Keep­ing Incu­ba­tors and Work­sta­tions Contamination-Free

Maintaining a contamination-free incubator is essential in microbiology and cell culture labs. Even low levels of residual bacteria or fungi can compromise cell viability, distort experimental data, or lead to failed cultures. Incubators in multi-user labs show a 70% higher contamination rate when internal surfaces were not decontaminated at least monthly. Contamination isn’t just an inconvenience – it’s a fundamental threat to experimental integrity and reproducibility. Effective incubator decontamination, done routinely, is therefore a cornerstone of good laboratory practice.

Decontaminating a CO₂ incubator or hypoxia workstation requires a combination of manual cleaning of accessible internal surfaces, regular disinfection using approaches such as hydrogen peroxide fogging, and periodic professional fumigation. High-risk areas include water pans, door gaskets, fan assemblies, and interior surfaces that can harbor microbes. Tools like MycoFog (a hydrogen peroxide fogger) help reduce microbial load between experiments, supporting cleaner workflows, and more reliable cell culture results.

This article focuses on cell incubators and workstations used in research settings. We’ll explore where contamination commonly occurs, why basic cleaning alone often falls short, and what to consider when developing your decontamination strategy. If you manage daily cell culture work or a busy core facility, understanding how to decontaminate incubators effectively will help you maintain consistency, reduce contamination risk, and improve experimental outcomes.

In lab settings, ‘cleaning’, ‘disinfection’, ‘decontamination’, and ‘sterilization’ are related but distinct terms. 

Cleaning is the physical removal of dirt, debris, organic material, and contaminants from surfaces or equipment using water, detergents, or mechanical action, reducing the bioburden but not necessarily killing microorganisms.

Disinfection is the process of using chemical agents (e.g., alcohol, bleach) or heat to kill or inactivate most pathogenic microorganisms (except some bacterial spores) on inanimate surfaces, lowering the risk of infection without guaranteeing complete sterility

Decontamination refers to the broader removal or neutralization of hazardous substances, including biological agents, chemicals, or radioactive materials, from surfaces or equipment to make them safe for handling, often involving cleaning and disinfection steps. Just like disinfection it doesn’t guarantee the absolute kill of every organism, but it significantly lowers the bioburden to minimize interference with experiments or cultures.

Sterilization is the complete elimination or destruction of all forms of microbial life (including hardy spores). It requires rigorous, validated methods - such as high-heat cycles or gaseous agents such as ethylene oxide or formaldehyde - and is typically reserved for critical tasks like preparing surgical instruments or sterilizing equipment in biosafety level facilities. 

CO₂ incubators and hypoxia workstations are rarely (if ever) sterilized, because true sterilization involves long downtimes or extreme conditions incompatible with routine use or indeed materials that make up the incubator. Instead, laboratories tend to rely on regular cleaning and disinfection to control contamination. 

Decontamination measures such as chemical disinfectants or fogging can be applied more readily than a full sterilization procedure, and with considerably less disruption and cost. 

MycoFog is a high-level decontamination tool, not a sterilizer. It does not claim to eradicate every microbe or spore in the chamber (as an autoclave or high-heat cycle would). Instead, it offers a practical way to significantly reduce microbial load via hydrogen peroxide vapor, without the downtime, harsh conditions, or indeed toxicity risks associated with traditional fumigation or full sterilization. This makes it ideal for routine use between ‘deep cleans’, especially when working with sensitive cultures or back-to-back experiments.

Even minimal contamination can have serious consequences in cell culture and microbiology work. In cell culture, for example, an undetected mycoplasma infection can alter cell metabolism and gene expression, leading to false conclusions. Bacterial or fungal contaminants may outcompete cultured cells. In microbiology experiments, background contaminants can obscure target organism growth or yield misleading data. Thus, a regimen of routine decontamination is not just about cleanliness, it’s about safeguarding the integrity of your research.

Decontamination helps reduce these risks without the cost or downtime of full sterilization. When done consistently, it becomes integral to maintaining reproducibility and lab safety. In fact, increasing the frequency of decontamination has a measurable impact: one 2022 study found that implementing thorough incubator cleaning/disinfection on a monthly schedule led to an approximately 60% reduction in contamination occurrences. The same study noted that incubators lacking regular wipe-downs had significantly higher microbial loads, underscoring the value of frequent surface decontamination. Simply put, consistent incubator decontamination preserves cell viability, prevents culture losses, and avoids costly project setbacks over time.

