mixed effects linear regression) to evaluate relationships between the occurrence of parasites, wild bird contact with chickens, farm management practices, soil, and weather. These analyses reveal a very complex system of factors that affect the frequency of parasite infections. Important factors include: contact between chickens and soil, the breeds of chickens in a flock, chicken age, flock density, wind, and surrounding farms. Our models represent a change in knowledge for farmers that did not previously have information about what factor(s) influenced risk of parasitic disease for their poultry. These models will ultimately help to form "best practices" for poultry farming in open environments that will maximize chicken health and minimize the need for chemical interventions (e.g. antibiotics and parasiticides). We have prepared some of these model results in manuscripts that are currently under peer-review. This information is also being prepared for communication to stakeholders through extension bulletins created by eOrganic (Oregon State University).

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Smith, O.M., Edworthy, A., Taylor, J.M., Jones, M.S., Tormanen, A., Kennedy, C.M., Fu, Z., Latimer, C.E., Cornell, K.A., Michelotti, L.A., Sato, C., Northfield, T.D., Snyder, W.E., Owen, J.P. (2020) Agricultural intensification and landscape simplification increase food safety risks imposed by wild birds on produce farms. J. Applied Ecology. doi.org/10.1111/1365-2664.13723
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Smith, O.M., Taylor, J.M., Echeverri, A., Northfield, T., Cornell, K.A., Jones, M.S., Latimer, C.E., Owen, J.P., Snyder, W.E., Kennedy, C.M. (2021). Big wheel keep on turnin: Linking grower attitudes, farm management, and delivery of avian ecosystem services. Biological Conservation. doi.org/10.1016/j.biocon.2021.108970
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Smith, O.M., Olimpi, E., Navarro-Gonzalez, N., Cornell, K., Frishkoff, L., Northfield, T., Bowles, T., Edworthy, A., Eilers, J., Fu, Z., Garcia, K., Gonthier, D., Jones, M., Kennedy, C M., Latimer, C., Owen, J.P., Sato, C., Taylor, J., Wilson-Rankin, E., Snyder, W.E., Karp, D. (2021) A trait-based framework for predicting foodborne pathogen spillover from wild birds. Ecological Applications.
  • Type: Journal Articles Status: Under Review Year Published: 2021 Citation: Smith, O. M., Kennedy, C.M., Echeverri, A., Karp, D., Latimer, C., Taylor, J., Wilson-Rankin, R., Owen, J.P., Snyder, W. (2021) Complex landscapes stabilize farm bird communities and their expected ecosystem services. J. Applied Ecology.
  • Type: Journal Articles Status: Under Review Year Published: 2021 Citation: Cornell, K.A., Smith, O.M., Crespo, R., Jones, M.S., Snyder, W.E., Owen, J.P. (2021) Prevalence patterns for enteric parasites of chickens managed in open environments of the Western United States. Avian Diseases.


