Potential Zoonoses Associated with Birds


This document provides information about potential zoonotic exposure while working with birds or their products (e.g., fecal samples). This list of infectious agents here is not exhaustive but provide guidance about some common zoonotic agents seen in birds. Safe work practices are provided as guidelines for staff and researchers working with animals, animal facilities, or animal products.

Researchers planning field work should also visit EHS’ website on field research safety: https://ehs.cornell.edu/research-safety/general-laboratory-safety/field-research-safety

Zoonotic Pathogens

  • Avian Mycobacterium
    • Organisms: Mycobacterium spp.
    • Clinical Signs:
      • Animals – Asymptomatic; Diarrhea and wasting.
      • Humans – Asymptomatic to night sweats, weight loss, abdominal pain, fatigue, diarrhea, and cough in people with immunosuppression or preexisting lung damage.
      • Transmission: Inhalation of aerosols or ingestion of food or water contaminated with feces of infected birds. 
  • Avian Chlamydiosis or Psittacosis
    • Organisms: Chlamydophila spp.
    • Clinical Signs:
      • Animals – Asymptomatic to lethargy, anorexia, and ruffled feathers; ocular and nasal discharge and diarrhea are possible.
      • Humans – Flu-like symptoms (fever, chills, headache, muscle ache, cough); can evolve into pneumonia
    • Transmission: Ingestion or inhalation of feces or respiratory secretions.
    • Prevention: Minimize inhalation of aerosols such as dust particles

NOTE: Psittacosis is a reportable disease.

  • Low Pathogenic Avian Influenza Virus (LPAI)
    • Organism: Avian Influenza Virus
      • Clinical Signs:
        • Animals – Respiratory signs (coughing, dyspnea, cyanosis); diarrhea; neurological signs.
        • Humans – Flu-like symptoms (fever, chills, headache, muscle ache, cough); can evolve into pneumonia.
      • Transmission: Aerosol route; Direct contact with feces, oronasal secretions, or contaminated environment.
      • Control: Persons who have contact with birds infected with LPAI are quarantined from interaction with other birds for 5 days.
  • Highly Pathogenic Avian Influenza Virus (HPAI)
    • Organism: H5N1 and H7N1
      • Clinical Signs:
        • Animals- Mortality approaching 100% within 48 hours of exposure for chicken flocks
        • Humans- Mild to severe flu-like symptoms
      • Transmission: Very contagious among birds via saliva, nasal secretions, feces, and contaminated surfaces
      • Controlculling of the flock is recommended due to the potential economic impact. Persons who have contact with birds infected with HPAI are quarantined from interaction with other birds for 5 days. 

NOTE: Avian Influenza (both LPAI and HPAI) is a reportable disease and is required to be reported to USDA and State authorities.

  • Enteric pathogens
    • ​​​​​​​Organisms: Salmonella spp., Cryptosporidium spp. and Campylobacter spp
    • Clinical Signs:
      • Animals – Asymptomatic or Diarrhea.
      • Humans – Diarrhea, nausea, vomiting, abdominal pain.
    • Transmission: Accidental ingestion of food or water contaminated with feces of infected birds.

Safe Work Practices

  1. Good Personal Hygiene
    • Wash hands after working with animals or animal products and when leaving animal facilities.
    • Do not eat, drink, apply cosmetics, or use tobacco products in animal facilities.
  2. Personal Protective Equipment (PPE)
    • Use proper PPE for the proposed task (e.g., disposable gown, nitrile gloves, facemask, respirator, safety glasses). Maintain dedicated protective clothing and footwear while working with animals or in animal facilities. Do not wear the same protective clothing outside of the animal facility.
    • Wear disposable gloves and safety glasses during procedures that increase the likelihood of exposure to zoonotic agents (e.g., handling of birds or contaminated surfaces or equipment). Exercise increased caution when handling sick animals (i.e., animals showing clinical signs such as diarrhea or ruffled feathers).
    • Use medical masks for routine care and N95 masks for protection during “aerosolizing procedures” (e.g., high-pressure hosing).
  3. Animal Care
    • Isolate sick or infected animals when possible.
    • Handle and care for sick or infected animals last.
  4. Cleaning and Disinfection
    • Maintain clean, dry, and uncluttered animal areas and workspace.
    • Disinfect laboratory and animal room surfaces after each use. Use disinfectants approved by facility managers and suitable for the potential agents identified in this information sheet.
    • Dispose of deceased animals, animal products, items contaminated by animal products, contaminated bedding, and laboratory waste in a facility-approved manner
  5. Proper Sharps Handling
    • Work only with one uncapped needle at a time and immediately dispose of after use in sharps receptacle.
    • Avoid recapping needles whenever possible.
  6. Medical Attention
    • In an emergency, call 911 or 607-255-1111 from a campus phone. if you suspect any exposure or if you develop any symptoms associated with infection with zoonotic agents (e.g., fever, malaise, diarrhea, abdominal pain).
      1. For students, seek medical attention at Cornell Health or a local primary care provider. Cornell Health is available by phone at 607-255-5155 (a 24-hour phone consultation line).
      2. For faculty and staff, seek a medical evaluation with a local primary care provider or urgent care. Cornell Health does not see employees for post-exposure care. 
      3. Cornell Health Occupational Medicine (607-255-6960) may provide counseling prior to working with birds
  7. Allergies
    • Handling of bedding and animal products may aggravate allergies. Proper use of PPE reduces but does not eliminate the risk of developing allergies. Refer to the Allergy Prevention web page (see References) for further information.


  1. Allergen Prevention http://www.research.cornell.edu/Care/documents/OHS/AllergyPreventionFactSheet.pdf
  2. Cornell Health Occupational Medicine, 607-255-6960 or https://health.cornell.edu/services/occupational-medicine
  3. Zoonoses in pet birds: review and perspectives https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668993/pdf/1297-9716-44-36.pdf
  4. Avian Influenza in Birds
  5. ​​​​​​​2022 Detections of Highly Pathogenic Avian Influenza https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/avian/avian-influenza/2022-hpai
  6. USDA-APHIS Guidelines for Avian Influenza Viruses https://www.selectagents.gov/compliance/guidance/avian/docs/AIV_Guidelines_180220.pdf