Endoscope Reprocessing in Veterinary Practice: What “Clean” Really Means, and Why Your Team’s Health Depends on It
Flexible endoscopes are some of the most valuable tools in a veterinary hospital—and also some of the most misunderstood from an infection-control standpoint. They’re long, narrow, multi-lumen devices designed to travel through biologically messy environments: mucus, saliva, blood, bile, feces, urine, and biofilm-friendly moisture. That combination is why endoscopes demand a reprocessing mindset that’s closer to a “mini sterile processing department” than a typical wipe-down-and-go workflow.
In veterinary medicine, reprocessing is often performed by the most essential people in the building—technicians and assistants—under the highest time pressure, in spaces that were never designed for chemical disinfection. That’s the recipe for two kinds of risk: patient-to-patient cross-contamination and occupational exposure (especially when aldehyde-based disinfectants are used without proper engineering controls).
This article is meant to read like continuing education material: it explains what high-quality endoscope reprocessing looks like, why the details matter, and where the real-world compliance traps live—particularly around glutaraldehyde and OPA ventilation and the OSHA liability that follows.
“Disinfected” vs “Sterilized”: The Language Matters (Clinically and Legally)
In veterinary practice, the word sterilized is commonly used to mean “we cleaned it really well.” But sterilization has a specific meaning: the complete elimination of all forms of microbial life, including bacterial spores. Flexible endoscopes in routine veterinary use are typically processed with high-level disinfection (HLD), not sterilization.
High-level disinfection is designed to eliminate vegetative bacteria, mycobacteria, fungi, and viruses—but it is not the same as sterilization. Using the word “sterilized” in SOPs, staff training, client communications, or documentation can become a liability if your actual process is HLD and a contamination event occurs. The safest approach is to standardize your internal language:
- “High-level disinfected endoscope” (accurate)
- Avoid “sterilized scope” unless you truly used a validated sterilization method compatible with that device and documented it
This isn’t semantics. It’s about aligning what you say with what you do.
The Non-Negotiable Truth: Cleaning Is the Step That Makes Disinfection Work
If there’s one principle every hospital should engrain into training, it’s this: you can’t disinfect dirt. High-level disinfectants are not magic. If protein and bioburden remain in channels, disinfectant contact becomes incomplete and inconsistent—and organisms can persist, especially in protected microenvironments.
Reprocessing failures commonly happen when:
- bedside pre-cleaning is skipped (bioburden dries and hardens),
- channel brushing is incomplete,
- contact times are shortened “just this once,”
- drying is rushed (moisture + storage = biofilm opportunity).
The best reprocessing programs treat cleaning as the “procedure” and disinfection as the “final validation step.”
A Practical, Defensible Reprocessing Flow (What “Good” Looks Like)
A defensible workflow is one you can teach, repeat, document, and audit. In plain language, the core phases are:
1) Immediate pre-cleaning at point of use.
Right after the procedure, wipe the insertion tube, flush channels with detergent solution, and prevent drying. Dry debris becomes tomorrow’s biofilm.
2) Leak testing and inspection.
Leak test per the scope’s IFU. Damaged scopes are not just “image quality problems”—they’re reprocessing failures waiting to happen because fluid ingress compromises internal spaces you can’t adequately clean.
3) Manual cleaning (the real work).
Use the correct enzymatic detergent, correct brushes, and correct technique for all channels. Then rinse thoroughly. Manual cleaning is where most contamination events are either prevented—or quietly guaranteed.
4) High-level disinfection using an approved chemistry.
This is where chemical selection, test-strip verification (when required by product IFU), contact time, temperature, and complete channel fill become critical.
5) Rinsing, drying, and storage.
Residual chemical must be rinsed per IFU. Then the scope must be dried (often including alcohol flush and forced air as recommended by IFU) and stored in a way that discourages recontamination and moisture retention.
If you can’t confidently teach every step above to a new technician—and verify competency—you don’t have a system; you have a habit.
Choosing the High-Level Disinfectant: What’s Common vs What’s Usually Approved
Veterinary practices typically encounter four chemistry “families” for HLD:
Glutaraldehyde (aldehyde-based)
Glutaraldehyde has long been used for HLD, and it remains commonly approved by endoscope manufacturers. It’s effective when used correctly—but it is also a well-known occupational hazard that can drive significant compliance risk if vapors are not controlled.
OSHA’s guidance for glutaraldehyde emphasizes engineering controls like local exhaust ventilation (e.g., fume hoods) and keeping glutaraldehyde baths under ventilation where possible.
OPA (ortho-phthalaldehyde; aldehyde-based)
OPA is widely used for flexible endoscopes and is also commonly manufacturer-approved. It typically requires no activation and has less odor than glutaraldehyde, but it remains a chemical exposure risk and should be treated with the same seriousness regarding ventilation and handling.
Advanced Hydrogen Peroxide (AHP) liquid solutions
These can look attractive because they reduce aldehyde exposure concerns. However, manufacturer compatibility is the hinge point. Many scope manufacturers do not broadly approve every AHP liquid for every scope model and channel design. Using an unapproved chemistry can become an ugly problem when a scope fails or a contamination incident is investigated.