There is no one-size-fits-all rule for decontamination frequency. It depends on usage patterns, incubator type, and the contamination sensitivity of the work being carried out. However, general guidelines can be adopted:

Daily to weekly
Perform quick wipe-downs of high-contact surfaces (door handles, door gasket, inner door, shelving) with 70% ethanol or another suitable disinfectant. In high-use or shared incubators, daily spot-cleaning of spills and weekly surface wipes are recommended; in lower-use settings, a weekly or biweekly wipe-down may suffice. Regular surface hygiene significantly lowers the background microbial burden.

Monthly
Conduct a full internal clean, disinfection and decontamination about once a month. This should include removing shelves and trays, cleaning the fan or HEPA filter cover, disinfecting the water reservoir, and wiping all interior walls and ceiling. A structured monthly cleaning cycle targets hidden contamination and has been shown to dramatically cut down microbial levels. Indeed, most manufacturer guidelines recommend such monthly deep cleans to maintain optimal incubator and workstation performance and reduce contamination risk.

Between experiments
In busy labs or critical experiments, consider bio-decontamination between experiments. For example run a hydrogen peroxide fogging cycle or use a disinfectant spray before the next batch of cultures is introduced. Studies indicate that without such interim decontamination, microbial load in a humid CO₂ incubator can rebound to pre-clean levels in a matter of a few days. Supplemental disinfection between full sterilization or cleaning cycles is strongly recommended by experts to prevent rapid recontamination.

Immediately as needed
If a spill occurs (e.g. a flask of media tips over) or if you suspect contamination in a culture, clean and decontaminate the incubator right away rather than awaiting the next scheduled clean. Prompt action can stop a localized incident from seeding a chamber-wide problem. Remove any contaminated item, wipe up spills with disinfectant, and consider running a fogging or UV cycle (if available) to treat the air and surfaces after the manual clean.

Ultimately, you should adjust frequency based on factors such as laboratory traffic (more users means more frequent decontamination required), incubator type (humidified water-jacketed models need more attention than dry incubators), experiment demands (long-term or sensitive cultures justify stricter contamination control), and any recent contamination events (a history of contamination may warrant temporarily stepping up cleaning frequency until resolved). 

Regular decontamination – not just cursory cleaning – is key to preserving cell viability and maintaining the incubator consistently safe for cultures.

CO₂ incubators and hypoxia workstations provide a warm, humid environment where microbes can thrive. Understanding where contamination tends to lurk will help you target your decontamination efforts effectively:

Door gaskets and frame
The incubator door seal (gasket) often accumulates moisture, nutrients from media drips, and dust. It’s a common hiding spot for mould and bacteria. Unfortunately, gaskets are also frequently missed during routine cleaning, allowing microbes to persist. Make a point to regularly wipe and inspect the door seal and the inner door frame. Even trained staff often overlook such crevices, highlighting the need for complementary methods to reach those surfaces.

Interior walls, shelves, and corners
The inner chamber surfaces can collect condensation and small splashes. Microorganisms (from culture vessel openings, or carried on gloves and tools) can land on these surfaces. Shelving, especially corners and undersides, can harbour residues. Regular manual cleaning is important but be aware that manual wiping may not reach every corner or crack in the chamber. Fogging or vapor-phase decontamination can help reach those areas that wipes miss.

Fan and sensor openings
If your incubator has a circulation fan or airflow plenums, these components can spread contaminants if they themselves get contaminated. The fan blades, fan housing, and any air ducts should be cleaned or replaced according to the manufacturer’s schedule. Microbes can hide in these recesses and then get blown over all your cultures. Similarly, sensor chambers or humidity sensor ports can accumulate dust or fungus – check manufacturer guidelines for cleaning those delicate parts (often 70% IPA wipes or specialized swabs are recommended).

Water pan, or humidification system
Standing water used for humidity is one of the biggest contamination reservoirs. A warm water pan can rapidly grow bacteria, mould, and even algae if not maintained. Studies confirm that humidified incubators tend to have higher contamination burdens than dry incubators, with Gram-negative bacteria and fungi commonly found in neglected water trays. To mitigate this: use only sterile distilled water in pans, add antimicrobial agents (like copper sulphate or commercial incubator water additives) as recommended, and change/clean the water tray frequently (weekly or biweekly). If you see any slimy biofilm or deposits in the pan, that’s a red flag to clean it immediately. In high-traffic labs, consider emptying and refilling the water reservoir weekly and autoclaving or replacing the pan periodically.

