Abstract
Parasite mixed infections remain a relatively unexplored field in part due to the difficulties of unraveling complex mixtures of parasite DNA using classical methods of sequencing. Next-generation amplicon sequencing (NGS) is a powerful tool for exploring mixed infections of multiple genetic variants of the same parasite in clinical, environmental (water or soil), or food samples. Here, we provide a method for NGS-based detection of mixed parasite infections which uses the Blastocystis SSU rRNA gene as an example and includes steps for parasite concentration, DNA extraction, sequencing library preparation, and bioinformatic analysis.
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Acknowledgments
This work was supported by USDA-ARS Project No: 8042-32000-100-00-D.
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Maloney, J.G., George, N.S., Molokin, A., Santin, M. (2021). An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example. In: de Pablos, L.M., Sotillo, J. (eds) Parasite Genomics. Methods in Molecular Biology, vol 2369. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1681-9_5
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