20 Sobsey

Overview of Pathogens Associated with AFOs: What Organisms and Why? : 

Overview of Pathogens Associated with AFOs: What Organisms and Why? Mark D. Sobsey University of North Carolina Chapel Hill, NC Email: Sobsey@email.unc.edu

What Pathogens and Why?Answer: Zoonoses: 

What Pathogens and Why? Answer: Zoonoses Zoonoses: microorganisms of animal origin that can also infect humans Animal-to-human transmission Human-to-animal Human-to-human by the same pathogens Transmission routes: Direct contact Indirect contact Food Water Air Other environmental media and routes

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AIR; BIOAEROSOLS Pathogen Sources and Transmission Pathways from Animal Agriculture

Animal Wastes Potentially Contain Human Pathogens at High Concentrations: 

Animal Wastes Potentially Contain Human Pathogens at High Concentrations Agricultural animals can harbor and shed high concentrations of viruses, bacteria and parasites that are pathogenic for humans Levels of human pathogens in animal manures can be millions to billions/gram of feces Antibiotic use also causes high proportions of antibiotic-resistant bacteria in animal wastes Animal waste pathogens have caused disease and death in humans via: Contaminated food Farm workers and other people with animal contact Environmental contamination: notably water and air

Some Known Zoonotic Pathogens Causing Infection and/or Disease: 

Some Known Zoonotic Pathogens Causing Infection and/or Disease Viruses: rotaviruses, reoviruses, noroviruses, SARS, hepatitis E virus, (para)myxoviruses (Swine flu, “bird flu, Nipah, etc.) Bacteria: Salmonella, E. coli O157:H7, Yersinia enterocolitica, Campylobacter spp., Mycobacterium avium Protozoan parasites: Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii Helminths: Trichuris trichuria, Taenia spp., Echinococcus spp. Prions: Bovine spongiform encephalopathic agent (BSE); variant Creuzfeldt Jacob Many are responsible for known cases and outbreaks of foodborne and waterborne diseases Consequences: temporary morbidity to mortality, especially in high-risk individuals

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Some Zoonotic Viral Pathogens Viruses Animals?_____ Hepatitis E virus swine, rats, etc. Reoviruses mice, others (type 3) Rotaviruses probably (bovine) Adenoviruses maybe? Caliciviruses probably (bovine; swine) Orthomyxoviruses (influenza) yes (swine, avian, etc.)* Coronavirus: SARS yes (civets, others) ________________________________________________________________________________________________________________________________________ Prions - spongiform encephalopathogens: Yes (bovine, others) ________________________________________________________________________________________________________________ *An international problem Avian (or other animal) + swine → human pandemic influenza Bird flu: avian → human

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Some Zoonotic Bacterial Pathogens Bacterium/Group Animals Other sources Salmonella spp. yes no (except S. typhi) no no Campylobacter spp. yes yes Escherichia coli yes no Aeromonas hydrophila yes yes Yersinia enterocolitica yes yes Vibrio cholerae; other Vibrio spp. yes yes Brucella yes no Leptospira yes no Mycobacteria spp. (non-tubercular) rare (rising?) yes

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Some Zoonotic Parasitic Pathogens Parasite________________________________________ Protozoan: Cryptosporidium parvum yes Giardia lamblia yes Entamoeba histolytica rare Balantidium coli yes (pigs) Toxoplasma gondii yes Helminths: Trichuris trichiura pigs Ascaris suum yes (pigs) Strongyloides stercoralis yes (dogs & others) Taenia spp. cattle & pigs Echinococcus spp. Dogs + others

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Potential Bioaerosols from Animal Agriculture Includes all classes of microbes: Prions: ex: BSE (Mad Cow Disease agent) Viruses: ex. Myxoviruses (influenza viruses) Bacteria and other procaryotes: ex. Salmonella Unicellular Eucaryotes (Protists): Protozoans: ex. Amebae (Acanthamoeba spp.) Fungi: ex. Histoplasma capsulatum, Cryptococcus neoformans Algae: ex. Microcystis aeruginosa Bacteria endotoxins (Gram-negative bacterial cells) Fungal Toxins (Mycotoxins) and -(13)-D-Glucans

Zoonotic Pathogen Issues to Address: 

Zoonotic Pathogen Issues to Address Which zoonoses are foodborne pathogens; how/where do they contaminate food? Which zoonoses are waterborne; how/where do they contaminate water Which zoonoses are airborne; how/where do they contaminate air What are the principal microbes of animal (AFO) origin that can contaminate the environment and cause human disease what are their origins and sources? What are the pathways of exposure and transmission to people? What is the contribution of AFOs, and pastureland systems to the total burden of infectious disease from these organisms? What features are most important to the ability of zoonotic pathogens to survive in the environment?

Zoonotic Pathogen Issues to Address: 

Zoonotic Pathogen Issues to Address Can strains of zoonotic microorganisms that infect humans be differentiated from those that are not infectious to humans? To what extent and how do animal pathogens evolve (mutate) and interact to become human pathogens? Do current public health, animal agriculture and environmental practices protect the public from exposure to zoonotic pathogens? What analytical methods and indicators are available to detect, quantify and identify the pathogens and monitor treatment and control processes? What are the most effective Rx processes, management practices and systems for these pathogens to protect the environment How can management of sources and exposure pathways control the potential for human exposure?

Zoonotic Pathogen Issues to Address: 

Zoonotic Pathogen Issues to Address Which pathogens fall outside the current “prevention and control envelope”? What are the appropriate research and regulatory approaches to address this issue? Which zoonotic pathogens are candidates for future concerns and evaluation with respect to human health risks from animal agriculture?

