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Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions

BACKGROUND: Cyclospora 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 cyclosporias...

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Autores principales: Cinar, Hediye Nese, Qvarnstrom, Yvonne, Wei-Pridgeon, Yuping, Li, Wen, Nascimento, Fernanda S., Arrowood, Michael J., Murphy, Helen R., Jang, AhYoung, Kim, Eunje, Kim, RaeYoung, da Silva, Alexandre, Gopinath, Gopal R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129617/
https://www.ncbi.nlm.nih.gov/pubmed/27899155
http://dx.doi.org/10.1186/s13071-016-1896-4
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author Cinar, Hediye Nese
Qvarnstrom, Yvonne
Wei-Pridgeon, Yuping
Li, Wen
Nascimento, Fernanda S.
Arrowood, Michael J.
Murphy, Helen R.
Jang, AhYoung
Kim, Eunje
Kim, RaeYoung
da Silva, Alexandre
Gopinath, Gopal R.
author_facet Cinar, Hediye Nese
Qvarnstrom, Yvonne
Wei-Pridgeon, Yuping
Li, Wen
Nascimento, Fernanda S.
Arrowood, Michael J.
Murphy, Helen R.
Jang, AhYoung
Kim, Eunje
Kim, RaeYoung
da Silva, Alexandre
Gopinath, Gopal R.
author_sort Cinar, Hediye Nese
collection PubMed
description BACKGROUND: Cyclospora 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. METHODS: To 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. RESULTS: We 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. CONCLUSIONS: SNPs 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1896-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-51296172016-12-12 Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions Cinar, Hediye Nese Qvarnstrom, Yvonne Wei-Pridgeon, Yuping Li, Wen Nascimento, Fernanda S. Arrowood, Michael J. Murphy, Helen R. Jang, AhYoung Kim, Eunje Kim, RaeYoung da Silva, Alexandre Gopinath, Gopal R. Parasit Vectors Research BACKGROUND: Cyclospora 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. METHODS: To 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. RESULTS: We 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. CONCLUSIONS: SNPs 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-016-1896-4) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-29 /pmc/articles/PMC5129617/ /pubmed/27899155 http://dx.doi.org/10.1186/s13071-016-1896-4 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cinar, Hediye Nese
Qvarnstrom, Yvonne
Wei-Pridgeon, Yuping
Li, Wen
Nascimento, Fernanda S.
Arrowood, Michael J.
Murphy, Helen R.
Jang, AhYoung
Kim, Eunje
Kim, RaeYoung
da Silva, Alexandre
Gopinath, Gopal R.
Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title_full Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title_fullStr Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title_full_unstemmed Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title_short Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
title_sort comparative sequence analysis of cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129617/
https://www.ncbi.nlm.nih.gov/pubmed/27899155
http://dx.doi.org/10.1186/s13071-016-1896-4
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