S1076: Fly Management in Animal Agriculture Systems and Impacts on Animal Health and Food Safety

(Multistate Research Project)

Status: Active

S1076: Fly Management in Animal Agriculture Systems and Impacts on Animal Health and Food Safety

Duration: 10/01/2018 to 09/30/2023

Administrative Advisor(s):

NIFA Reps:

Statement of Issues and Justification

Federal funding priorities are focused on major issues of national concern, climate change, food safety, food security, biofuels, and obesity.  Entomologists play a key and vital role in helping to solve many of these national concerns by evaluating the potential impact of climate change on insect populations and how these changes can threaten the health and well-being of humans and animals, and compromise the nation’s safe and secure food supply. Few insects are more influenced by anthropogenic effects than nuisance and pest flies; the house fly, stable fly, horn fly, face fly and blow flies. There is a significant body of literature on the biology and economic impact of these pests but this multidisciplinary project examines closely predictive models influencing pest distribution in light of climate change, the effects of the microbial community of pest populations, and the dispersal of pathogenic microorganisms that compromise a safe and secure food supply. Advances developed in the course of this project will lead to the development of new and innovative pest management technologies to mitigate these threats.

Biting and nuisance flies are among the most important pests in livestock and poultry production systems.  These flies are responsible for damage and control costs in excess of a billion dollars per year in the United States (e.g., see Taylor et al. 2012).  In addition to the direct damage these flies inflict upon livestock, their presence as a byproduct of confined livestock and poultry operations has been repeatedly cited as a nuisance, especially when flies enter the vicinity of human habitations and urban environments. Law suits, zoning limitations and animosity between farmers and home owners have resulted (Thomas and Skoda 1993).  In spite of their ubiquitous presence, importance as pests, and association with diseases of humans and livestock, our knowledge of the biology of these species is seriously wanting and available control technologies remain inadequate. The recent sequencing of the house fly genome and of the stable fly genome offer great potential for the identification of new opportunities for managing these pests. 

House flies are considered to be the #1 nuisance pest associated with dairy and other confined animal operations (Geden and Hogsette 1994, Hinkle and Hickle 1999). House flies are capable of carrying more than 65 disease organisms that affect humans and animals (Greenberg 1971), such as the virulent Escherichia coli strain O157:H7 (Sasaki et al. 2000). In poultry production, house flies can transmit Salmonella among flocks; and the spotting of eggs with fly specks may reduce the eggs’ market value. Stable flies are among the most serious pests of cattle worldwide. With their painful bites, they can reduce weight gains of cattle on finishing rations up to 20% (Campbell et al. 1977). The total impact to U.S. cattle industries is estimated to exceed $2 billion dollars annually (Taylor et al. 2012).  Given the economic importance of nuisance and biting flies, control of their populations is critically important.  For decades insecticides have provided economical control of these pests.  However, the evolution of insecticide resistance compromises the control achieved in many locations around the USA. 

Stable flies develop as maggots in a wide array of decomposing organic matter, including soiled animal bedding and soiled feed debris that accumulates wherever cattle are confined (Moon, 2002). Populations build exponentially by continuous reproduction from spring to fall in northern temperate localities (Beresford and Sutcliffe, 2010; Taylor et al., 2012). Dairy farm surveys indicate calf hutch bedding is a prominent source of stable flies around dairies (Schmidtmann, 1988), and choice of bedding material can minimize stable fly production (Schmidtmann, 1991). More recently, it has also become apparent that feed debris and manure that accumulate during winter are important sources of stable flies, especially where overwintered debris piles remain intact into the following summer (Broce et al., 2005; Talley et al., 2009; Taylor and Berkebile, 2011). 

The face fly is the primary pest of pastured cattle in most state north of the 35th parallel. Adult face flies overwinter in attics and out-buildings and colonize cattle in the spring (Krafsur and Moon 1997).  The face fly feeds on lachrymal and mucosal secretions of the eyes and nose of cattle. Gravid flies lay eggs exclusively in fresh cattle dung pats, and the life cycle can be completed in as little as 14 days. When face flies are abundant, cattle change grazing habits, which often results in poor utilization of pasture.  In addition to the annoyance and irritation associated with its feeding habits, the face fly is the primary means of transmission of Moraxella bovis, the causative agent of infectious bovine keratoconjunctivitis (IBK), also known as pinkeye (Glass et al. 1982, Glass and Gerhardt 1983, Krafsur and Moon 1997).  Face fly infestations were estimated to cause annual losses of more than $53 million (Drummond et al. 1981). Action threshold levels of 10-15 flies per face were established to reduce the spread of pinkeye and maximize animal comfort (Krafsur & Moon 1997).  In the northeast face fly numbers often exceed 100 flies per face. 

