The Experts below are selected from a list of 585 Experts worldwide ranked by ideXlab platform
Joel Barratt - One of the best experts on this subject based on the ideXlab platform.
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investigation of us cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved cyclospora genotyping system against 2019 Cyclosporiasis outbreak clusters
Epidemiology and Infection, 2021Co-Authors: Katelyn Houghton, Joel Barratt, Travis Richins, Anne Straily, Ryan Threlkel, Betelehem Bera, Jayne Kenneally, Brooke ClemonsAbstract:Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US Cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of Cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined Cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.
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evaluation of an ensemble based distance statistic for clustering mlst datasets using epidemiologically defined clusters of Cyclosporiasis
Epidemiology and Infection, 2020Co-Authors: Fernanda S Nascimento, Katelyn Houghton, Joel Barratt, Shannon M Casillas, Mateusz M Plucinski, Julia Kelley, Carolyne BennettAbstract:Outbreaks of Cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of Cyclosporiasis.
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development of a workflow for identification of nuclear genotyping markers for cyclospora cayetanensis
Parasite, 2020Co-Authors: Katelyn Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.
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Development of a workflow for identification of nuclear genotyping markers for
'EDP Sciences', 2020Co-Authors: Katelyn A. Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes
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mitochondrial junction region as genotyping marker for cyclospora cayetanensis
Emerging Infectious Diseases, 2019Co-Authors: Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Eldin Talundzic, John R Barta, Julia Whale, Jessica N Hofstetter, Shannon Casillas, Yvonne QvarnstromAbstract:Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of Cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during Cyclosporiasis outbreak investigations.
Longxian Zhang - One of the best experts on this subject based on the ideXlab platform.
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advances in Cyclosporiasis diagnosis and therapeutic intervention
Frontiers in Cellular and Infection Microbiology, 2020Co-Authors: Zhaohui Cui, Longxian ZhangAbstract:Cyclosporiasis is caused by the coccidian parasite Cyclospora cayetanensis and is associated with large and complex food-borne outbreaks worldwide. Associated symptoms include severe watery diarrhea, particularly in infants, and immune dysfunction. With the globalization of human food supply, the occurrence of Cyclosporiasis has been increasing in both food growing and importing countries. As well as being a burden on the health of individual humans, Cyclosporiasis is a global public health concern. Currently, no vaccine is available but early detection and treatment could result in a favorable clinical outcome. Clinical diagnosis is based on cardinal clinical symptoms and conventional laboratory methods, which usually involve microscopic examination of wet smears, staining tests, fluorescence microscopy, serological testing, or DNA testing for oocysts in the stool. Detection in the vehicle of infection, which can be fresh produce, water, or soil is helpful for case-linkage and source-tracking during Cyclosporiasis outbreaks. Treatment with trimethoprim-sulfamethoxazole (TMP-SMX) can evidently cure C. cayetanensis infection. However, TMP-SMX is not suitable for patients having sulfonamide intolerance. In such case ciprofloxacin, although less effective than TMP-SMX, is a good option. Another drug of choice is nitazoxanide that can be used in the cases of sulfonamide intolerance and ciprofloxacin resistance. More epidemiological research investigating Cyclosporiasis in humans should be conducted worldwide, to achieve a better understanding of its characteristics in this regard. It is also necessary to establish in vitro and/or in vivo protocols for cultivating C. cayetanensis, to facilitate the development of rapid, convenient, precise, and economical detection methods for diagnosis, as well as more effective tracing methods. This review focuses on the advances in clinical features, diagnosis, and therapeutic intervention of Cyclosporiasis.
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mitochondrial genome sequence variation as a useful marker for assessing genetic heterogeneity among cyclospora cayetanensis isolates and source tracking
Parasites & Vectors, 2019Co-Authors: Yaqiong Guo, Ynes R. Ortega, Longxian Zhang, Yuanfei Wang, Xiaolan Wang, Yaoyu FengAbstract:Background Cyclospora cayetanensis is an important enteric pathogen, causing diarrhea and food-borne Cyclosporiasis outbreaks. For effective outbreak identification and investigation, it is essential to rapidly assess the genetic heterogeneity of C. cayetanensis specimens from cluster cases and identify the likely occurrence of outbreaks.
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comparative genomics reveals cyclospora cayetanensis possesses coccidia like metabolism and invasion components but unique surface antigens
BMC Genomics, 2016Co-Authors: Kevin Tang, Dawn M. Roellig, Michael Frace, Shiyou Liu, Michael J Arrowood, Huajun Zheng, Delynn M Moss, Longxian ZhangAbstract:Background Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of Cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of C. cayetanensis and inferred its metabolism and invasion components based on comparative genomic analysis.