Progress 09/01/19 to 08/31/20

Outputs
Target Audience: The target audience during this reporting period consisted of poultry farmers and producers, as well as poultry breeders. The efforts to reach the target audience included presentation of research seminars to peer scientists, as well as preparation and delivery of research reports to participating farmers. PI-Owen presented research findings to farmers and producers attending the annual "Poultry Institute" meeting at Washington State University. He also presented research findings to avian disease researchers at Hy-Line International, which is a poultry breeding company that supplies some of the most commonly used breeds of chickens on poultry farms. These efforts directly communicated important research findings to stakeholders at the production level and the research level. For participating farmers, we reported summary statistics on the parasites and pathogens found on each farm. In addition, we described the basic biology and associated health risks (poultry or human) associated with the parasites detected. These reports provided cooperating farmers with essential information to use in developing mitigation strategies. Changes/Problems:Major changes include: major problems or delays that may have a significant impact on the rate of expenditure; significant deviations from research schedule or goals; The global pandemic with the COVID-19 virus was a critical impediment to progress on this research project during the reporting period. Based on State mandates, Washington State University required a period of suspension on research activities in both the field and lab. After establishment of strict protocols, research activities could be resumed. However, those protocols (e.g. limitations on the number of people in vehicles and lab spaces) greatly slowed the work rate. Also, many cooperating farmers were not willing to continue farm visits for ongoing collection of field data, due to concerns about the COVID-19 virus. Together, these events effectively stopped field-related research for 2019-2020. As a result, work that was intended to aAs described in the section - Plans for the Next Reporting Period - our analyses have indicated that soil properties are not strong predictors of parasites on these farms. As a result, we are shifting focus to potential effects of different chicken breeds on parasite infection. This does not affect the approved use of animals in this project. In the original proposal and animal use protocol, we planned to expose chicks from a single chicken breed (White Leghorn) to a parasite (Eimeria spp., Coccidia) and bacteria (Salmonella) maintained in different soil types (treatments). In the revised approach, we will be exposing chicks from multiple chicken breeds to the same parasite (Eimeria spp., Coccidia) and the bacteria Campylobacter jejuni. The change to C. jejuni was based on the frequent occurrence of this pathogen in poultry flocks in our field study and the fact that it is a common cause of foodborne illness in people. The numbers of animals used, and their treatment in the experiments (i.e. infections and sample collection), will not be significantly changed from the original protocol. As in the original proposal, these experiments will be conducted in a campus laboratory animal vivarium under supervision of the WSU campus veterinarian. We will obtain fertilized eggs from local hatcheries that are used by farmers involved in this study and hatch them in the Owen lab. As described in the original proposal, the Owen lab has an incubator (Brinsea 190 capacity OVA-easy) and is able to hatch eggs. We will hatch eggs from 7 chicken breeds observed on farms in this project--(i) Sex-link red, (ii) Sex-link black, (iii) Rhode Island red, (iv) Buff Orpington, (v) Wyandotte, (vi) White Leghorn, (vii) Ameraucana. We will expose the chicks to infections following the same protocols described in the original proposal and we will test each breed 3 times. Estimated numbers of animals that will be used are as follows: Infection experiments will use 5 chicks/breed/infection type x 7 breeds x 2 infection types/replicate x 3 replicates (= 210 chicks) and Negative Controls will use 5 chicks/breed x 7 breeds/replicate x 3 replicates (= 105 chicks). This total number of chicks (n = 315), the experimental replication, and the number of treatment levels match what was originally proposed. What opportunities for training and professional development has the project provided?Three M.S. students and 3 undergraduate research assistants have been involved with this research. Field samples were collected by Mr. Kevin Cornell between 2017 and 2019. He completed and successfully defended his M.S. thesis in the spring of 2020. A second M.S. student (Ms. Johnna Eilers) has been analyzing observational data on wild bird contact with chickens. She will complete and defend her thesis in spring 2021. A third M.S. student (Ms. Kendra Chambless) has been evaluating health data collected from chickens in the field to examine potential health metrics that may be used to evaluate flock conditions in organic production systems. Her work has included the use of blood cell counts and enzyme-linked immunosorbent assays for quantifying antibody diversity. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period we will be implementing experiments related to Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms. The experiments will be a deviation from the original proposal, based on analyses of field data and technical challenges due to the COVID-19 pandemic (please see Changes/Problems section of REEport). Briefly, the original objective entailed testing different soil types for effects on survival and infectivity of parasites and pathogens found on farms. Analyses of soil properties from field samples collected during the previous 3 years did not reveal consistent effects of soil on parasites and pathogens. We suspect this is due to wide variation in flock management (e.g. flock age, size and rotation frequency). In addition, we do not expect that it will not be feasible to repeatedly visit farms for repeated soil collection, due to COVID-19 concerns. As a result, we will not conduct experiments focused on soil effects. Instead, we will focus on effects of chicken breed, which is another important farm variable that we predict will affect parasite persistence. We observed that roughly half of the farms in this study used a single chicken breed in flocks, which is consistent with practices of conventional poultry farms. In contrast, the remaining farms kept flocks with multiple chicken breeds that were often "heritage" varieties (i.e. older breeds not found in typical commercial production). We observed 15 different chicken breeds across the farms. These observations reveal that farmers vary in their choices of breeds for their flocks. Published studies of standard, commercial chicken breeds have shown breed effects on resistance to some parasites. However, there is very little known about parasite resistance among the chicken breeds observed in this study. Given that chicken breed selection is within the farmer's control, we believe it is highly valuable to identify any breeds that inherently provide strong parasite resistance. During the next reporting period we will conduct comparative, experimental infection studies of the common chicken breeds observed on farms in this study. These experiments will achieve the same basic outcome as the original objective, because the data will allow farmers to identify factors that potentially affect the occurrence of parasites in their flocks. This revised approach may be more useful for farmers, given that selection of chicken breeds for production can be easily manipulated in comparison to modifying flock interaction with the soil. Finally, these can be accomplished without reliance on field samples, which will make it achievable regardless of COVID-19 restrictions.