Biological Factors Contributing to Pathogen (Re-)Emergence: 

Biological Factors Contributing to Pathogen (Re-)Emergence Genetic changes due to mutation Genetic changes due to recombination, reassortment, and other gene “swapping” Changes in gene expression Changes in human and animal hosts that alter pathogen properties, including host range and infectivity Environmental changes altering pathogen-host interactions

Factors Influencing Zoonotic Pathogen Risks: 

Factors Influencing Zoonotic Pathogen Risks Pathogen adaptability Increasing reservoir/routes of introduction into the environment “Proximity” of reservoir to water/human exposure Persistence of pathogen in the environment and resistance to control measures Human behavior factors Outcome factors (infectivity, severity of adverse health impacts) Public health factors potential contribution of an exposure route to overall burden of disease

Other Factors Contributing to Zoonotic Risks: 

Other Factors Contributing to Zoonotic Risks Human intrusion into sylvan and other undeveloped regions Intense human exposure to animals from agriculture and other activities (e.g., pets, including exotic ones) Increased urbanization and animal vector attraction Growing immune compromised human and animal populations Global climate change and other ecological alterations Changing and severe weather Continued use of antibiotics for therapeutic and non-therapeutic purposes Travel, migration and importation of humans and animals International trade in animals, foods and other and animal products Bioterrorism

Practices and Systems for Animals, Food and the Environment: 

Practices and Systems for Animals, Food and the Environment Which management and other practices will be protective? Current practices adequate? New or better approaches needed to protect human health? Can zoonotic pathogens be best managed at the source? Prevention measures (vaccines, drugs, genetic manipulation?) Animal health interventions Human health interventions Through animal husbandry and management practices? Food safety practices: HACCP, pre-/post-harvest processes? Waste Rx, water pollution control & environmental management.? Waste Rx, runoff management, riparian buffers, DW water Rx Are optimum combinations of all/some multiple barriers the best approach?

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Animal Manure Management Systems for CAFOs: Potential Environmental Impacts Typical animal production and manure management systems can cause environmental pollution from pathogens Food, water, soil and air pollution possible Typical solid and liquid waste management: Store liquids in anaerobic lagoons; store “dry” wastes in piles months (sometimes only weeks) land apply (sprayfields and spreaders) at nutrient-controlled rates for N or P “Non-discharge” systems: often a misnomer On- and off-farm contamination is possible and sometimes occurs documented excess microbe levels and WBDOs US EPA estimates CAFOs and their wastes to be major contributors to impairment of surface water quality; TMDLs

Some Bioaerosol Materials and Exposure Routes: 

Some Bioaerosol Materials and Exposure Routes Animals, including fur, feathers, skin flakes, etc. Feed Litter and bedding Barn exhausts Spray irrigation of liquid wastes Land spreading of manure solids Waste treatment processes, especially mixing and other mechanical processes

Microbial Reductions by Liquid Animal Waste Treatment Processes and Management Systems: 

Microbial Reductions by Liquid Animal Waste Treatment Processes and Management Systems Most evaluated only for fecal coliform bacteria reductions little/no data on bacterial pathogens, viruses and parasites Many achieve moderate (90-99%) pathogen reductions: high pathogen levels remain in treated liquids and solids Some achieve high (>99.99%) pathogen reductions: high temperature (thermophilic and composting) processes Alkaline (lime) stabilization at pH >11 Some give ineffective (<90%) microbial reductions Overland flow; other biological systems of short residence time Survival, transport and fate of pathogens after land application and other post-treatment management options is poorly characterized

Animal Solid Waste Management and Pathogens: 

Animal Solid Waste Management and Pathogens Pathogen levels decline with time in stored manure reductions poorly characterized for different storage conditions and pathogens Composting increases rate of pathogen reduction Pathogen reductions of >99.99% are expected Land application method and rate and environmental conditions will influence pathogen survival on land/in soil Stored manure can attract vectors pathogen recontamination by animals and other vectors (e.g., birds, mice, flies) is a concern vectors spread pathogens to other places, animals & people Physical handling of dry manure can increase airborne dissemination of pathogens (bioaerosols)

Issues and Needs to Address: 

Issues and Needs to Address Animal waste management systems can cause pathogen contamination of land, air and surface and ground waters Greater risks of pathogen contamination during/after precipitation How can systems be further improved to reduce pathogen levels in foods, reaching off-farm environmental media or contacting humans? Is the EPA CAFO regulation an adequate step? Probably not for pathogens NPDES permits, Best Practicable Control Technologies, Best Available Technologies, Best Management Practices, Effluent Guidelines and Total Maximum Daily Loads Identifying BMPs for pathogen reduction and containment Understand pathogen contamination and human health risks Characterize pathogen fate in Rx processes and management systems Assess pathogen impacts on environmental media and human health

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Where will future emerging pathogens come from? Humans Animals: Zoonotic origin Environment: reservoirs New (existing) pathogens will be recognized New agents will be created Greater impacts of existing pathogens will be recognized Pathogens will continue to evolve and adapt

Goals/Approaches to Address Pathogens from AFOs: 

Goals/Approaches to Address Pathogens from AFOs Provide guidance to stakeholders Characterize current systems and address current issues Anticipate and identify potential future problems: Which present, emerging and re-emerging pathogens? Which exposure routes? Which management and other practices will be protective? Disease surveillance, diagnosis and response measures What surveillance systems are` best to detect new zoonoses? How can new and (re-)emerging pathogens be best detected? What disease surveillance, investigation and response systems will best detect, diagnose and contain/rid zoonotic pathogens? How can agriculturalists, microbiologists, veterinarians, physicians, epidemiologists, biosecurity specialists and other public health and environmental specialists best work together?

Need for a Risk-based Approach: 

Need for a Risk-based Approach Risk Assessment: Essential Steps