Jul 11, 2014

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive

BioRxiv : the Preprint Server for Biology
Anthony O Olarerin-George, John B Hogenesch

Abstract

Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Because they are small, they can escape filtration in culture media. Because they lack cell walls, they are resistant to commonly used antibiotics. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series (or projects) in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥ 100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. Interestingly, series using poly(A)-selection, which should bias against mycoplasma detection, had comparable contamination rates as non-poly(A)-selected series. We also examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes ( P < 0.001) were significantly associated with mycoplasma-mapped read counts. Lastly, to estimate the potential...Continue Reading

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Mentioned in this Paper

Study
Research
Filtration
Mycoplasma
Antibiotic throat preparations
Antifungal Antibiotics, Topical
Ncbi Taxonomy
Cell Culture Techniques
Nutrients
Mycoplasmatales (bacterium)

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