An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

Jenny G Maloney; Nadja S George; Aleksey Molokin; Monica Santin

doi:10.1007/978-1-0716-1681-9_5

An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

Methods Mol Biol. 2021:2369:67-82. doi: 10.1007/978-1-0716-1681-9_5.

Authors

Jenny G Maloney¹, Nadja S George², Aleksey Molokin², Monica Santin²

Affiliations

¹ United States Department of Agriculture, Agricultural Research Service, Environmental Microbial Food Safety Laboratory, Beltsville, MD, USA. jenny.maloney@usda.gov.
² United States Department of Agriculture, Agricultural Research Service, Environmental Microbial Food Safety Laboratory, Beltsville, MD, USA.

PMID: 34313984
DOI: 10.1007/978-1-0716-1681-9_5

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.

Keywords: Blastocystis; Illumina Miseq; Mixed infections; NGS; Next-generation amplicon sequencing; Parasites; Protist; Subtypes.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Blastocystis* / genetics
Coinfection*
Genes, rRNA
High-Throughput Nucleotide Sequencing
Parasitic Diseases*