# Presentation: 237437

## 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

- 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

## Pathogen Sources and Transmission    Pathways from Animal Agriculture

**AIR; BIOAEROSOLS**

## 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

- 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: C*ryptosporidium 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

## 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

## 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

## 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

## 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

- 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

- 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

- 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

- 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

- 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

- 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

- 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?

## 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

- 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

- 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

- 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

- 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

## 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

- 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

- Risk Assessment: Essential Steps