Contamination is a tough issue that concerns almost every clinical laboratory and research lab. LAMP is a simple molecular test, requiring little hands-on work and some expertise, but that doesn’t mean contamination doesn’t exist there either! As a matter of fact, in low tech testing settings and especially when using LAMP, contamination must be taken extremely seriously. An ounce of prevention early can save you a ton of trouble later on! In this article, we’ll go over how such contamination can arise, what to look out for and how to prevent it in testing setups and also what to do once you notice you have some contamination problems.
LAMP, just like PCR and other nucleic acid amplification methods, works by making more copies of a specific segment of DNA based on a template of the same nucleic acid sequence. Billions of these copies are generated in a single, tiny reaction, leading to a fluorescent or colorful result that we can interpret. These copies of an original template that are generated through amplification are called amplicons, they’re small DNA molecules, chemically exceptionally stable, much more than the RNA of a virus for example. In a true positive test, the DNA amplification kicks off based on the presence of a template sequence in the sample, the viral RNA. If, for some reason, a small amount of amplicons from previous finished reactions gets into the reaction tubes from whatever source, you will get a false positive reaction that wasn’t triggered by the presence of a template sequence from the virus, but from an amplicon. In this case, you essentially can’t separate a true positive from a false positive and your results become unreliable and useless.
While DNA amplicons don’t have legs and can’t jump into reactions that you are preparing on a bench, they can linger on surfaces, be present in reagents, cling to pipettes and your gloves and most of all be in the air in the form of an aerosol. There’s several kinds of danger happening here and you want to make sure you always think about how risky any given action or behavior is when it comes down to contamination, you want to be taking sensible preventative measures and avoid the worst practices that make running into a problem only a matter of time.
A small, low tech LAMP lab and a high-throughput lab have lots of differences. When it comes to contamination though, key things have to be observed even in the most basic testing setups. We’ve established that DNA being generated in these LAMP tests can act as a template for further false amplification, and that’s the key source of contamination. The more reactions you run, the higher the risk is, essentially. Luckily, there’s a few things you can do to substantially decrease the risk.
If you see that your negative control has turned positive, contamination is a certainty. Higher than normal positive rates in recent samples that are negative upon retesting in a different lab are also a clear sign that contamination is present. A contamination problem can be building up for weeks before tipping over into noticeable symptoms, and even then it takes a keen eye and making connections to realize that contamination is what you’re dealing with.
Once you do spot a problem, don’t put it off. You want to find out the following things as soon as possible:
Getting rid of a present contamination is much harder than taking preventative measures. But it’s possible. A key item is to find the source of contamination, and get rid of it. Then, a 10% bleach solution becomes your best friend to solve the problem.
Work in a well ventilated environment and wear a mask and a lab coat – bleach is nasty, the fumes are irritating and the droplets can bleach your clothes. Avoid bleaching aluminium surfaces.
For maximum effectiveness, mix the bleach fresh before every use and leave the bleach on surfaces for 10 minutes. Wipe down your reagents, door handles, pipettes and machines with bleach on tissue paper. If contamination is coming from the pipettes, find out if it’s possible to disassemble the pipettes (from the documentation or by contacting the manufacturer) and if so, soak the barrels of the pipettes in bleach overnight. Ideally, incorporate a bleach-cleaning step into your daily or weekly routine, depending on the severity of the problem. Persistence is key when getting rid of contamination.