Reducing cross-contamination requires more than selecting an effective disinfectant. It depends on standardized cleaning procedures, staff training, proper facility design, and consistent adherence to biosecurity protocols.
Here are five commonly overlooked areas where cross-contamination can occur—and practical strategies to reduce the risk.
Cross-contamination can affect much more than animal health.
Disruption of ongoing research
Loss of valuable animal colonies
Increased diagnostic testing
Additional labor and sanitation costs
Delays in study timelines
Biosecurity breaches
Regulatory findings during inspections or accreditation visits
The Guide for the Care and Use of Laboratory Animals emphasizes that sanitation, husbandry, facility design, and personnel practices all contribute to maintaining animal health and supporting reliable research outcomes.
Source: National Academies Press. Guide for the Care and Use of Laboratory Animals, 8th Edition
https://nap.nationalacademies.org/catalog/12910/guide-for-the-care-and-use-of-laboratory-animals
Today’s rodent enclosures are primarily made of polysulfone, a tough, autoclavable plastic known for its chemical durability. Polysufone is also naturally opaque. Over the last several years, cage manufacturers have made alterations in the structure/design of their cages. The cages have become clearer and have added more features. This has created some challenges when using certain disinfectants specifically when autoclaving out is introduced.
Through collaborative testing with leading cage suppliers, and at end user facilities, Contec and Virox have confirmed Peroxigard RTU and Peroxigard diluted from Concentrate are excellent and safe disinfectants for the reprocessing of these newer cages when using the appropriate processes.
Transport carts move throughout the facility, from receiving areas to housing rooms, procedure spaces, and cage wash. If they are not cleaned and disinfected between uses, they can become vehicles for transferring microorganisms between animal populations
Animal transport carts
Cage transport racks
Feed carts
Waste collection carts
Mobile procedure equipment
Clean and disinfect carts between designated areas.
Establish separate carts for clean and dirty workflows where practical.
Include wheels, handles, and undersides in cleaning SOPs.
Verify disinfectant contact times according to the manufacturer's instructions.
Door handles
Push plates
Light switches
Computer keyboards
Touchscreen monitors
Time clocks
Refrigerators and freezer handles
Because multiple employees interact with these surfaces throughout the day, they can contribute to indirect pathogen transmission.
The Centers for Disease Control and Prevention (CDC) recommends routine cleaning and disinfection of frequently touched surfaces as part of an effective environmental infection prevention program.
Source: CDC. Environmental Infection Control Guidelines
https://www.cdc.gov/infection-control/hcp/environmental-control/index.html
Equipment that moves between rooms can bypass many of the controls designed into barrier facilities.
Scales
Procedure tables
Anesthesia machines
Imaging equipment
Laptops and tablets
Vacuum units
Tool kits
Unless equipment is properly cleaned before entering another room, contaminants can travel with it.
Clean and disinfect shared equipment before transfer.
Maintain room-specific equipment whenever possible.
Use checklists to verify equipment decontamination.
Clearly label equipment assigned to restricted areas.
Personal protective equipment (PPE) protects both personnel and animals—but only when it is used correctly.
Touching contaminated gowns while removing gloves
Reusing disposable PPE
Carrying contaminated shoe covers into clean areas
Improper donning and doffing sequences
Inadequate hand hygiene during transitions
The National Institutes of Health Office of Laboratory Animal Welfare (OLAW) emphasizes that occupational health and safety programs, including PPE and personnel practices, should be based on risk assessment and integrated into the overall animal care and use program.
Source: OLAW. Guide for the Care and Use of Laboratory Animals resources
https://olaw.nih.gov/guidance/guide
Post visual PPE instructions at entry points.
Reinforce hand hygiene during every room transition.
Observe staff periodically for technique.
Include PPE competency assessments in onboarding and annual refresher training.
Ironically, the tools used for cleaning can become sources of contamination if they are not managed appropriately.
Mop heads
Buckets
Reusable wipes
Brushes
Squeegees
Spray bottles
Using the same cleaning tools in multiple areas without appropriate laundering, replacement, or disinfection can spread contaminants rather than remove them.
The CDC recommends maintaining and cleaning environmental services equipment to prevent contamination of surfaces during routine cleaning.
Source: CDC. Environmental Infection Control Guidelines
https://www.cdc.gov/infection-control/hcp/environmental-control/index.html
Use color-coded cleaning tools by area or function.
Replace damaged or worn equipment promptly.
Store clean and used equipment separately.
When contamination events are investigated, the root cause is often not a failure of the disinfectant itself. Instead, it may involve:
Inconsistent SOPs
Improper contact times
Missed high-touch surfaces
Equipment moving between rooms
Workflow shortcuts
Insufficient staff training
Documentation gaps
The American Association for Laboratory Animal Science (AALAS) emphasizes training and professional development as essential components of quality laboratory animal care programs, reinforcing the importance of consistent personnel practices alongside facility sanitation.
Source: AALAS
https://www.aalas.org/
Reducing cross-contamination requires a comprehensive approach that integrates products, people, and processes.
• Are cleaning responsibilities clearly assigned?
• Are high-touch surfaces identified in SOPs?
• Is shared equipment cleaned before entering another room?
• Are transport carts included in routine sanitation schedules?
• Are cleaning tools dedicated to specific areas?
• Are PPE procedures regularly observed and reinforced?
• Are employees trained on why these practices matter—not just how to perform them?
Facilities that routinely review these questions are better positioned to maintain biosecurity, protect research integrity, and support animal welfare.
Cross-contamination does not always begin with major procedural failures. More often, it starts with small, routine actions that are easy to overlook.
By focusing on transport equipment, high-touch surfaces, shared equipment, PPE transitions, and cleaning tools, vivarium managers can address some of the most common pathways for contamination.
Combined with evidence-based SOPs, validated disinfectants, ongoing staff training, and regular program reviews, these practices can help create a more resilient sanitation program—one that supports research continuity, regulatory compliance, and the health of both animals and personnel.
Every vivarium has unique workflow challenges. Through our Process Improvement Program, featuring a Complimentary Contamination Control Assessment (CCA), our specialists can help you identify potential contamination risks and recommend cleaning and disinfection solutions that support your SOPs, compliance goals, and research objectives.
Cross-contamination occurs when microorganisms, allergens, or other contaminants are unintentionally transferred from one animal, room, piece of equipment, or surface to another, potentially affecting animal health, research integrity, and biosecurity.
Common sources include transport carts, shared equipment, high-touch surfaces, improperly managed cleaning tools, and incorrect PPE use during room transitions.
Facilities can reduce risk by implementing validated cleaning SOPs, disinfecting shared equipment, cleaning high-touch surfaces routinely, using dedicated cleaning tools, reinforcing PPE practices, and providing ongoing staff training.
High-touch surfaces are contacted frequently by multiple employees throughout the day, making them potential reservoirs for indirect pathogen transmission if they are not cleaned and disinfected routinely.
AAALAC does not prescribe a single protocol. Instead, it evaluates whether institutions have science-based sanitation, biosecurity, and personnel practices that support animal welfare and align with the Guide for the Care and Use of Laboratory Animals.