The horn fly is an obligate blood-sucking parasite of cattle and is considered a serious pest of pastured cattle in US (Drummond 1988).  Horn fly feeding annoys cattle, alters their grazing habits, and decreases both milk production and weight gains.  Horn fly numbers as high as 10,000 per animal have been reported and they feed 10 to 12 times per day.  Horn flies oviposit exclusively in fresh dung, and they do so immediately after it has been deposited (Bruce 1964).  The fly can complete development in 9-12 days, with 50% adult survival at 5 weeks.  Horn flies diapause beneath dung pats during the winter months.  Horn fly control leads to increased milk production and calf growth (Jonsson and Mayer 1999). Unlike other kinds of flies that just visit cattle for brief moments, adult horn flies reside on their host animals, which makes then especially vulnerable to control. Organic dairy farmers rely on essential oil repellents to alleviate horn fly problems, but success of these products is limited. Horn flies have been incriminated in the transmission of bovine mastitis, also known as summer mastitis (Oliver et al. 1998, Gillespie et al. 1999, Edwards et al. 2000).  In NC, 53% of horn flies collected from cattle were positive for S. aureus, and 39% of the cows were positive for the same genotype found in the flies (Anderson et al. 2012).  

In 2003, the Northeastern IPM Center Livestock and Field Crop working group created a list of prioritized needs (http://northeastipm.org/work_livepriority.cfm). The group indicated that the “development of new integrated management of key pests of livestock and poultry in confined and pasture settings” was a top priority with specific reference to “stable fly breeding and migration in pasture systems” and “fly control methods for pasture and feedlot situations.” Ten of the working group’s 17 assessed needs and seven of the top 10 directly referred to muscid flies, including house flies, stable flies, and face flies as top priorities. The objectives of the current proposal address 10 of the 17 needs.  Coordinated extension of the research outcomes derived from this proposal to stakeholders will address 2 additional priorities of this working group. 

In 2001, research and extension needs for IPM of arthropods of veterinary importance that were identified as part of a USDA sponsored workshop in Lincoln, Nebraska nearly 20 years ago (Geden and Hogsette 1999) were reevaluated, updated, and the updated document is now available at: http://www.ars.usda.gov/Services/docs.htm?docid=10139.  This document describes the IPM needs of eight animal commodity groups including poultry, dairy, beef cattle, and swine.  For each of these commodity groups, muscid flies are noted as a very significant pest, and the working group makes strong recommendations for increased research and extension efforts to reduce the considerable economic losses resulting from pest activities.  This workgroup also noted the decline to critical levels of extension personnel nationally, particularly related to domestic animal production.  Increasing coordination and collaboration among veterinary entomologists nationally is needed to more efficiently disseminate research findings and management recommendations.  

Successful completion of this project will provide a better understanding of the interactions between livestock production systems and the life cycles of pestiferous flies. Exploitation of these interactions will provide economically feasible and environmentally friendly technology for reducing the impact of flies on livestock production and human health. The project will provide quantitative data to analyze fly borne spread of pathogens from animal production systems into the urban environment. The project will develop new control technologies for biting and nuisance flies and will assess the fly resistance to insecticides that are currently available or under development.  New technological innovations and comprehensive pest management information will be disseminated to producers through a multistate coordinated effort to provide the broadest reach for project outcomes thereby increasing the health and quality of livestock and reducing the economic impact of these pest flies. 

The expertise to accomplish the objectives of this project exists within the university and USDA-ARS systems.  However, expertise is widely dispersed with few states having more than one livestock entomologist and many having none. A Multistate Project will serve to coordinate this research effort, maximizing synergy and minimizing duplicated effort. 

This project will replace the existing Multistate Project S-1060: Fly Management in Animal Agriculture Systems and Impacts on Animal Health and Food Safety (2013-2018).


