Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » Research » Publications at this Location » Publication #377107
Research Project: Zoonotic Parasites Affecting Food Animals, Food Safety, and Public Health

Location: Environmental Microbial & Food Safety Laboratory

Title: An Illumina MiSeq based amplicon sequencing method for the detection of mixed parasite infections using the Blastocystis SSU rRNA gene as an example

Author
item Maloney, Jenny
item George, Nadja
item Molokin, Aleksey
item Santin-Duran, Monica

Submitted to: Methods in Molecular Biology
Publication Type: Book / Chapter
Publication Acceptance Date: 4/18/2021
Publication Date: 8/28/2021
Citation: 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. Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-1681-9_5.
DOI: https://doi.org/10.1007/978-1-0716-1681-9_5

Interpretive Summary: Parasite mixed infections are the presence of multiple genetic variants of the same parasite in a single sample. Mixed infections are difficult to study partly because of the technical limitations of classical sequencing methods leaving the field of mixed infections largely unexplored. Next generation amplicon sequencing (NGS) is a powerful tool for exploring mixed infections in clinical, environmental (water or soil), or food samples. Here, we provide a method for NGS based detection of mixed parasite infections. This method uses the Blastocystis SSU rRNA gene as an example and includes steps for parasite concentration, DNA extraction, sequencing library preparation, and bioinformatic analysis. This method is beneficial to scientists, regulators, and industry professionals interested in understanding the role mixed infections in parasite transmission, sources of contamination, host specificity, and pathogenicity.

Technical 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.