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Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples.

ABSTRACT: Cyclospora cayetanensis, a coccidian apicomplexan parasite, causes large outbreaks of foodborne diarrheal disease globally. Tracking the source of C. cayetanensis oocyst contamination in food items is essential to reduce, even prevent outbreaks. We previously showed that a genotyping method based on mitochondrial single nucleotide polymorphism (SNP) profiles had discriminatory power in classifying C. cayetanensis clinical isolates. In food specimens, low level contamination by oocysts and difficulties in DNA extraction present significant challenges in genotyping method development. Here, we report the development of a highly sensitive, custom-designed, targeted sequencing method based on the Illumina AmpliSeq platform; our method was capable of consistently generating near-complete mitochondrial genome sequences of C. cayetanensis from foods with low levels of contamination. To simulate environmentally observed contamination levels in foods, we seeded various food matrices, such as fresh produce and prepared dishes, with known quantities of oocysts, and isolated genomic DNA from washed food samples. Using the Ampliseq Targeted Sequencing method, we obtained near-complete mitochondrial genome sequences of C. cayetanensis from food samples seeded with as low as five to ten oocysts and used the data in downstream analysis. The flexibility of the AmpliSeq platform could potentially allow for more genomic targets to be added to achieve higher discriminatory power. This level of sensitivity in capturing high resolution genome data from contaminated food samples is a critical milestone towards the potential development of a comprehensive genotyping method for C. cayetanensis.

SUBMITTER: Cinar HN

PROVIDER: S-EPMC9676520 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples.

Cinar Hediye Nese HN Gopinath Gopal G Almería Sonia S Njoroge Joyce M JM Murphy Helen R HR da Silva Alexandre A

Heliyon 20221113 11

Cyclospora cayetanensis, a coccidian apicomplexan parasite, causes large outbreaks of foodborne diarrheal disease globally. Tracking the source of C. cayetanensis oocyst contamination in food items is essential to reduce, even prevent outbreaks. We previously showed that a genotyping method based on mitochondrial single nucleotide polymorphism (SNP) profiles had discriminatory power in classifying C. cayetanensis clinical isolates. In food specimens, low level contamination ...[more]

PMID: 36419667

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Project description:BackgroundCyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis. The apicoplast of C. cayetanensis, a relict non-photosynthetic plastid with an independent genome, provides an attractive target to discover sequence polymorphisms useful as genetic markers for detection and trace back analysis of the parasite. Distinct differences in the apicoplast genomes of C. cayetanensis could be useful in designing advanced molecular methods for rapid detection and, subtyping and geographical source attribution, which would aid outbreak investigations and surveillance studies.MethodsTo obtain the genome sequence of the C. cayetanensis apicoplast, we sequenced the C. cayetanensis genomic DNA extracted from clinical stool samples, assembled and annotated a 34,146 bp-long circular sequence, and used this sequence as a reference genome in this study. We compared the genome and the predicted proteome to the data available from other apicomplexan parasites. To initialize the search for genetic markers, we mapped the raw sequence reads from an additional 11 distinct clinical stool samples originating from Nepal, New York, Texas, and Indonesia to the apicoplast reference genome.ResultsWe identified several high quality single nucleotide polymorphisms (SNPs) and small insertion/deletions spanning the apicoplast genome supported by extensive sequencing reads data, and a 30 bp sequence repeat at the terminal spacer region in a Nepalese sample. The predicted proteome consists of 29 core apicomplexan peptides found in most of the apicomplexans. Cluster analysis of these C. cayetanensis apicoplast genomes revealed a familiar pattern of tight grouping with Eimeria and Toxoplasma, separated from distant species such as Plasmodium and Babesia.ConclusionsSNPs and sequence repeats identified in this study may be useful as genetic markers for identification and differentiation of C. cayetanensis isolates found and could facilitate outbreak investigations.

Dataset Information

Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples.

Publications

Targeted next generation sequencing of <i>Cyclospora cayetanensis</i> mitochondrial genomes from seeded fresh produce and other seeded food samples.

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