Contents and labware
Sometimes the source of contamination is not the incubator itself but what’s put inside it. Culture flasks or plates with loose lids, contaminated stock solutions, or even a researcher’s gloves can introduce microbes. Once inside, though, those microbes will colonize the incubator surfaces. Always use good aseptic technique when loading cultures, consider disinfecting the exterior of gloves with 70% IPA before handling cell cultures, quarantine any suspect cultures, and decontaminate the chamber after any known contamination incident.

Traditional incubator cleaning (manual wipe-downs with disinfectant, or occasional high-heat sterilization cycles if available) is essential but not fool proof. Some challenges include:

Human error and missed areas
As noted, manual cleaning is only as effective as the thoroughness of the person doing it. It’s easy to miss hidden or hard-to-reach surfaces. Studies in hospital settings have shown that even diligent staff often miss critical spots during cleaning, underscoring the need for “no-touch” adjunct methods. An incubator has many crevices (door seals, screw holes, sensor covers) where microbes can hide from a quick wipe.

Rapid recontamination
After you clean an incubator, it doesn’t stay sterile for long. Every time the door opens, there’s a chance for airborne microbes or spores to enter. In a busy lab, dozens of door openings a day can quickly introduce new microbes. If surfaces are not continuously protected or frequently decontaminated, the microbial load can bounce back fast. This is why solely relying on monthly cleanings might still leave gaps – microbes can recolonize in the interim.

Downtime of heat sterilization cycles
Some incubators feature an overnight 90°C sterilization cycle or UV decontamination program. While effective, these cycles render the incubator unusable for many hours and require removal of cultures and heat-sensitive components. Labs with only one or two incubators may find it impractical to take units out of service for a full day routinely. Thus, high-temperature sterilization might be done only infrequently, if ever, creating periods where the incubator is just routinely cleaned and potentially accumulating low-level contamination.

Chemical disinfectant limitations
Not all disinfectants kill all types of organisms. For example, 70% ethanol, common for wipe-downs, works well against vegetative bacteria but may not kill spores or certain fungi effectively. Bleach can kill spores but is corrosive to stainless steel and electronics, so it’s usually not recommended inside incubators. Many labs use a hydrogen peroxide solution or specialized incubator disinfectant for deeper cleaning, which offers broader kill but still requires contact with surfaces to be effective.

Given these challenges, modern contamination control strategies increasingly combine manual cleaning with “augmented” decontamination tools to fill the gaps. This is where MycoFog and similar systems come into play.

MycoFog is a portable hydrogen peroxide fogger designed specifically for bio-decontaminating laboratory workspaces like CO₂ incubators and the HypoxyLab workstation. It addresses many of the shortcomings of manual cleaning by delivering a fine mist of hydrogen peroxide that permeates the incubator’s interior contact surfaces that wipes, or UV light might miss. Hydrogen peroxide is a well-established disinfectant, known to be effective against a broad spectrum of organisms, including bacteria, viruses, and fungi (even spores at sufficient concentration and exposure). By dispersing it as a fog, MycoFog achieves uniform coverage within the chamber.

As noted, MycoFog is not a replacement for a certified sterilization process. However, it provides what can be considered a high-level disinfection or decontamination. It can dramatically reduce microbial load without the need for heat or extended downtime. This makes it extremely useful for routine decontamination between deep cleans or between experiments. Many labs struggle most with between-use contamination rather than major outbreaks – exactly the scenario MycoFog was designed for. Instead of waiting for a quarterly sterilization cycle, researchers can run a quick fogging cycle to refresh the incubator’s cleanliness on a weekly or even daily basis as needed.

Broad surface coverage
Manual scrubbing can fail to reach internal corners, seams, fan blades, or the top ceiling of the incubator. Hydrogen peroxide fogging achieves broad distribution by virtue of filling the space with vapor that settles on every exposed surface. The fog droplets can even penetrate into tiny gaps and around objects. This “no-touch” decontamination complements your regular cleaning – after you physically clean removable parts, a MycoFog treatment can ensure the entire chamber, including crevices, get disinfected consistently.

