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Leonard SR, Mammel MK, Almeria S, Gebru ST, Jacobson DK, Peterson AC, Barratt JLN, Musser SM. Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for Genotyping Cyclospora cayetanensis. Microorganisms 2024; 12:848. [PMID: 38792677 PMCID: PMC11124223 DOI: 10.3390/microorganisms12050848] [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: 03/12/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
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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Affiliation(s)
- Susan R. Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (M.K.M.); (S.A.); (S.T.G.)
| | - Mark K. Mammel
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (M.K.M.); (S.A.); (S.T.G.)
| | - Sonia Almeria
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (M.K.M.); (S.A.); (S.T.G.)
| | - Solomon T. Gebru
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (M.K.M.); (S.A.); (S.T.G.)
| | - David K. Jacobson
- Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (D.K.J.); (A.C.P.); (J.L.N.B.)
| | - Anna C. Peterson
- Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (D.K.J.); (A.C.P.); (J.L.N.B.)
| | - Joel L. N. Barratt
- Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (D.K.J.); (A.C.P.); (J.L.N.B.)
| | - Steven M. Musser
- Office of the Center Director, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA;
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Richins T, Houghton K, Barratt J, H. Sapp SG, Peterson A, Qvarnstrom Y. Comparison of two novel one-tube nested real-time qPCR assays to detect human-infecting Cyclospora spp. Microbiol Spectr 2023; 11:e0138823. [PMID: 37819113 PMCID: PMC10715049 DOI: 10.1128/spectrum.01388-23] [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: 03/30/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Human-infecting Cyclospora spp. cause gastrointestinal distress among healthy individuals contributing to morbidity and putting stress on the economics of countries and companies in the form of produce recalls. Accessible and easy-to-use diagnostic tools available to a wide variety of laboratories would aid in the early detection of possible outbreaks of cyclosporiasis. This, in turn, will assist in the timely traceback investigation to the suspected source of an outbreak by informing the smallest possible recall and protecting consumers from contaminated produce. This manuscript describes two novel detection methods with improved performance for the causative agents of cyclosporiasis when compared to the currently used 18S assay.
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Affiliation(s)
- Travis Richins
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Parasitic Disease Branch, Atlanta, USA
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | | | - Joel Barratt
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Parasitic Disease Branch, Atlanta, USA
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Sarah G. H. Sapp
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Parasitic Disease Branch, Atlanta, USA
| | - Anna Peterson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Parasitic Disease Branch, Atlanta, USA
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Parasitic Disease Branch, Atlanta, 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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Peterson A, Richins T, Houghton K, Mishina M, Sharma S, Sambhara S, Jacobson D, Qvarnstrom Y, Cama V. The limit of detection of the BioFire® FilmArray® gastrointestinal panel for the foodborne parasite Cyclospora cayetanensis. Diagn Microbiol Infect Dis 2023; 107:116030. [PMID: 37572510 PMCID: PMC10530562 DOI: 10.1016/j.diagmicrobio.2023.116030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/20/2023] [Accepted: 07/15/2023] [Indexed: 08/14/2023]
Abstract
Cyclosporiasis is a foodborne diarrheal illness caused by the parasite Cyclospora cayetanensis. The BioFire® FilmArray® gastrointestinal (FilmArray GI) panel is a common method for diagnosing cyclosporiasis from clinical stool samples. The currently published limit of detection (LOD) of this panel is in genome equivalents; however, it is unclear how this relates to the number of C. cayetanensis oocysts in a clinical sample. In this study, we developed a technique to determine the LOD in terms of oocysts, using a cell sorter to sort 1 to 50 C. cayetanensis oocyst(s) previously purified from three human stool sources. We found the FilmArray GI panel detected samples with ≥20 C. cayetanensis oocysts in 100% of replicates, with varying detection among samples with 1, 5, or 10 C. cayetanensis oocysts. This method provides a parasitologically relevant LOD that should enable comparison among C. cayetanensis detection techniques, including the FilmArray GI panel.