Impacts
What was accomplished under these goals? Project Impact: Organic production of chicken eggs and meat is a rapidly growing practice nationwide. Organic chicken egg sales more than doubled from 2014 (~166 million dozen sold) to 2017 (~399 million dozen sold). These sales reflect an increase in market value from ~$419 million to ~$887 million. Sales of chicken meat (broilers) from organic farms increased from ~$372 million in 2014 to ~$1.1 billion in 2017 (USDA National Agricultural Statistics Service). These statistics reveal that organic poultry production has grown to become a high value component of the poultry market. Importantly, many farmers are producing chickens under pastured and outdoor conditions, even though they lack USDA organic certification. A key motivation for the production of chickens in these kinds of "open environments" is the appeal to consumers that believe it is healthier and more humane to raise chickens with access to foraging opportunities outdoors. An important barrier to the growth of the organic poultry market is the potential for parasitic and infectious disease to negatively affect production. Many parasites and pathogens that affect chickens are transmitted via feces or wildlife. These infectious organisms are controlled in conventional production systems by keeping chickens indoors where the farmer can control chicken contact with the ground, remove feces, and block out wildlife. Under organic production, chickens are able to roam outdoors where they can encounter soil, feces, insects, worms, and wild birds that are all potential sources of parasites and pathogens. This poses a serious risk to organic poultry production that has not been well characterized. As a result, it has remained unclear what disease burdens may affect the organic poultry market, and there is a lack of essential information to anticipate those risks and develop strategies to minimize disease impacts. The central objective of this research project has been to determine what parasites and pathogens may affect organic poultry production and limit the growth of the industry. In this project we have worked directly with poultry farmers that use open environment production methods (e.g. pasture foraging). We have quantified the parasites and pathogens occurring in flocks on these cooperating farms, while also quantifying chicken contact with wild bird species that may introduce these infectious organisms onto farms. While many cooperating farmers initially reported that their chickens are "free of parasites" and "healthy", we found that parasites are common and widespread in flocks raised in open environments. Of the 30 farms sampled over a 3-year period, we found at least one parasite species in every flock. Most flocks harbored over 3 parasite species co-infecting chickens. Importantly, these parasites included Eimeria species, which are considered the most economically costly intestinal parasites for poultry production. We found Eimeria species in 97% of the flocks tested and these flocks were not immunized against the parasite. Campylobacter species of bacteria, which are found in feces and are a leading cause of foodborne illness in people, were detected in 68% of flocks, which suggests a downstream risk to human health. Our analysis of flock management practices suggest that Eimeria infections become more common among flocks that are moved frequently in larger pastures. This suggests that Eimeria could be managed by altering the placement and movement of chickens foraging outdoors. Finally, an analysis of wild bird contacts revealed that, of 91 wild bird species observed near poultry flocks, only 15 species exhibited regular contact with chickens. These high-contact wild bird species included American Robin, House sparrow, Red-winged blackbird, Brewer's blackbird, Rock pigeon, House finch, and Barn swallow--all of which have been confirmed to carry parasites and pathogens that infect chickens. These observations suggest it may be possible for farmers to develop targeted mitigation strategies to discourage wild bird contact with chickens, while also supporting bird diversity that is an important ecosystem service that many organic farmers seek to strengthen. These accomplishments represent a change in knowledge for farmers that previously lacked information about (i) the diversity and abundance of parasites that may affect flocks in open environments and (ii) the wild bird species that most frequently interact with chickens on the farm to create avenues for parasite introduction. With this change in knowledge, farmers and researchers will be better equipped to develop mitigation strategies to limit the impacts of these parasitic diseases and lower the barriers to growth of the organic poultry market.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Smith, O.M., Snyder, W.E., Owen, J.P. (2020) Are we overestimating risk of enteric pathogen spillover from wild birds to humans? Biological Reviews. 10.1111/brv.12581
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Seminar: "Unpacking the Infection Risks for Organic and Pastured Poultry". The Poultry Institute, Annual Meeting  Washington State University (Puyallup, WA)
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Seminar: "Diverse Infections Will Require Diverse Defenses: Poultry Immunogenetics, Antibodies and Inflammation". Hy-Line International (Des Moines, Iowa)


