Quarantine Protocols:
Automated Health Screening Workflows

Why Quarantine Is Essential

Every new animal entering your facility is a potential carrier of adventitious agents — pathogens that could devastate your existing colony, compromise research data, and require costly decontamination. The Guide for the Care and Use of Laboratory Animals requires that all animals undergo a quarantine period and health assessment before introduction into a colony.

A well-defined quarantine program protects not only animal welfare but also research integrity. Subclinical infections can alter immune responses, tumor growth, behavior, and metabolism — confounding experimental results without any visible signs of disease.

Physical separation is the cornerstone of effective quarantine:

• Dedicated rooms: Quarantine must be in a separate room or suite with independent ventilation (ideally negative pressure relative to the main colony)
• Equipment isolation: Use dedicated cages, water bottles, feeders, and handling equipment that never enters the main colony
• PPE requirements: Dedicated gowns, gloves, shoe covers, and masks for quarantine areas. Change PPE between quarantine and main colony areas.
• Traffic flow: Designate a one-way workflow: care for quarantine animals last in the daily rounds, after main colony animals
• Access control: Restrict quarantine access to essential personnel only. Maintain a visitor log.

Quarantine duration varies based on several factors:

• Mice and rats (commercial vendors with health reports): 14 days minimum
• Mice and rats (non-approved or unknown sources): 28-30 days minimum
• Guinea pigs and hamsters: 14-21 days
• Rabbits: 14-21 days
• Non-human primates: 30-60 days (with TB testing requirements)

Additional considerations:

• Acclimation period: Add 3-7 days for behavioral and physiological recovery from shipping stress before any experimental use
• Screening turnaround: Quarantine duration must be long enough to receive all health screening results
• Incubation periods: Some pathogens have incubation periods longer than the minimum quarantine; your veterinarian should assess risk

Health screening panels should be tailored to your species, source, and facility requirements:

• Serology: ELISA or immunofluorescent antibody (IFA) testing for species-specific pathogens. For mice: MHV, MPV, MNV, Sendai, PVM, Ectromelia, Clostridium piliforme, Mycoplasma pulmonis. For rats: SDAV, KRV, CAR bacillus, Mycoplasma pulmonis.
• Parasitology: Fecal flotation for endoparasites (Aspiculuris, Syphacia), tape test for pinworms, skin scraping for ectoparasites (mites, lice)
• PCR testing: Nucleic acid testing for specific agents not reliably detected by serology (e.g., Helicobacter spp., MNV)
• Bacterial culture: Fecal culture for Salmonella, Campylobacter, and other enteric pathogens when indicated
• Clinical examination: Physical assessment by a veterinarian or trained technician

Daily monitoring is critical for early detection of disease in quarantined animals:

• Body condition scoring: Assess body condition on a 1-5 scale; animals scoring below 2 require immediate veterinary attention
• Activity level: Note any lethargy, hunched posture, or reluctance to move
• Coat and skin: Look for rough coat, alopecia, lesions, or evidence of barbering/fighting
• Respiration: Listen for sneezing, nasal discharge, or labored breathing
• Fecal quality: Check for diarrhea, mucoid feces, or blood
• Food and water intake: Monitor consumption patterns for changes

Use standardized observation forms and record all findings. Any abnormality should be reported to veterinary staff and documented with the date, observer, finding, and action taken.

Sentinel animals provide ongoing surveillance beyond initial quarantine screening:

• Selection: Use young (4-6 week old), immunocompetent, specific pathogen-free (SPF) animals of the same species as the colony being monitored
• Exposure method: Transfer soiled bedding from colony cages to sentinel cages weekly. This ensures sentinels are exposed to fecal, urinary, and respiratory pathogens circulating in the colony.
• Number: Typically 2 sentinel animals per rack or per room, depending on facility size
• Testing interval: Test sentinels quarterly (every 3 months) for a comprehensive pathogen panel
• Rotation: Replace sentinel animals annually or after testing; never return tested sentinels to the colony

Before releasing animals from quarantine, verify that all clearance criteria are met:

• Negative screening results: All health screening tests must be negative for excluded pathogens
• Minimum duration: The minimum quarantine period must have elapsed
• Clinical health: Animals must be in good clinical health with no signs of disease
• Treatments completed: Any required prophylactic treatments (e.g., anti-parasitic medication) must be completed
• Veterinary approval: The attending veterinarian must authorize the release from quarantine

Document the clearance decision with the date, authorizing veterinarian, screening results summary, and any conditions or restrictions on the animals' use.

The final step is a documented transfer from quarantine to the main colony:

• Health certificate: Issue a health certificate for each animal or shipment, documenting quarantine history, screening results, and clearance approval
• System update: Update the animal management system to change the animal's status from "quarantine" to "active colony"
• Cage transfer: Transfer animals to clean cages in the main colony area. Do not reuse quarantine cages without proper decontamination.
• Monitoring: Continue daily health observations for 7 days after transfer to detect any delayed-onset illness

Frequently Asked Questions