Draft Hybrid Genome Assembly of a Canadian Cyclospora cayetanensis Isolate

Yanta, Christine A.; Pollo, Stephen M. J.; Barta, John R.; Reiling, Sarah J.; Wasmuth, James D.; Guy, Rebecca A.

doi:10.1128/mra.01072-21

Cited by 5 publications

(4 citation statements)

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“…In order to improve the genotyping ability of the TADS scheme, novel markers that display a greater sequencing success rate and higher entropy should replace the least sensitive and discriminatory markers, Nu_CDS1, Nu_CDS2, and Nu_CDS4. Research should focus on identifying new markers through comparative analyses of whole genome sequences available to date, including the newly published hybrid assembly of a Canadian C. cayetanensis isolate [24] and four other Canadian genomes generated (unpublished). Additionally, comparative analyses should focus on finding discriminatory markers that further differentiate the isolates that are grouping into persistent clusters observed over several years.…”

Section: Discussionmentioning

confidence: 99%

Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations

et al. 2022

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Cyclospora cayetanensis is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the potential sources of infection have relied solely on epidemiological data. To supplement the epidemiological data with genetic information, we genotyped 169 Canadian cyclosporiasis cases from stool specimens collected from 2010 to 2021 using an existing eight-marker targeted amplicon deep (TADS) scheme specific to C. cayetanensis as previously described by the US Centers for Disease Control and Prevention (CDC). This is the first study to genotype Canadian Cyclospora cayetanensis isolates, and it focuses on evaluating the genotyping performance and genetic clustering. Genotyping information was successfully collected with at least part of one of the markers in the TADS assay for 97.9% of specimens, and 81.1% of cyclosporiasis cases met the minimum requirements to genetically cluster into 20 groups. The performance of the scheme suggests that examining cyclosporiasis cases genetically will be a valuable tool for supplementing epidemiological outbreak investigations and to minimize further infections. Further research is required to expand the number of discriminatory markers to improve genetic clustering.

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Section: Discussionmentioning

confidence: 99%

Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations

et al. 2022

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“…Despite such limitations, researchers studying limited supplies of C. cayetanensis have made commendable progress characterizing strains, genomes, and advancing detection. Several C. cayetanensis draft genomes have been characterized and published [ 3 , 4 , 5 , 6 , 7 , 8 , 9 ] and molecular typing efforts have given rise to powerful genotyping tools [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ] for epidemiological analysis, such as outbreak tracing. As described below, methods such as these and others are now being used to detect C. cayetanensis from various sources of infection.…”

Section: The Scarcity Of Oocysts Slows Research Progressmentioning

confidence: 99%

“…The first published draft genome sequence for C. cayetanensis , reported by Qvarnstrom et al (2015) [ 4 ] provided an assembly consisting of ~44 Mb, including a full-length mitochondrial genome of ~6.3 Kb and an apicoplast genome of ~24 Kb. Since then, advances in Next Generation Sequencing (NGS) technologies and bioinformatics have fostered additional draft genome assemblies, complete mitochondrial and apicoplast genomes of C. cayetanensis [ 3 , 5 , 6 , 7 , 8 , 9 , 10 , 57 ]. Several other studies have made strides on C. cayetanensis genomics and diagnostics, focusing on genotyping assays for use with stool and produce samples and molecular techniques to improve detection and sequencing (also cited above).…”

Section: What Can We Learn From Such Surrogates?mentioning

confidence: 99%

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

et al. 2022

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Cyclospora cayetanensis is an enigmatic human parasite that sickens thousands of people worldwide. The scarcity of research material and lack of any animal model or cell culture system slows research, denying the produce industry, epidemiologists, and regulatory agencies of tools that might aid diagnosis, risk assessment, and risk abatement. Fortunately, related species offer a strong foundation when used as surrogates to study parasites of this type. Species of Eimeria lend themselves especially well as surrogates for C. cayetanensis. Those Eimeria that infect poultry can be produced in abundance, share many biological features with Cyclospora, pose no risk to the health of researchers, and can be studied in their natural hosts. Here, we overview the actual and potential uses of such surrogates to advance understanding of C. cayetanensis biology, diagnostics, control, and genomics, focusing on opportunities to improve prevention, surveillance, risk assessment, and risk reduction. Studying Eimeria surrogates accelerates progress, closing important research gaps and refining promising tools for producers and food safety regulators to monitor and ameliorate the food safety risks imposed by this emerging, enigmatic parasite.

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“…There are no known methods of propagating C. cayetanensis in the laboratory, and it is time-consuming and difficult to isolate oocysts from clinical specimens; thus, whole genome sequencing is not a practical option for determining genetic linkages among specimens [12,13]. The U.S. Centers for Disease Control and Prevention (CDC) has been implementing a multi-locus sequence typing (MLST) scheme to genetically cluster C. cayetanensis clinical fecal specimens to supplement epidemiologic information when investigating outbreaks [14].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for Genotyping Cyclospora cayetanensis

Leonard,

Mammel,

Almeria

et al. 2024

Microorganisms

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Cyclospora cayetanensis is a foodborne parasite that causes cyclosporiasis, an enteric illness in humans. Genotyping methods are used to genetically discriminate between specimens from cyclosporiasis cases and can complement source attribution investigations if the method is sufficiently sensitive for application to food items. A very sensitive targeted amplicon sequencing (TAS) assay for genotyping C. cayetanensis encompassing 52 loci was recently designed. In this study, we analyzed 66 genetically diverse clinical specimens to assess the change in phylogenetic resolution between the TAS assay and a currently employed eight-marker scheme. Of the 52 markers, ≥50 were successfully haplotyped for all specimens, and these results were used to generate a hierarchical cluster dendrogram. Using a previously described statistical approach to dissect hierarchical trees, the 66 specimens resolved into 24 and 27 distinct genetic clusters for the TAS and an 8-loci scheme, respectively. Although the specimen composition of 15 clusters was identical, there were substantial differences between the two dendrograms, highlighting the importance of both inclusion of additional genome coverage and choice of loci to target for genotyping. To evaluate the ability to genetically link contaminated food samples with clinical specimens, C. cayetanensis was genotyped from DNA extracted from raspberries inoculated with fecal specimens. The contaminated raspberry samples were assigned to clusters with the corresponding clinical specimen, demonstrating the utility of the TAS assay for traceback efforts.

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Draft Hybrid Genome Assembly of a Canadian Cyclospora cayetanensis Isolate

Cited by 5 publications

References 10 publications

Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations

Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for Genotyping Cyclospora cayetanensis

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