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Affiliation(s)
- Anna Peterson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA.
| | - Travis Richins
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Katelyn Houghton
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Margarita Mishina
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - Suresh Sharma
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Influenza Division, Immunology and Pathogenesis Branch, Atlanta, GA, USA
| | - David Jacobson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, USA
| | - Vitaliano Cama
- Centers for Disease Control and Prevention, Global Health Center, Division of Parasitic Diseases and Malaria, Laboratory Science and Diagnostic Branch, Atlanta, GA, 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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6
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Jacobson DK, Low R, Plucinski MM, Barratt JLN. An improved framework for detecting discrete epidemiologically meaningful partitions in hierarchically clustered genetic data. BIOINFORMATICS ADVANCES 2023; 3:vbad118. [PMID: 37744999 PMCID: PMC10517639 DOI: 10.1093/bioadv/vbad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/26/2023]
Abstract
Motivation Hierarchical clustering of microbial genotypes has the limitation that hierarchical clusters are nested, where smaller groups of related isolates exist within larger groups that get progressively larger as relationships become increasingly distant. In an epidemiologic context, investigators must dissect hierarchical trees into discrete groupings that are epidemiologically meaningful. We recently described a statistical framework (Method A) for dissecting hierarchical trees that attempts to minimize investigator bias. Here, we apply a modified version of that framework (Method B) to a hierarchical tree constructed from 2111 genotypes of the foodborne parasite Cyclospora, including 639 genotypes linked to epidemiologically defined outbreaks. To evaluate Method B's performance, we examined the concordance between these epidemiologically defined groupings and the genetic partitions identified. We also used the same epidemiologic clusters to evaluate the performance of Method A, plus two tree-dissection methods (cutreeHybrid and cutreeDynamic) available within the Dynamic Tree Cut R package, in addition to the TreeCluster method and PARNAS. Results Compared to the other methods, Method B, TreeCluster, and PARNAS were the most accurate (99.4%) in identifying genetic groups that reflected the epidemiologic groupings, noting that TreeCluster and PARNAS performed identically on our dataset. CutreeHybrid identified groups reflecting patterns in the wider Cyclospora population structure but lacked finer, strain-level discrimination (Simpson's D: cutreeHybrid=0.785). CutreeDynamic displayed good strain discrimination (Simpson's D = 0.933), though lacked sensitivity (77%). At two different threshold/radius settings TreeCluster/PARNAS displayed similar utility to Method B. However, Method B computes a tree-dissection threshold automatically, and the threshold/radius settings used when executing TreeCluster/PARNAS here were computed using Method B. Using a TreeCluster threshold of 0.045 as recommended in the TreeCluster documentation, epidemiologic utility dropped markedly below that of Method B. Availability and implementation Relevant code and data are publicly available. Source code (Method B) and instructions for its use are available here: https://github.com/Joel-Barratt/Hierarchical-tree-dissection-framework.
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Affiliation(s)
- David K Jacobson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Ross Low
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
- Oak Ridge Institute of Science and Education, Oak Ridge, TN, 37830, United States
| | - Mateusz M Plucinski
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
| | - Joel L N Barratt
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30329, United States
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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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Ahart L, Jacobson D, Rice M, Richins T, Peterson A, Zheng Y, Barratt J, Cama V, Qvarnstrom Y, Montgomery S, Straily A. Retrospective evaluation of an integrated molecular-epidemiological approach to cyclosporiasis outbreak investigations - United States, 2021. Epidemiol Infect 2023; 151:e131. [PMID: 37466070 PMCID: PMC10540164 DOI: 10.1017/s0950268823001176] [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: 02/10/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Cyclosporiasis results from an infection of the small intestine by Cyclospora parasites after ingestion of contaminated food or water, often leading to gastrointestinal distress. Recent developments in temporally linking genetically related Cyclospora isolates demonstrated effectiveness in supporting epidemiological investigations. We used 'temporal-genetic clusters' (TGCs) to investigate reported cyclosporiasis cases in the United States during the 2021 peak-period (1 May - 31 August 2021). Our approach split 655 genotyped isolates into 55 genetic clusters and 31 TGCs. We linked two large multi-state epidemiological clusters (Epidemiologic Cluster 1 [n = 136 cases, 54 genotyped] and Epidemiologic Cluster 2 [n = 42 cases, 15 genotyped]) to consumption of lettuce varieties; however, product traceback did not identify a specific product for either cluster due to the lack of detailed product information. To evaluate the utility of TGCs, we performed a retrospective case study comparing investigation outcomes of outbreaks first detected using epidemiological methods with those of the same outbreaks had TGCs been used to first detect them. Our study results indicate that adjustments to routine epidemiological approaches could link additional cases to epidemiological clusters of cyclosporiasis. Overall, we show that CDC's integrated genotyping and epidemiological investigations provide valuable insights into cyclosporiasis outbreaks in the United States.