Related, Current and Previous Work

See attachment for complete Related, Current and Previous Work section due to the character limit


  1. New technologies for management of biting and nuisance flies in organic and conventional systems
    Comments: a. Novel push-pull strategies (NE, NC, USDA-NE, USDA-FL) b. Evaluation of improved monitoring systems (USDA-NE, CA, TN, NM) c. Novel toxicants, biopesticides, and delivery systems (TX, USDA-FL, USDA-NE, FL, NE, PA, NM) d. Non-pesticide management options (mechanical) (FL, NC, NE, USDA-NE, USDA-FL, USDA-TX, PA, TN)
  2. Insecticide resistance detection and management
    Comments: a. Assessment of insecticide resistance (TX, NY, USDA) b. Leveraging the Stomoxys and Musca genomes for novel control measures (NY, USDA)
  3. Investigation of the microbial ecology, epithelial immunity, and vector competence of biting and nuisance flies
    Comments: a. Identification of the key bacterial strains and their metabolites playing a major role in oviposition and larval development of stable flies (TX, KS, USDA) b. Investigation of the innate immune response of filth flies (KS, USDA) c. Consequences of fly-bacteria interactions: selection effects and evolutionary outcomes (USDA, TX) d. Animal and human pathogen acquisition, dispersal and deposition by muscid flies (NC, MA, KS)
  4. Characterize population biology of biting and nuisance flies
    Comments: a. Characterize effects of climate and landscape features on dispersal (KS, TX, USDA NC) b. Phenological and environmental effects on biting and nuisance fly populations (FL, KS, TN, USDA)
  5. Extension and community engagement
    Comments: a. Improve project website to maximize extension and community engagement b. Demonstrate research value to stakeholders and funding decision-makers c. Seek funding to support these extension/outreach efforts by developing proposals that will be submitted to various granting agencies including our Regional IPM Centers.


Measurement of Progress and Results


  • 1a. Create multistate pest management strategies for biting and nuisance livestock flies, identify repellants and attractants that will provide extended efficacy, and conduct trials and create reports looking at repellants.
  • 1b. Develop sensor systems and algorithms for machine learning and define and quantify animal responses for monitoring
  • 1c. Develop autodissemination device to deliver novel toxicants (pyriproxyfen) and biopesticides (Beauveria bassiana) for fly control and publish efficacy testing and extension outputs on results of product performance
  • 1d. We will expand target pest range for the walk thru fly trap, measure production parameters of dairy cattle with and without fly traps in the southern region, develop and test a portable management device for stable flies, develop and test a multibehavior and visual olfactory trap, improve fly kill times through genetic selection of Beauveria, conduct efficacy testing of selected Beauveria strains for activity on target and non-target insects, conduct efficacy testing of entomopathogenic bacteria against house flies and stable flies, enhance our understanding of the interactions among flies and their associated pathogens and parasitoids, determine whether natural populations of parasitoids from high temperature locations are heat adapted, and assess heritability for horn fly resistance (hfr) in animals and identify hfr traits.
  • 2a. We will improve our understanding of house fly and stable fly resistance profiles across the U.S. and the relative efficacy of new insecticides for fly control. We will establish baseline susceptibility to abamectin and other new insectices in fly populations across the U.S.
  • 2b. Identification of the mutations responsible for stable fly and house fly resistance
  • 3a. We will identify the key bacterial strains and/or the metabolites essential for stable fly development
  • 3b. We will determine differences in gene expression profiles across larvae of four important veterinary pests (house flies, horn flies, stable flies, face flies) and how these profiles are related to their utilization of bacteria in manure. We will also generate new information about the antimicrobial peptides stored in the crop of the adult house fly and how they are involved in the destruction of pathogens imbibed and sent to the crop
  • 3c. Identification of components of fly and bacterial genomes that are important for promoting and inhibiting interactions between flies and bacteria; generate surveys of bacterial taxa that respond to different thermal environments when in association with flies and the general phenotypic qualities of fly associated bacteria
  • 3d. Determine if flies harbor and/or as serve as vectors of foodborne pathogens, livestock-associated pathogens and other microbes; identify pathogens associated with human and avian diseases that are carried by house flies in poultry facilities; assess the transmission of Salmonella between and among flies and cantaloupe; determine the role of the crop in pathogen harborage and transmission by house flies; provide a monitoring system to document the incidence or prevalence of mastitis and pinkeye in organic and conventional dairy cattle; catalogue the various genotypes of mastitis and pinkeye specific bacteria
  • 4a. Application of new technology to document fly dispersal factors in pasture.
  • 4b. Population dynamic models for stable flies relative to developmental substrates
  • 4c. Publications on genetic structure and distribution of Culicoides sonorensis; DNA barcodes, phylogenetic trees, and distribution maps for tabanid identification; population structure, gene flow, and dispersal patterns of stable flies within North America
  • 5a. Improvements to our project website (Insect Pests of Animals – www.veterinaryentomology.org) to more effectively provide pest management training and education to animal producers, extension personnel, funding agencies, and decision makers. Content will be developed to support extension and community engagement goals. Content may range from documents to videos to interactive displays
  • 5b. Economic impact statements for flies of veterinary importance; update of the Research and Extension Needs for IPM of Arthropods of Veterinary Importance document last reviewed in 2001; and one-page impact statements that clearly state value of this multistate research project.
  • 5c. Project members will write funding proposals to the various Regional IPM Centers to support development of Pest Management Strategic Plans or that support other extension and community engagement goals of this project. Project members will include in research proposals a request for funds to support the production of research impact statements and for the development of relevant educational content for the multistate project website.

