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Durigan M, Ewing-Peeples L, Almeria S, Balan KV, Grocholl J, Irizawa S, Mammel M. Detection of Cyclospora cayetanensis in Food and Water Samples: Optimized Protocols for Specific and Sensitive Molecular Methods from a Regulatory Agency Perspective. J Food Prot 2024; 87:100291. [PMID: 38701974 DOI: 10.1016/j.jfp.2024.100291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/29/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cyclospora cayetanensis is a coccidian parasite of the phylum Apicomplexa that causes cyclosporiasis, a human-specific gastrointestinal disease. Unlike most enteric pathogens, C. cayetanensis does not infect via direct fecal-oral transmission between humans because shed oocysts must be exposed to environmental triggers prior to becoming infectious. The development of specific and sensitive detection methods for C. cayetanensis is crucial to effectively address data gaps and provide regulatory support during outbreak investigations. In this study, new more specific molecular markers for the detection of C. cayetanensis were developed based on updated genomic databases of Apicomplexa mitochondrial sequences. Novel alternative reagents and supplies, as well as optimization protocols, were tested in spiked produce and agricultural water samples. The selected Mit1C primers and probe combined showed at least 13 mismatches to other related species. The new optimized qualitative real-time PCR assay with modifications to sample processing and replacement of discontinued items produced results comparable to the previously validated methods. In conclusion, the new optimized qualitative Mit1C real-time PCR assay demonstrated an increase in its specificity in comparison to other detection methods previously published, while it showed to be robust and as sensitive as the previously validated method at the FDA. This study has also expanded the array of PCR reagents that can be used to detect C. cayetanensis in produce and agricultural water samples and provided several improvements to the method for detection in agricultural water including replacements for discontinued items and a new dialysis filter for water filtration.
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Affiliation(s)
- Mauricio Durigan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA.
| | - Laura Ewing-Peeples
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Sonia Almeria
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Kannan V Balan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - John Grocholl
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA; Goldbelt C6, Chesapeake, VA 23320, USA
| | - Sachi Irizawa
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD 20742, USA
| | - Mark Mammel
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
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González-Gómez JP, Lozano-Aguirre LF, Medrano-Félix JA, Chaidez C, Gerba CP, Betancourt WQ, Castro-Del Campo N. Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis. Parasitol Res 2023; 122:2641-2650. [PMID: 37676306 DOI: 10.1007/s00436-023-07963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.
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Affiliation(s)
- Jean P González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Luis F Lozano-Aguirre
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A, 62210, Cuernavaca, Morelos, México
| | - José A Medrano-Félix
- Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional Para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a El dorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, Mexico
| | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Charles P Gerba
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Walter Q Betancourt
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México.
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Reyes GA, Chavez RA, Stasiewicz MJ. Modeling Preharvest Cyclospora cayetanensis Sampling and Testing for Various Water and Produce Sampling Plans. J Food Prot 2023; 86:100161. [PMID: 37742835 DOI: 10.1016/j.jfp.2023.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/07/2023] [Accepted: 09/10/2023] [Indexed: 09/26/2023]
Abstract
As of August 2023, the two U.S. Food and Drug Administration (FDA) official detection methods for C. cayetanensis are outlined in the FDA Bacteriological Analytical Manual (BAM) Chapters 19b (produce testing) and 19c (agricultural water testing). These newly developed detection methods have been shown to not always detect contamination when present at low levels. Yet, industry and regulators may choose to use these methods as part of their monitoring and verification activities while detection methods continue to be improved. This study uses simulation to better understand the performance of these methods for various produce and water sampling plans. To do so, we used published FDA test validation data to fit a logistic regression model that predicts the methods' detection rate given the number of oocysts present in a 10-L agricultural water or 25 g produce sample. By doing so, we were able to determine contamination thresholds at which different numbers of samples (n = 1, 2, 4, 8, 16, and 32) would be adequate for detecting contamination. Furthermore, to evaluate sampling plans in use cases, a simulation was developed to represent C. cayetanensis contamination in agricultural water and on cilantro throughout a 45-day growth cycle. The model included uncertainty around the contamination sources, including scenarios of unintentionally contaminated irrigation water or in-field contamination. The results demonstrate that in cases where irrigation water was the contamination source, frequent water testing proved to be more powerful than produce testing. In scenarios where contamination occurred in-field, conducting frequent produce testing or testing produce toward the end of the season more reliably detected contamination. This study models the power of C. cayetanensis detection methods to understand the sampling plan performance and how these methods can be better used to monitor this emerging food safety hazard.
