How to Prevent Contamination in the Lab

Everyone’s had their run-ins with contamination in the lab. There are two main types of contamination—biological (bacteria or fungi) and chemical—both of which can easily ruin your day, making cell cultures unusable and skewing your experimental results. Below, we’ll review many of the ways you can avoid spreading contamination throughout your lab. 

Sterilize your equipment

The most common preventative measures against contamination in the lab is sterilization. Autoclaving, which involves applying intense heat and pressure, is used in most labs to clean equipment and consumables. When autoclaving, don’t forget to use containers that are specialized for the elevated heat and pressure of autoclave cycles; polypropylene is usually a suitable material for autoclave bins, while Pyrex glass and metal can also be autoclaved without breaking or warping. For all containers, remember to apply labels to that won’t fail under the extreme temperatures and pressure of the cycle you’re using, and that are appropriate for the surface of your containers (applying a thermal-transfer printout will also give you the greatest resistance against smudging caused by heat).

Sterilization should occur frequently at the bench as well. A 70% solution of ethanol, sprayed over your bench or inside your biosafety cabinet, will remove almost all bacterial and fungal contaminants, while using a diluted concentration of bleach will disinfect just as effectively. When cleaning consumables and equipment prior to placing them in a biosafety cabinet, make sure you give a few minutes to off-gas them, as ethanol can still linger in the air. Here, chemical-resistant labels will ensure they stay affixed when coated with the sterilizing agent and using a thermal-transfer printout will resist the smudging that comes with exposure to ethanol and bleach.

Check the quality of your water and air

Consistently checking the quality of the air and water in your lab can save you from unwanted hassles later on, when contamination begins to creep into your cultures. Systems like XiltriX can keep track of possible contaminants in the air of your lab and incubators, alerting you instantly though a cloud-based system whenever something unusual appears. For baths and incubators, using autoclaved water is necessary, and it’s worth changing at least once a week. There are several antibiotic solutions that can be applied as well, such as SigmaClean®,which will prevent the growth of bacteria and fungi. In cases where the water is suspected of contamination, especially mycoplasma, there are fluorescence-based or polymerase chain reaction (PCR)-based kits that can detect the contaminant. Mycoplasma is especially difficult to catch, since it’s hard to detect by eye, even using a microscope. Frequently testing samples of all your cell lines, even if they don’t look contaminated, could save you a lot of hassle, particularly when your cell-based experiments are giving you results that don’t make sense compared with your old findings.

For IVF labs, volatile organic compounds (VOCs) are also considered airborne contaminants. VOCs, like aldehydes and alcohols, can come from a variety of sources, including certain kinds of furniture, plasticware that hasn’t been off-gassed, and even perfume. These VOCs can have a particularly negative effect on birth rates, so making sure they’re eliminated is important for any IVF lab. Reducing VOCs could also theoretically help standardize experiments with any type of cell that is as sensitive to them as human eggs, sperm, and embryos are.

Consider antibiotics

Not everyone is on board using antibiotics for cell culture. Some antibiotics, like penicillin/streptomycin (PenStrep), induce genome-wide changes in gene expression and regulation.¹ Because of resistance, they also don’t guarantee that your cultures will remain contaminant-free. However, many still rely on antibiotics to ensure the purity of their cultures, yielding consistent results regardless of their off-target effects. Remember, when using antibiotics, it’s always a good idea to test the effect of the antibiotics on your experimental output to see if they inadvertently affect the system you’re working on.

Organize your lab

No matter how many methods you use to avoid contamination, nothing will work consistently unless you plan ahead. When preparing for an experiment, it’s always important to set aside everything that must be decontaminated beforehand; this ensures that nothing needs to be cleaned last-minute, risking both contamination and ruining the timing of your assay. Organizing your stocks of bottles and other solutions also prevents dust buildup, which can spread bacterial and fungal cells to your samples. A great way to keep everything organized and scheduled is using a laboratory information management system (LIMS), which will help keep track of your inventory and schedule decontamination protocols. To get the most out of your LIMS, it’s key to identify important samples and reagents with barcode or radio-frequency identification (RFID) labels, as this will make it easy to know what should and shouldn’t be kept on your bench, in addition to managing the things you need prior to working under sterile conditions. For PCR or any other technique that’s sensitive to chemical contaminants, it’s worth setting aside a set of dedicated pipettes, in a clean and safe location, for that specific technique.  

Use common sense measures

Don’t forget to use proper protective equipment, especially when you’re working in sterile conditions. It’s not just to protect yourself from your own samples and chemicals; it’s also to protect your cells and samples from you! Wearing gloves, a lab coat, lab glasses (when appropriate), and hair ties will avoid particles, like keratin and bacteria from your skin, falling into your tubes, vials, and plates. Also, clean up when you’re done! Traces of cell lines left on the bench can cross-contaminate your samples, as can chemicals, such as formaldehyde, which once wrecked the quantitative PCR results of a certain lab that will not be named here. It’s also unbelievably aggravating—and potentially dangerous—when someone leaves unknown powder around the measuring scale, which can contaminate the lab’s air supply.  

Keeping your lab clean can be difficult, especially in large labs performing multiple assays simultaneously. However, if you can organize your workflow and inventory, in addition to implementing the basic tenets of sterile technique, you stand a good chance of keeping your cells and reagents free of contaminants, reducing the effort, time, and money lost due to tainted supplies and failed experiments.