Outcomes or Projected Impacts

  • 1a. Distribute information on new push-pull products and strategies for improved animal health to stakeholders.
  • 1b. Improved surveillance methods for pestiferous flies and introduction of new technologies for insect monitoring that are adoptable by the industry.
  • 1c. Reduce fly populations on livestock farms using new toxicants and delivery systems and generate new pesticide options for livestock producers
  • 1d. Develop fly management system with minimal use of pesticide; provide improved control of horn flies on dairies; make available new heat-tolerant strains of parasitoids for use in augmentative biocontrol programs against filth flies; provide an improved non-pesticide control agent that could be used in conjunction with other biological control to reduce filth fly pests on poultry facilities; provide recommendations on the compatibility of B. bassiana with fly parasitoids.
  • 2a. Development of fly baseline susceptibility to abamectin in house fly populations; surveys of abamectin resistance in house flies; identification of permethrin resistance in stable fly populations across the U.S.; develop and disseminate to livestock producers overall insecticide resistance management plans including new compounds for fly control, such as abamectin.
  • 2b. Improved insecticide resistance management strategies based on improved understanding of resistant populations
  • 3a. Augment stable fly control efforts through the identification of biological requirements for larval development
  • 3b. Inform efforts to identify targets or mitigation points for filth fly larval population reduction; gain information about how the fly imbibes various pathogens into the crop and what happens to them while there, which will shed further light on the role of the crop in pathogen transmission.
  • 3c. Data will be applied to risk assessment regarding the ability of certain flies to regularly harbor specific microbes, and how those microbes are harbored and transmitted; we will provide information necessary for controlling the development of nuisance and biting flies, and for restricting the role that flies play as vectors of pathogenic bacteria
  • 3d. Projects will impart a greater understanding of the role that house flies serve as carriers and transmitters of pathogens under several conditions (livestock operations, produce farms, food safety), which can help in mitigation strategies. Such strategies include integrated management programs for food safety at diversified farms and confined livestock health and safety
  • 4a. Fly dispersal is actuated by repellent use and in the absence of host animal, dispersing fly mortality increases.
  • 4b. Improved predictive models for stable fly life history parameters and population dynamics; improved understanding of parameters defining the quality of stable fly developmental substrates.
  • 4c. Nation-wide distribution map for Culicoides sonorensis; ecological distribution and molecular phylogeny of Tabanus species; identification of populations associated with different phenotypes (e.g., geography, collection site, age).
  • 5a. Industry stakeholders (livestock and poultry producers, and others involved in animal agriculture) and university/government researchers accessing the project website will have increased awareness and knowledge of pest management strategies. Project members will have an enhanced connection to animal producers, extension agents, and decision makers.
  • 5b. Pest Management Strategic Plans and the revised Research and Extension Needs for IPM of Arthropods of Veterinary Importance document will focus future research efforts towards areas of greatest concern and impact to animal producers.
  • 5c. Project members will successfully acquire funding to support project goals, particularly those related to extension of project outcomes and development of training and education content for the project website


