Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing

Parasites & Vectors
H N CinarAlexandre J da Silva

Abstract

Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing. We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline. This approach allowed us to sequence complete mitochondrial genomes from the ...Continue Reading

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Citations

Oct 2, 2021·PloS One·Matthew S TuckerBenjamin M Rosenthal

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Datasets Mentioned

BETA
KP231180
MG831586
MG831587
MG831588
PRJNA357477

Methods Mentioned

BETA
PCR
fluorescence microscopy
electrophoresis
amplicon sequencing

Software Mentioned

MAFFT
GenomeTrakr
MEGA7
CFSAN SNP - Pipeline
Geneious
Muscle
ClustalW
CLC workbench
MEGA
CLC Genome Workbench Toolkit

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