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Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes
Parasites & vectors, 2015Co-Authors: Kevin Tang, Longxian Zhang, Yaoyu Feng, Yaqiong Guo, Lori A. Rowe, Dawn M. Roellig, Michael Frace, Shiyou Liu, Lihua XiaoAbstract:Background Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of Cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.
Ynes R. Ortega - One of the best experts on this subject based on the ideXlab platform.
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mitochondrial genome sequence variation as a useful marker for assessing genetic heterogeneity among cyclospora cayetanensis isolates and source tracking
Parasites & Vectors, 2019Co-Authors: Yaqiong Guo, Ynes R. Ortega, Longxian Zhang, Yuanfei Wang, Xiaolan Wang, Yaoyu FengAbstract:Background Cyclospora cayetanensis is an important enteric pathogen, causing diarrhea and food-borne Cyclosporiasis outbreaks. For effective outbreak identification and investigation, it is essential to rapidly assess the genetic heterogeneity of C. cayetanensis specimens from cluster cases and identify the likely occurrence of outbreaks.
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documented foodborne outbreaks of infection with cyclospora cayetanensis
2017Co-Authors: Ynes R. Ortega, Lucy J RobertsonAbstract:Since the characterization of Cyclospora in 1992, foodborne outbreaks have been reported with increasing frequency worldwide. The developed world has often experienced outbreaks of Cyclosporiasis that have been associated with consumption of fresh products that have been imported from an endemic location for Cyclospora, particularly Central or South America. In several instances, the products had not produced following Good Agricultural Practice (GAP), Good Hygienic Practice (GHP), Sanitation Standard Operating Procedures (SSOPs), and Good Manufacturing Practice (GMP) (see Chap. 7). As a result of these outbreaks, importation from implicated crops have been denied port of entry and import alerts have been issued.
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assessing and controlling the risk of cyclospora cayetanensis in the food chain
2017Co-Authors: Ynes R. Ortega, Lucy J RobertsonAbstract:In order to minimize the likelihood of foodborne infection with Cyclosporiasis the whole food-chain, from production to consumption, needs to be considered. By using a Hazard Analysis and Critical Control Point (HACCP) approach, it is possible to identify where control measures can be most usefully implemented that will have the greatest effect at reducing risk. Legislation regarding food control in general is in place, and application of the steps of quantitative microbial risk assessment is also possible, but this is a data-demanding tool, and we currently have many gaps in our knowledge on the epidemiology of Cyclospora that need to be filled. Due to the association of Cyclosporiasis outbreaks in North America with specific products imported from countries south in the Americas, particular import restrictions have been implemented. However, such trade restrictions have not been applied in Europe or elsewhere, presumably due to the lack of documented outbreaks. In this chapter we discuss not only the legislation and tools available to reduce the likelihood of foodborne transmission, including information on practical measures that could be implemented at the early stages of the food-chain where it appears that much of the contamination occurs that is subsequently associated with outbreaks, and also in cruise ships where other factors may be important for the infection epidemiology. As well as risk assessment, risk management and risk communication are important aspects for controlling the risk from Cyclospora, and other pathogens, in the food-chain.
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doi:10.4269/ajtmh.13-0535 Copyright © 2014 by The American Society of Tropical Medicine and Hygiene Cyclospora cayetanensis in a Pediatric Hospital in Morelia, México
2016Co-Authors: Guadalupe E. Orozco-mosqueda, O A. Martı́nez-loya, Ynes R. OrtegaAbstract:Abstract. Cyclospora cayetanensis, a coccidian parasite, can cause gastrointestinal illness in humans and is characterized by watery and persistent diarrhea and abdominal pain. Cyclosporiasis has been associated with traveler’s diarrhea. The infection is acquired through food and waterborne transmission, particularly by consumption of contaminated fresh fruits and vegetables. In the present study, stool samples from 8,877 children were examined for ova and parasites at the Pediatric Hospital of Morelia in Michoacán, Mexico, during 2000–2009. Sixty children (0.67%) had Cyclospora in their stools. Diarrhea (45.8%), abdominal pain (39.6%), and vomiting (18.8%) were the most frequent symptoms of cases with Cyclosporiasis. Most of the cases (93.3%) were observed during June–August, the rainy season. In 45 children, Cyclospora was the only parasitic pathogen detected (75%); 15 children were co-infected with commensal, pathogenic, or both groups of parasites. Our findings suggest that C. cayetanensis is endemic to Michoacán and shows characteristically temporal patterns
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Cyclospora cayetanensis in a Pediatric Hospital in Morelia, Mexico
The American journal of tropical medicine and hygiene, 2014Co-Authors: Guadalupe E. Orozco-mosqueda, Orlando A. Martínez-loya, Ynes R. OrtegaAbstract:Cyclospora cayetanensis, a coccidian parasite, can cause gastrointestinal illness in humans and is characterized by watery and persistent diarrhea and abdominal pain. Cyclosporiasis has been associated with traveler's diarrhea. The infection is acquired through food and waterborne transmission, particularly by consumption of contaminated fresh fruits and vegetables. In the present study, stool samples from 8,877 children were examined for ova and parasites at the Pediatric Hospital of Morelia in Michoacán, Mexico, during 2000-2009. Sixty children (0.67%) had Cyclospora in their stools. Diarrhea (45.8%), abdominal pain (39.6%), and vomiting (18.8%) were the most frequent symptoms of cases with Cyclosporiasis. Most of the cases (93.3%) were observed during June-August, the rainy season. In 45 children, Cyclospora was the only parasitic pathogen detected (75%); 15 children were co-infected with commensal, pathogenic, or both groups of parasites. Our findings suggest that C. cayetanensis is endemic to Michoacán and shows characteristically temporal patterns.