(1):1a. Assess products for evaluation and establish protocols. Conduct field tests demonstrating PPS. Evaluate and refine products in initial field trials. 1b. Identify best attractants for stable fly traps. Evaluate digital imaging tools to quantify images. Conduct feasibility testing of sensors and robotic quantification methods. Develop sensors in laboratory and algorithms. Conduct attractant assays in laboratory and field. 1c. Identify novel toxicants and delivery systems. Evaluate novel toxicants and delivery systems in lab and field and develop a novel toxicant autodissemination device for testing. 1d. Develop expertise in production of P. protegens. Conduct bioassays on effects of B. bassiana-infected pupae on parasitoid adults and immatures. Survey poultry systems for naturally occurring Beauveria bassiana isolates; screen and select isolates for further testing. Identify livestock with putitive hfr traits and their offspring. Initiate field trials on economic impact of biting flies on dairies. Complete P. protegens bioassay with house flies. Assess ability of parasitoids to detect and avoid pathogen infected fly pupae. Conduct B. bassiana bioassays with M. raptor and M. zaraptor. Testing compatibility of selected B. bassiana strains with biological control agents completed. Testing compatibility of selected strains with biological control agents completed. Continue monitoring of putative hfr cattle. Initiate genetic testing of hfr cattle. 2a. Develop assay protocols and establish LC50 and LC99 values for to be able to monitor abamectin susceptibility in field populations of house flies. Sample stable flies for permethrin resistance in at least 8 states, with 5 states sampled across multiple years. Monitor resistance levels in field populations for current and new insecticides. 2b. Use bulk segregant analysis to identify the loci responsible insecticide resistance and identify genes for further study. Validate the mutations responsible for resistance. 3a. Obtain and process diverse stable fly development substrates for metagenomic analysis. Culture, isolate, and sequence Herpetomonas spp. nov. 3b. Generate, analyze, and validate transcriptomes and microbiomes. Identify and characterize AMPs used in the house fly crop. 3c. Determine which bacteria are associated with filth flies. Identify immune genes in filth fly genomes. Characterize the effects of bacteria on fly behavior and development. Identify taxa for study in different thermal environments and preliminary collection of data on thermal performance. 3d. Identify study sites and the integrated roles of flies, cattle, and/or produce in pathogen transmission. Design and assess experiments for fly to fly and fly to food transmission of pathogens. Characterize the fly populations on cooperating dairies and conduct diagnostics on collected flies to characterize the disease specific bacteria. Identify importance of peptides in fly crop function and ability of fly to imbibe, store and regurgitate pathogens. Initiate fly control measures on the participating farms and continue disease monitoring. Complete screening of flies from poultry facilities for common pathogenic bacteria. 4a. Quantify pasture-based fly dispersal based on distance, endurance, age, and feeding status. 4b. Complete laboratory diet and field substrate studies. 4c. Complete midge collections and sequencing. Identify population structure and gene flow of stable flies. 5a. Develop a framework for management of the project website, including type of content to make available and responsibility for update of this content. 5b. Identify opportunities for funds to produce Pest Management Specific Plans. Work with animal producers and industry representatives to initiate workshops to develop these Specific Plans. Identify flies for which economic impacts are most critically needed and organize project members into teams to assess the economic impacts of these important pest flies. 5c. Identify opportunities for funding from Regional IPM Centers. Encourage project members to include support for development of extension content (both online and print) as part of any suitable funding proposal.

(4):1a. Execute final field trials and develop recommendations. 1b. Evaluate sensors in the field. Field test algorithms. Conduct attraction field assays and develop extension programs and guides. 1c. Evaluate novel toxicants and delivery systems in the field. Develop a novel toxicant autodissemination device and testing. 1d. Complete field trials on economic impact of biting flies on dairies. Complete P. protegens bioassays with stable flies. Conduct bioassays with S. cameroni and S. endius. Develop a B. basssiana autodissemination device and testing completed. Development of autodissemination devices and testing completed. 2a. Continue to monitor resistance levels in field populations for current and new insectides. Obtain stable fly resistance data from missing states. 2b. Continue to validate the mutations responsible for resistance. 3a. Identify common microflora among diverse larval substrates. 3b. Continue analysis and validation of transcriptomes and microbiomes. 3d. Replicated field season monitoring disease incidence and prevalence on the farms and continue monitoring fly population densities following control measures. Conduct stakeholder interviews on study outcomes and summarize results. Complete assessment of the vector competence of house flies for low pathogenic avian influenza virus. 4c. Complete midge data analysis. Identify barcodes, distribution maps and species complexes of Tabanus species. Describe dispersal and phenotype associations of stable flies. 5a. Update and modernize project website. Maximize reach of website through availability of content that stakeholders find valuable. 5b. Finalize and publish Pest Management Strategic Plans. Complete economic impact analyses for important pest flies associated with animal agriculture.

Projected Participation

View Appendix E: Participation

Outreach Plan


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