Peracetic acid (PAA) liquid solutions
Peracetic acid is a powerful oxidizer and is used in some reprocessing systems. The same warning applies: not all approaches are manufacturer-approved for all scopes, and PAA can raise material compatibility concerns if used outside validated systems.
Bottom line: in practice, most manufacturers primarily approve glutaraldehyde and OPA for flexible endoscopes, and deviations should be justified against the scope IFU and your documented risk assessment.
The Real Regulatory Exposure: OSHA Ventilation, Aldehydes, and the Liability You Can’t Ignore
For most veterinary hospitals, the most immediate regulatory risk in endoscope reprocessing isn’t “infection control policing.” It’s occupational exposure—particularly when aldehyde-based solutions are used in spaces without adequate ventilation and controls.
OSHA’s hospital guidance on glutaraldehyde is blunt about the direction of travel: use local exhaust ventilation, keep baths under ventilation where feasible, and control vapor at the source.
Even if your practice is not a human hospital, the workplace hazard logic is the same: when staff are regularly exposed to irritating/sensitizing chemical vapors, the burden shifts to the employer to demonstrate that hazards are recognized and controlled. In the real world, that means your reprocessing area should not be a back counter next to laundry, a cramped closet, or a poorly ventilated “nook” with a soaking tray.
What does “out of compliance” look like in veterinary reprocessing spaces?
Common patterns that create risk:
- soaking trays used in open air without local exhaust
- lids left off basins “just during turnover”
- no documented ventilation performance
- staff reporting throat/eye irritation as “normal”
- no written SOPs or training documentation for hazardous chemical handling
What’s the financial risk of an OSHA enforcement action?
OSHA publishes maximum penalties that can be assessed per violation. As of the current posted schedule (inflation-adjusted amounts effective after Jan. 15, 2025), maximums include: $16,550 per serious (or other-than-serious/posting) violation, $165,514 per willful or repeated violation, and $16,550 per day for failure to abate beyond the abatement date.
That matters because ventilation issues rarely appear alone. A single visit can uncover multiple citable items tied to the same workflow: inadequate ventilation/engineering controls, inadequate hazard communication, missing PPE policies, lack of training documentation, poor labeling, missing spill response planning, etc. Penalties can also escalate quickly if OSHA classifies issues as repeated or willful, or if abatement is delayed (daily penalties).
In short: the financial risk is not “a slap on the wrist.” It can be a multi-thousand to six-figure exposure depending on the classification and how many items are cited—plus the indirect costs of remediation, downtime, and staff turnover.
Why This Matters More Right Now: Biosecurity Pressure from Real Equine Disease Events
Reprocessing rigor becomes even more important when your caseload includes high biosecurity pressure—especially equine patients moving through referral networks, show circuits, and multi-horse facilities.
Recent EHV-1 activity (what it signals for practices)
A multistate EHV-1 outbreak linked to events in Texas (originating around Waco) was widely reported in late 2025, with confirmed cases across multiple states. This is the kind of scenario that reminds everyone: pathogens move faster than schedules change, and clinics become “mixing bowls” without intending to.
Even when a virus spreads primarily via direct contact and fomites like buckets, tack, hands, and clothing, the broader lesson is that infection prevention systems must hold under stress—when patient volume is high, turnaround is rushed, and the hospital is tired.
S. equi (Strangles) and endemic risk realities
Strangles remains a persistent, highly contagious disease challenge in equine populations. AAEP guidance explicitly references vaccination on premises where strangles is a persistent endemic problem or where horses are at high risk of exposure.
Texas is a practical example of why “endemic-premises” language matters: high horse density, constant movement, frequent commingling, and seasonal peaks in cases discussed by Texas A&M’s diagnostic lab outreach all support a higher baseline risk environment and the need for proactive prevention strategies.
The connection to endoscope reprocessing is simple: when high-consequence infectious agents are in your ecosystem, “pretty good” cleaning becomes unacceptable—because small process shortcuts can become outbreak accelerants through contaminated surfaces, wet storage, rushed handling, and poorly controlled reprocessing spaces.
Bringing It Home: What a “Practice-Manager Defensible” Program Looks Like
A reprocessing program that protects patients and staff is built on a few pillars:
- A written SOP that matches reality. If your SOP says “sterilize” but you do HLD, fix the language. If your SOP says “ventilated area” but you have no local exhaust, fix the facility.
- Manufacturer-first chemical selection. Start with what the endoscope IFU supports. In practice, many manufacturers primarily approve glutaraldehyde and OPA—so if you want to move away from aldehydes for staff safety reasons, treat that as a structured project: IFU review, compatibility confirmation, and documented transition.
- Ventilation as a safety system, not a suggestion. If you use aldehydes, implement engineering controls consistent with OSHA’s glutaraldehyde guidance (local exhaust ventilation, controlling vapors at the source, keeping baths under ventilation where feasible).
- Competency-based training and documentation. Your best defense is repeatability: checklists, competency sign-offs, logs that match IFU contact times, and an audit rhythm that finds drift early.
- Drying and storage treated as clinical steps. Moisture and poor storage defeat your best disinfection. Drying isn’t “nice to have”—it’s part of preventing biofilm and recontamination.