Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing
Abstract Background 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...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | Parasites & Vectors |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13071-020-3997-3 |
| _version_ | 1818254045572235264 |
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| author | Hediye Nese Cinar Gopal Gopinath Helen R. Murphy Sonia Almeria Mauricio Durigan Dajung Choi AhYoung Jang Eunje Kim RaeYoung Kim Seonju Choi Jeongu Lee Yurim Shin Jieon Lee Yvonne Qvarnstrom Theresa K. Benedict Henry S. Bishop Alexandre da Silva |
| author_facet | Hediye Nese Cinar Gopal Gopinath Helen R. Murphy Sonia Almeria Mauricio Durigan Dajung Choi AhYoung Jang Eunje Kim RaeYoung Kim Seonju Choi Jeongu Lee Yurim Shin Jieon Lee Yvonne Qvarnstrom Theresa K. Benedict Henry S. Bishop Alexandre da Silva |
| author_sort | Hediye Nese Cinar |
| collection | DOAJ |
| description | Abstract Background 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. Methods 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. Results This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study. Conclusions Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source. |
| first_indexed | 2024-12-12T16:49:43Z |
| format | Article |
| id | doaj.art-15c8655047f6488898f6627c9754e497 |
| institution | Directory Open Access Journal |
| issn | 1756-3305 |
| language | English |
| last_indexed | 2024-12-12T16:49:43Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Parasites & Vectors |
| spelling | doaj.art-15c8655047f6488898f6627c9754e4972022-12-22T00:18:23ZengBMCParasites & Vectors1756-33052020-03-0113111210.1186/s13071-020-3997-3Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencingHediye Nese Cinar0Gopal Gopinath1Helen R. Murphy2Sonia Almeria3Mauricio Durigan4Dajung Choi5AhYoung Jang6Eunje Kim7RaeYoung Kim8Seonju Choi9Jeongu Lee10Yurim Shin11Jieon Lee12Yvonne Qvarnstrom13Theresa K. Benedict14Henry S. Bishop15Alexandre da Silva16Center for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and PreventionDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and PreventionDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and PreventionCenter for Food Safety and Applied Nutrition, U.S. Food and Drug AdministrationAbstract Background 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. Methods 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. Results This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study. Conclusions Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.http://link.springer.com/article/10.1186/s13071-020-3997-3Cyclospora cayetanensisMitochondria genomeGenotypingNext-generation sequencing |
| spellingShingle | Hediye Nese Cinar Gopal Gopinath Helen R. Murphy Sonia Almeria Mauricio Durigan Dajung Choi AhYoung Jang Eunje Kim RaeYoung Kim Seonju Choi Jeongu Lee Yurim Shin Jieon Lee Yvonne Qvarnstrom Theresa K. Benedict Henry S. Bishop Alexandre da Silva Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing Parasites & Vectors Cyclospora cayetanensis Mitochondria genome Genotyping Next-generation sequencing |
| title | Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing |
| title_full | Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing |
| title_fullStr | Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing |
| title_full_unstemmed | Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing |
| title_short | Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing |
| title_sort | molecular typing of cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next generation sequencing |
| topic | Cyclospora cayetanensis Mitochondria genome Genotyping Next-generation sequencing |
| url | http://link.springer.com/article/10.1186/s13071-020-3997-3 |
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