Contamination of cell cultures is easily the most common problem encountered in cell culture laboratories, sometimes with very serious consequences.  Cell culture contaminants can be divided into two main categories, chemical contaminants such as impurities in media, sera, and water, endotoxins, plasticizers, and detergents, and biological contaminants such as bacteria, molds, yeasts, viruses, mycoplasma, as well as cross contamination by other cell lines.  While it is impossible to eliminate contamination entirely, it is possible to reduce its frequency and seriousness by gaining a thorough understanding of their sources and by following good aseptic technique.

This section provides an overview of major types of biological contamination:

Cross-Contamination

While not as common as microbial contamination, extensive cross-contamination of many cell lines with HeLa and other fast growing cell lines is a clearly-established problem with serious consequences.  Obtaining cell lines from reputable cell banks, periodically checking the characteristics of the cell lines, and practicing good aseptic technique are practices that will help you avoid cross-contamination.  DNA fingerprinting, karyotype analysis, and isotype analysis can confirm the presence or absence of cross-contamination in your cell cultures.

Using antibiotics

Antibiotics should not be used routinely in cell culture, because their continuous use encourages the development of antibiotic resistant strains and allows low-level contamination to persist, which can develop into full-scale contamination once the antibiotic is removed from media, and may hide mycoplasma infections and other cryptic contaminants.  Further, some antibiotics might cross react with the cells and interfere with the cellular processes under investigation.  

Antibiotics should only be used as a last resort and only for short term applications, and they should be removed from the culture as soon as possible.  If they are used in the long term, antibiotic-free cultures should be maintained in parallel as a control for cryptic infections.