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Affiliation(s)
- Lauren Ahart
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - David Jacobson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Marion Rice
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Travis Richins
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Anna Peterson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Yueli Zheng
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Eagle Global Scientific, San Antonio, TX, USA
| | - Joel Barratt
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan Montgomery
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anne Straily
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Leonard SR, Mammel MK, Gharizadeh B, Almeria S, Ma Z, Lipman DJ, Torrence ME, Wang C, Musser SM. Development of a targeted amplicon sequencing method for genotyping Cyclospora cayetanensis from fresh produce and clinical samples with enhanced genomic resolution and sensitivity. Front Microbiol 2023; 14:1212863. [PMID: 37396378 PMCID: PMC10311907 DOI: 10.3389/fmicb.2023.1212863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Outbreaks of cyclosporiasis, an enteric illness caused by the parasite Cyclospora cayetanensis, have been associated with consumption of various types of fresh produce. Although a method is in use for genotyping C. cayetanensis from clinical specimens, the very low abundance of C. cayetanensis in food and environmental samples presents a greater challenge. To complement epidemiological investigations, a molecular surveillance tool is needed for use in genetic linkage of food vehicles to cyclosporiasis illnesses, estimation of the scope of outbreaks or clusters of illness, and determination of geographical areas involved. We developed a targeted amplicon sequencing (TAS) assay that incorporates a further enrichment step to gain the requisite sensitivity for genotyping C. cayetanensis contaminating fresh produce samples. The TAS assay targets 52 loci, 49 of which are located in the nuclear genome, and encompasses 396 currently known SNP sites. The performance of the TAS assay was evaluated using lettuce, basil, cilantro, salad mix, and blackberries inoculated with C. cayetanensis oocysts. A minimum of 24 markers were haplotyped even at low contamination levels of 10 oocysts in 25 g leafy greens. The artificially contaminated fresh produce samples were included in a genetic distance analysis based on haplotype presence/absence with publicly available C. cayetanensis whole genome sequence assemblies. Oocysts from two different sources were used for inoculation, and samples receiving the same oocyst preparation clustered together, but separately from the other group, demonstrating the utility of the assay for genetically linking samples. Clinical fecal samples with low parasite loads were also successfully genotyped. This work represents a significant advance in the ability to genotype C. cayetanensis contaminating fresh produce along with greatly expanding the genomic diversity included for genetic clustering of clinical specimens.
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Affiliation(s)
- Susan R. Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Mark K. Mammel
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | | | - Sonia Almeria
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Zhihai Ma
- Chapter Diagnostics, Menlo Park, CA, United States
| | - David J. Lipman
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Mary E. Torrence
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Chunlin Wang
- Chapter Diagnostics, Menlo Park, CA, United States
| | - Steven M. Musser
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
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Abstract
The apicomplexan parasite Cyclospora cayetanensis causes seasonal foodborne outbreaks of the gastrointestinal illness cyclosporiasis. Prior to the coronavirus disease-2019 pandemic, annually reported cases were increasing in the USA, leading the US Centers for Disease Control and Prevention to develop a genotyping tool to complement cyclosporiasis outbreak investigations. Thousands of US isolates and 1 from China (strain CHN_HEN01) were genotyped by Illumina amplicon sequencing, revealing 2 lineages (A and B). The allelic composition of isolates was examined at each locus. Two nuclear loci (CDS3 and 360i2) distinguished lineages A and B. CDS3 had 2 major alleles: 1 almost exclusive to lineage A and the other to lineage B. Six 360i2 alleles were observed – 2 exclusive to lineage A (alleles A1 and A2), 2 to lineage B (B1 and B2) and 1 (B4) was exclusive to CHN_HEN01 which shared allele B3 with lineage B. Examination of heterozygous genotypes revealed that mixtures of A- and B-type 360i2 alleles occurred rarely, suggesting a lack of gene flow between lineages. Phylogenetic analysis of loci from whole-genome shotgun sequences, mitochondrial and apicoplast genomes, revealed that CHN_HEN01 represents a distinct lineage (C). Retrospective examination of epidemiologic data revealed associations between lineage and the geographical distribution of US infections plus strong temporal associations. Given the multiple lines of evidence for speciation within human-infecting Cyclospora, we provide an updated taxonomic description of C. cayetanensis, and describe 2 novel species as aetiological agents of human cyclosporiasis: Cyclospora ashfordi sp. nov. and Cyclospora henanensis sp. nov. (Apicomplexa: Eimeriidae).