Progress 09/01/18 to 08/31/19

Outputs
Target Audience:The goal of the "An Ecological Approach to Disease Risk Management on Organic Poultry Farms" is to determine infectious disease risks encountered under conditions of organic poultry production. This includes risks of transmission from wild birds, how soil properties impact pathogen survival, and how management may reduce or encourage disease. Our target audience are free range, pasture raised, and backyard growers who use organic methods and rear flocks with outdoor access. Through the 2017 - 2019 field seasons we surveyed 30 farms across California, Oregon, Washington, and Idaho which varied in management, flock demographics, soil and habitat, and bird community composition. We collected individual fecal samples from chickens to test for human and avian parasites and pathogens. Additionally, we conducted wild bird point count surveys and contact observations, where we quantified wild bird communities on farms and species interacting with the chicken coop. In the 2018 field season we collected blood, trachea and cloaca swabs, ectoparasites, and physiological data from chickens. These broad datasets are now providing important insights into 1) the prevalence and intensity of enteric parasites and pathogens within flocks that are raised outdoors under organic conditions, 2) the influence of soil, wild birds, and farm-management practices on the prevalence and intensity of these pathogens, and 3) important insights into future areas of research and collaboration with the organic growers. These data are the first to assess individual- and flock-level parasite and pathogen loads across a broad geographic region of organic poultry growers, illuminating areas for future research and developing the tools for growers to reduce disease risk. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Three graduate students (Kevin Cornell , Kendra Chambless, and Johnna Eilers), as well as 3 undergraduate research assistants that previously assisted with diagnostics. Kevin Cornell conducted all initial field data collection activities between 2017 and 2019. He also has conducted all statistical analyses. Kendra Chambless is testing how soil properties affect the survival of chicken parasites and pathogens found in our study. Johnna Eilers will be collecting chicken and wild bird feces from farms to search for evidence that birds and chickens exchange pathogens. Furthermore, Campylobacter gene flow between chickens and birds will be tracked to see how Campylobacter populations change over time due to changes in wild bird populations. How have the results been disseminated to communities of interest?We have engaged grower-collaborators on this project and have had on-farm discussions with most growers to gauge their concerns associated with wild birds and organic management. At the end of each sampling round, we disseminated a confidential letter report to each grower describing the parasites and pathogens found in poultry, wild bird populations, soil properties, and brief synopsis of their farm with recommendations to improve poultry health. Papers are currently being developed and prepared to submit this year: K Cornell, O Smith, and J Owen. Etiology and Epidemiology of Coccidia on Organic Poultry Farms. Parasites & Vectors, in preparation. K Cornell, O Smith, and J Owen. Risks of Campylobacter spp. on Organic Poultry Farms: Strategies to Minimize Contamination and Improve Poultry Welfare. Poultry Science, in preparation. What do you plan to do during the next reporting period to accomplish the goals?Objective 1) Kevin Cornell is continuing to run analyses and develop manuscripts. With the help from Olivia Smith, we are including surrounding landscape variables classified using NLCD, CDL, and the gridded "livestock of the world" data layers in ArcGIS. Johnna Eilers is continuing field investigations that will further quantify bird communities on the farms and interacting with the coop. Objective 2) As noted above, Johnna Eilers will continue data collection on wild bird communities and diversity to bolster our analyses. Field data collection and diagnostics of parasites and pathogens in wild birds and chickens will be conducted during the 2020 field season. Objective 3) Kendra Chambless will be investigating how soil properties influence the survival of parasites and pathogens in soil. Laboratory in vitro experiments are being planned using soil collected from our farm collaborators. This shed light on potential nematophagous, ovicidal, and pathogen removal services that soil microbes provide. In turn, we hope to provide empirical strategies to improve parasite management on pasture. Objective 4) With the addition of new data from field and lab work in 2020 and help from Olivia Smith, we will improve upon our risk models and statistical methods. Future models analyzing spillover risk from wild birds will utilize landscape and farm management variables as potential drivers of "high risk" bird communities.