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Affiliation(s)
- Gustavo A Reyes
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ruben A Chavez
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Jacobson DK, Peterson AC, Qvarnstrom Y, Barratt JL. Novel insights on the genetic population structure of human-infecting Cyclospora spp. and evidence for rapid subtype selection among isolates from the USA. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 4:100145. [PMID: 37841306 PMCID: PMC10569985 DOI: 10.1016/j.crpvbd.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
Human-infecting Cyclospora was recently characterized as three species, two of which (C. cayetanensis and C. ashfordi) are currently responsible for all known human infections in the USA, yet much remains unknown about the genetic structure within these two species. Here, we investigate Cyclospora genotyping data from 2018 through 2022 to ascertain if there are temporal patterns in the genetic structure of Cyclospora parasites that cause infections in US residents from year to year. First, we investigate three levels of genetic characterization: species, subpopulation, and strain, to elucidate annual trends in Cyclospora infections. Next, we determine if shifts in genetic diversity can be linked to any of the eight loci used in our Cyclospora genotyping approach. We observed fluctuations in the abundance of Cyclospora types at the species and subpopulation levels, but no significant temporal trends were identified; however, we found recurrent and sporadic strains within both C. ashfordi and C. cayetanensis. We also uncovered major shifts in the mitochondrial genotypes in both species, where there was a universal increase in abundance of a specific mitochondrial genotype that was relatively abundant in 2018 but reached near fixation (was observed in over 96% of isolates) in C. ashfordi by 2022. Similarly, this allele jumped from 29% to 82% relative abundance of isolates belonging to C. cayetanensis. Overall, our analysis uncovers previously unknown temporal-genetic patterns in US Cyclospora types from 2018 through 2022 and is an important step to presenting a clearer picture of the factors influencing cyclosporiasis outbreaks in the USA.
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Affiliation(s)
- David K. Jacobson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna C. Peterson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel L.N. Barratt
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Almeria S, Chacin-Bonilla L, Maloney JG, Santin M. Cyclospora cayetanensis: A Perspective (2020-2023) with Emphasis on Epidemiology and Detection Methods. Microorganisms 2023; 11:2171. [PMID: 37764015 PMCID: PMC10536660 DOI: 10.3390/microorganisms11092171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Cyclospora cayetanensis infections are prevalent worldwide, and the parasite has become a major public health and food safety concern. Although important efforts have been dedicated to advance toward preventing and reducing incidences of cyclosporiasis, there are still several knowledge gaps that hamper the implementation of effective measures to prevent the contamination of produce and water with Cyclospora oocysts. Some of these data gaps can be attributed to the fact that access to oocysts is a limiting factor in C. cayetanensis research. There are no animal models or in vivo or in vitro culture systems to propagate the oocysts needed to facilitate C. cayetanensis research. Thus, researchers must rely upon limited supplies of oocysts obtained from naturally infected human patients considerably restricting what can be learnt about this parasite. Despite the limited supply of C. cayetanensis oocysts, several important advances have happened in the past 3 years. Great progress has been made in the Cyclospora field in the areas of molecular characterization of strains and species, generation of genomes, and development of novel detection methods. This comprehensive perspective summarizes research published from 2020 to 2023 and evaluates what we have learnt and identifies those aspects in which further research is needed.
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Affiliation(s)
- Sonia Almeria
- Center for Food Safety and Nutrition (CFSAN), Department of Health and Human Services, Food and Drug Administration, Office of Applied Research and Safety Assessment (OARSA), Division of Virulence Assessment, Laurel, MD 20708, USA
| | | | - Jenny G. Maloney
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA;
| | - Monica Santin
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA;
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Chacin-Bonilla L, Santin M. Cyclospora cayetanensis Infection in Developed Countries: Potential Endemic Foci? Microorganisms 2023; 11:540. [PMID: 36985114 PMCID: PMC10058255 DOI: 10.3390/microorganisms11030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Cyclospora cayetanensis infection has emerged as a significant public health concern worldwide. Developed countries are generally considered non-endemic for infection. However, sporadic cases and non-travel-related outbreaks of C. cayetanensis infections associated with domestically grown produce are becoming more common in developed countries. Cyclospora cayetanensis has been detected in fresh produce, surface water, wastewater, irrigation water, and soil in these countries, suggesting that the parasite may be more common in areas with advanced sanitation than previously thought and illustrating the potential risk for exposure and indigenous/autochthonous infections. The evidence suggests the possibility of foci of endemicity in developed countries, particularly in communities where sanitary conditions are compromised, and raises transmission issues that require further research to better define the risks for infection, how widespread C. cayetanensis may be in these areas, and to guide interventions against this infection. The main purpose of the present opinion was to evaluate the presence of cyclosporiasis in developed countries, which is a very important and ongoing issue in food safety.
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Affiliation(s)
- Leonor Chacin-Bonilla
- Instituto de Investigaciones Clinicas, Universidad del Zulia, Maracaibo 4001, Venezuela
| | - Monica Santin
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
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Tucker MS, Khan A, Jenkins MC, Dubey JP, Rosenthal BM. Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates. Microorganisms 2022; 10:1977. [PMID: 36296256 PMCID: PMC9608778 DOI: 10.3390/microorganisms10101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/16/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022] Open
Abstract
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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Affiliation(s)
| | | | | | | | - Benjamin M. Rosenthal
- Animal Parasitic Disease Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, BARC-East, Beltsville, MD 20705, USA
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