Ease of use and routine integration
MycoFog was engineered to be incredibly user-friendly. It is battery-operated and self-contained, meaning you don’t need to connect it to a gas line or power during use. The fogging cycle is automated and relatively quick (on the order of 2-4 hours). This makes it feasible to use between experiments without major downtime. For example, in a busy tissue culture lab, one could transfer cells to a secondary incubator, run the MycoFog in the primary incubator, and be back in operation later that same day – far faster than a heat sterilization cycle. In practice, labs can integrate MycoFog fogging as weekly or bi-weekly preventive measure, or as an on-demand cycle whenever a contamination concern arises, with minimal workflow disruption.

Validated efficacy and safety
How do you know MycoFog is actually working and not harming your equipment or cells? Extensive validation tests have been conducted using biological and chemical indicators to ensure the fogging process is both effective against microbes and safe for routine use. In efficacy tests, biological indicators (BIs) containing Geobacillus stearothermophilus spores were placed throughout incubator chambers and exposed to a MycoFog cycle. These spores are extremely resistant and are the benchmark for sterilization validation. The results showed no growth from the indicators inside the incubator after fogging (meaning a ≥6-log kill, as the spores were inactivated), whereas untreated control indicators did show growth. In multiple tests across different incubator models, all BI samples exposed to MycoFog’s fog were completely sterilized, while the control samples (kept outside) grew bacteria, confirming effective decontamination across the chamber (see MycoFog™ Efficacy & Safety Validation link below).

On the safety side, chemical sensors and indicators have verified that MycoFog’s hydrogen peroxide vapor breaks down to safe levels after each cycle. Continuous monitoring with an H₂O₂ gas sensor showed that by the end of the run (when the fog cycle and dwell time are complete), the residual peroxide concentration inside the incubator or workstation falls to the OSHA permissible exposure limit (PEL) for hydrogen peroxide gas. In other words, once the cycle finishes, it’s safe to open the incubator without risking exposure to high H₂O₂ levels. Additionally, peroxide-sensitive chemical indicator strips placed around the incubator consistently change colour during MycoFog treatment, providing visual confirmation of vapor distribution to those spots. These indicators, while not a substitute for biological kill data, show that the peroxide is reaching all corners of the chamber. They offer quick feedback that the process has run correctly and uniformly.

Finally, MycoFog has been tested for its material compatibility. Hydrogen peroxide at the concentrations used is generally gentle on stainless steel and incubator interiors, especially compared to harsher disinfectants like bleach or formaldehyde. There is no significant residue; H₂O₂ breaks down into water and oxygen. Electronics and sensors are typically safe as long as they are compatible with humid environments. 

Consistent incubator or hypoxia workstation decontamination is key to protecting cell cultures, reducing experimental variability, and avoiding costly delays. While manual cleaning and occasional high-temperature sterilization are important, they often lack the frequency or coverage needed to keep up with everyday lab demands. This is where tools like MycoFog add real value.

By delivering targeted, broad-spectrum decontamination between experiments, MycoFog bridges the gap between sporadic deep cleans. It significantly lowers microbial load on interior surfaces without taking the incubator offline for long periods. 

In fast-paced lab environments, effective decontamination must be thorough, efficient, and practical. A combination of smart manual practices (regular cleaning of spills, scheduled deep cleans) plus surface-wide solutions like hydrogen peroxide fogging will keep your CO₂ incubators and hypoxia workstations consistently cleaner with far less effort. The result is greater confidence in experimental results and fewer disruptions from contamination issues. Adopting convenient tools like MycoFog for routine use means you’re always a step ahead of contaminants, rather than reacting after the damage is done.

Contact us to learn how our solutions can elevate your research.

MycoFog Inc (2025). Use of Chemical Indicators to Validate the MycoFog® Biodecontamination System Cycle (White Paper) 

Mizuno M. et al. (2025). Cleaning methods for biosafety cabinet to eliminate residual mycoplasmas, viruses, and endotoxins after changeover. Regenerative Therapy

MycoFog (2024). MycoFog™ Efficacy & Safety Validation (Internal Validation Report v2.5) 

Meleties M. et.al.  (2023). Vaporized Hydrogen Peroxide Sterilization in the Production of Protein Therapeutics: Journal of Pharmaceutical Sciences

Borges E.D. et al.  (2019). Microbial contamination in assisted reproductive technology: source, prevalence, and cost. Journal of Assisted Reproduction and Genetics

Abatenh E. et al. (2018). Contamination in a Microbiological Laboratory. International Journal of Research Studies in Biosciences (IJRSB) 

Author: Justin Croft, July 2025