Impacts
What was accomplished under these goals? Objective 1: Characterize farm landscapes using GIS-based tools, and measure frequency/duration of contact between (i) poultry and wild birds and (ii) poultry and soil. Altogether, over two years of field work, MS student Kevin Cornell with help from field techs repetitively surveyed birds on 30 farms that reared chickens with full outdoor access and used organic methods. This included "contact" surveys which measured the behavior and frequency of bird utilizing the area where the chickens resided. Soil samples from within the actively used ground by the chickens and an adjacent sample from the same soil type but untouched by chickens, was collected and tested for physical and chemical properties. Based on aerial images, farmer surveys, and visual inspections we were able to quantify management and flock demographic parameters, such as flock densities, coop rotation frequencies, and breed diversity. We then used these data to build mixed effects models that compared farm management practices, wild bird contact, soil properties, flock demographics, and coinfections of multiple parasites to identify key areas of disease risk. We have found that wild bird abundance around the chicken coop is positively correlated with abundance on the rest of the farm and surrounding habitat; however, the diversity of birds utilizing chicken space was much lower than the total diversity of birds on the farm. Contact data has shown that only a handful of bird species (e.g. European starlings, Brewer's blackbirds, house sparrows) are responsible for the majority of interactions with chicken feed, water, foraging ground, housing, and coop. This data has enabled us to create an interface of high-risk species to focus future diagnostics on and incorporate known wild bird pathogen data to connect it with disease transmission risk for farms. Additionally, we have found that 25.6% of individuals tested positive for Campylobacter spp. and 0.8% Salmonella spp., important human pathogens. Collectively, our findings suggest that wild birds may pose a significant risk to the transmission and recycling of transmissible food-borne pathogens, warranting further investigation to improve food safety in organic systems. MS student Johnna Eilers is beginning a field experiment to track the transmission of Campylobacter spp. by repetitive sampling and sequencing of chickens and wild bird feces at single flock locations over the course of several seasons. This will provide definitive evidence that wild birds and chickens are exchanging Campylobacter and provide insights into the changes in Campylobacter population genetics over time. Soil samples collected from actively used pasture by chickens suggested that % organic matter in soil has a negative relationship with Campylobacter and Coccidia prevalence in poultry. Organic matter has been shown to be positively correlated with soil microbe abundance and diversity. Additionally, several in vitro experiments have identified specific fungi and microbes that degrade parasites and pathogens, including some evidence that increased microbe diversity removes pathogens quicker than less diverse soils. In our soil samples, we have found that soil in pasture used by chickens contains greater organic matter than adjacent soil samples that are untouched by chickens. This suggests a possible beneficial feedback system: where chicken-pasture management can improve organic matter in the soil, thus decreasing parasite and pathogen survivability while in free-living or intermediate stages. Collectively, this data warrants further investigation into organic matter, microbial diversity, and potentially other soil properties that might reduce environmental contamination of damaging poultry parasites and pathogens. We are in the process of running an in vitro experiment being led by graduate student Kendra Chambless to test these hypotheses. Objective 2: Determine on-farm wild bird diversity, while measuring parasites and pathogens in both wild birds and chickens. During the 2017, 2018, and 2019 field seasons, MS student Kevin Cornell and assistant field techs surveyed for birds on 30 farms: in farm plots, chicken coops, and adjacent habitat. This consisted of a total of 178 point count locations, observing 7393 birds, 126 species, and quantifying 1654 instances of bird contact with chicken space. Using statistical methods, we have found evidence that the abundance of bird species observed interacting with chicken flocks and total amount of contact with chicken space observed both have a positive correlation with Campylobacter prevalence within a chicken flock. Live sampling of wild bird feces using non-invasive techniques is underway for the 2020 field season. We surveyed 30 farms, containing 77 chicken flocks, for gatrointestinal parasites and pathogens (i.e. helminths, apicomplexans, and proteobacteria). A total of 1040 live individual feces samples were collected and shipped to labs for parasitology and bacteriology diagnostics. All parasites and pathogens observed were recorded and quantified. We found a diversity of parasites and pathogens, with Coccidia (Eimeria spp.) being the most common, found on 29/30 farms, in 74/77 of all sampled flocks, and in 653/1040 fecal samples. Four helminths were commonly found, including Ascaridia galli (399/1040 positive samples), Heterakis gallinarum (169/1040), Capillaria spp. (176/1040), and tapeworms (81/1040). Among these samples, coinfections were found to be common. Statistical evidence has suggested significant relationships between these parasite. For example, we have found evidence for a positive synergistic relationship between Capillaria spp. and Eimeria spp., where individuals infected with both parasites contained higher counts of both eggs and oocysts in individual feces, controlling for both chicken production type and flock spatial dependence. Objective 3: Characterize on-farm soil properties and coprophagous invertebrates, followed by determination of soil factors that degrade feces-borne infectious organisms. Chickens reared outside on natural soil, rather than hard surfaces and artificial bedding, presents unique risks and opportunities to better manage disease. Biotic and abiotic properties of soil have been shown to influence the survival of parasites and pathogens. To explore if soil properties may affect this on soil being used by organic poultry, we collected and tested 1040 chicken fecal samples and 32 soil samples. Using mixed effects models we compared the predictive power and importance of various soil physical chemical components, finding that % organic matter in the soil negatively correlated with the prevalence of Campylobacter spp. within a corresponding flock. This suggests that soils with greater organic matter and biotic abundance can help reduce environmental contamination, thus reducing the chance and amount of parasites and pathogens picked up by foraging chickens. Collectively, these findings lend promise for helping growers improve pasture health as a form of parasite and pathogen management in organic poultry. Objective 4: Use data collected from objectives 1-3 to develop a risk model for potential infectious diseases in poultry systems that utilize outdoor access for birds. Risk models are being developed by MS student Kevin Cornell and postdoc Olivia Smith to identify key parameters of disease risk in organic poultry systems.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Smith, OM, WE Snyder and JP Owen. In revision. Understanding food safety risks associated with wild birds: a meta-analysis and conceptual framework. Biological Reviews.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Smith, OM, CM Kennedy, JP Owen, CE Latimer, and WE Snyder. 2019. Highly diversified crop-livestock farming systems reshape wild bird communities. Ecological Applications, in press.
  • Type: Journal Articles Status: Other Year Published: 2020 Citation: K Cornell, O Smith, and J Owen. Etiology and Epidemiology of Coccidia on Organic Poultry Farms. Parasites and Vectors, in preparation.
  • Type: Journal Articles Status: Other Year Published: 2020 Citation: K Cornell, O Smith, and J Owen. Risks of Campylobacter spp. on Organic Poultry Farms: Strategies to Minimize Contamination and Improve Poultry Welfare. Poultry Science, in preaparation