Michael J Arrowood - One of the best experts on this subject based on the ideXlab platform.
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development of a workflow for identification of nuclear genotyping markers for cyclospora cayetanensis
Parasite, 2020Co-Authors: Katelyn Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.
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Development of a workflow for identification of nuclear genotyping markers for
'EDP Sciences', 2020Co-Authors: Katelyn A. Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes
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mitochondrial junction region as genotyping marker for cyclospora cayetanensis
Emerging Infectious Diseases, 2019Co-Authors: Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Eldin Talundzic, John R Barta, Julia Whale, Jessica N Hofstetter, Shannon Casillas, Yvonne QvarnstromAbstract:Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of Cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during Cyclosporiasis outbreak investigations.
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genotyping genetically heterogeneous cyclospora cayetanensis infections to complement epidemiological case linkage
Parasitology, 2019Co-Authors: Joel Barratt, Subin Park, Fernanda S Nascimento, Michael J Arrowood, Yvonne Qvarnstrom, Jessica N Hofstetter, Shannon Casillas, Mateusz M Plucinski, Richard S Bradbury, Eldin TalundzicAbstract:Sexually reproducing pathogens such as Cyclospora cayetanensis often produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness of C. cayetanensis infections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containing C. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of Cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P < 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of Cyclosporiasis.
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comparative genomics reveals cyclospora cayetanensis possesses coccidia like metabolism and invasion components but unique surface antigens
BMC Genomics, 2016Co-Authors: Kevin Tang, Dawn M. Roellig, Michael Frace, Shiyou Liu, Michael J Arrowood, Huajun Zheng, Delynn M Moss, Longxian ZhangAbstract:Background Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of Cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of C. cayetanensis and inferred its metabolism and invasion components based on comparative genomic analysis.
Fernanda S Nascimento - One of the best experts on this subject based on the ideXlab platform.
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evaluation of an ensemble based distance statistic for clustering mlst datasets using epidemiologically defined clusters of Cyclosporiasis
Epidemiology and Infection, 2020Co-Authors: Fernanda S Nascimento, Katelyn Houghton, Joel Barratt, Shannon M Casillas, Mateusz M Plucinski, Julia Kelley, Carolyne BennettAbstract:Outbreaks of Cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of Cyclosporiasis.
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development of a workflow for identification of nuclear genotyping markers for cyclospora cayetanensis
Parasite, 2020Co-Authors: Katelyn Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.
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Development of a workflow for identification of nuclear genotyping markers for
'EDP Sciences', 2020Co-Authors: Katelyn A. Houghton, Alexandre Lomsadze, Subin Park, Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Erik Vanroey, Eldin Talundzic, Mark Borodovsky, Yvonne QvarnstromAbstract:Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, Cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes
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mitochondrial junction region as genotyping marker for cyclospora cayetanensis
Emerging Infectious Diseases, 2019Co-Authors: Fernanda S Nascimento, Joel Barratt, Michael J Arrowood, Eldin Talundzic, John R Barta, Julia Whale, Jessica N Hofstetter, Shannon Casillas, Yvonne QvarnstromAbstract:Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of Cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during Cyclosporiasis outbreak investigations.
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genotyping genetically heterogeneous cyclospora cayetanensis infections to complement epidemiological case linkage
Parasitology, 2019Co-Authors: Joel Barratt, Subin Park, Fernanda S Nascimento, Michael J Arrowood, Yvonne Qvarnstrom, Jessica N Hofstetter, Shannon Casillas, Mateusz M Plucinski, Richard S Bradbury, Eldin TalundzicAbstract:Sexually reproducing pathogens such as Cyclospora cayetanensis often produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness of C. cayetanensis infections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containing C. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of Cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P < 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of Cyclosporiasis.