Progress 09/01/17 to 08/31/18

Outputs
Target Audience:The target audiences include organic poultry farmers, and researchers working in the areas of disease ecology and agriculture. Efforts to reach these audiences include the production of extension/outreach reports to individual farmers that describe (i) the measured levels of infection observed on their farms, (ii) the relevant biological background information for the observed disease risks, and (iii) suggested mitigation strategies to limit the effects of the parasites on their flocks. In addition, prelimary data were reported by a graduate student at the International Ornithonological Congress to draw researcher attention to the potential disease interactions between wild birds and poultry. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One M.S. student has been involved with sample and data collection from farms. The graduate student was assisted by a field technician. Two undergraduate students have been involved with data management, collection of blood cell data (via microscopic examination of blood films), and development/implementation of antibody screening in collected serum via enzyme-linked immunosorbent assays (ELISAs). How have the results been disseminated to communities of interest?Reports of detected parasites and pathogens have been provided to farmers involved with the project. These reports summarize the data recorded from the respective farm and provide a summary of the relevant background information on potential health effects that could impact the farmer. When possible, suggested strategies for mitigating health effects and future infection are included in the reports. What do you plan to do during the next reporting period to accomplish the goals?Based on the data collected in 2018, we will focus sample collection efforts in 2019 to target specific wild bird species that we believe are involved with parasite/pathogen exchange with poultry. In addition, we will begin empirical tests of the effects of soil properties on the persistence of the parasites observed in the field (Objective 3).

Impacts
What was accomplished under these goals? Twenty-eight organic poultry farms located across California, Oregon, and Washington States were visited to collect samples and data that are relevant to project objectives 1 and 2. The collected samples included flock fecal samples in the environment, blood samples from indvidual birds in each flock, and soil samples from areas with and without poultry. Fecal samples have provided direct detection of bacteria (Campylobacter and Salmonella), Coccida parasites, and intestinal worms. Additional data collected include point-counts of wild birds on the farm, and counts of wild bird contact with poultry. Finally, data on farm management were collected through the use of farmer surveys and interviews.

Publications