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Jacobson D, Barratt J. Optimizing hierarchical tree dissection parameters using historic epidemiologic data as 'ground truth'. PLoS One 2023; 18:e0282154. [PMID: 36827266 PMCID: PMC9955612 DOI: 10.1371/journal.pone.0282154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Hierarchical clustering of pathogen genotypes is widely used to complement epidemiologic investigations of outbreaks. Investigators must dissect trees to obtain genetic partitions that provide epidemiologists with meaningful information. Statistical approaches to tree dissection often require a user-defined parameter to predict the optimal partition number and augmenting this parameter can drastically impact resultant partition memberships. Here, we demonstrate how to optimize a given tree dissection parameter to maximize accuracy irrespective of the tree dissection method used. We hierarchically clustered 1,873 genotypes of the foodborne pathogen Cyclospora spp., including 587 possessing links to historic outbreaks. We dissected the resulting tree using a statistical method requiring users to select the value of a 'stringency parameter' (s), with a recommended value of 95% to 99.5%. We dissected this hierarchical tree across s-values from 94% to 99.5% (at increments of 0.25%), to identify a value that maximized partitioning accuracy, defined as the degree to which genetic partitions conform to known epidemiologic groupings. We show that s-values of 96.5% and 96.75% yield the highest accuracy (> 99.9%) when clustering Cyclospora sp. isolates with known epidemiologic linkages. In practice, the optimized s-value will generate robust genetic partitions comprising isolates likely derived from a common food source, even when the epidemiologic grouping is not known prior to genetic clustering. While the s-value is specific to the tree dissection method used here, the optimization approach described could be applied to any parameter/method used to dissect hierarchical trees.
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Affiliation(s)
- David Jacobson
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute of Science and Education, Oak Ridge, Tennessee, United States of America
- * E-mail:
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Richins T, Sapp SG, Ketzis JK, Willingham AL, Mukaratirwa S, Qvarnstrom Y, Barratt JL. Genetic characterization of Strongyloides fuelleborni infecting free-roaming African vervets ( Chlorocebus aethiops sabaeus) on the Caribbean island of St. Kitts. Int J Parasitol Parasites Wildl 2023; 20:153-161. [PMID: 36860205 PMCID: PMC9969202 DOI: 10.1016/j.ijppaw.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
Human strongyloidiasis is an important neglected tropical disease primarily caused by the nematode Strongyloides stercoralis, and to a lesser extent Strongyloides fuelleborni which mainly infects non-human primates. Zoonotic sources of infection have important implications for control and prevention of morbidity and mortality caused by strongyloidiasis. Recent molecular evidence suggests that for S. fuelleborni, primate host specificity is variable among genotypes across the Old World, and consequently that these types likely vary in their capacity for human spillover infections. Populations of free-roaming vervet monkeys (Chlorocebus aethiops sabaeus), introduced to the Caribbean Island of Staint Kitts from Africa, live in close contact with humans, and concern has arisen regarding their potential to serve as reservoirs of zoonotic infections. In this study, we sought to determine the genotypes of S. fuelleborni infecting St. Kitts vervets to explore whether they are potential reservoirs for human-infecting S. fuelleborni types. Fecal specimens were collected from St. Kitts vervets and S. fuelleborni infections were confirmed microscopically and by PCR. Strongyloides fuelleborni genotypes were determined from positive fecal specimens using an Illumina amplicon sequencing-based genotyping approach targeting the mitochondrial cox1 locus and 18S rDNA hypervariable regions I and IV of Strongyloides species. Phylogenetic analysis of resultant genotypes supported that S. fuelleborni from St. Kitts vervets is of an exclusively African variety, falling within the same monophyletic group as an isolate which has been detected previously in a naturally infected human from Guinea-Bissau. This observation highlights that St. Kitts vervets may serve as potential reservoirs for zoonotic S. fuelleborni infection, which warrants further exploration.
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Affiliation(s)
- Travis Richins
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA,Oak Ridge Associated Universities, Oak Ridge, TN, USA
| | | | - Jennifer K. Ketzis
- Biomedical Sciences, One Health Center for Zoonoses & Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Arve Lee Willingham
- Department of Veterinary Medicine, College of Agriculture & Veterinary Medicine, United Arab Emirates
| | - Samson Mukaratirwa
- Biomedical Sciences, One Health Center for Zoonoses & Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Yvonne Qvarnstrom
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA
| | - Joel L.N. Barratt
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA,Corresponding author.
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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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Development of a Molecular Marker Based on the Mitochondrial Genome for Detection of Cyclospora cayetanensis in Food and Water Samples. Microorganisms 2022; 10:microorganisms10091762. [PMID: 36144364 PMCID: PMC9504131 DOI: 10.3390/microorganisms10091762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
Cyclospora cayetanensis is a coccidian parasite that causes diarrheal illness outbreaks worldwide. The development of new laboratory methods for detection of C. cayetanensis is of critical importance because of the high potential for environmental samples to be contaminated with a myriad of microorganisms, adversely impacting the specificity when testing samples from various sources using a single molecular assay. In this study, a new sequencing-based method was designed targeting a specific fragment of C. cayetanensis cytochrome oxidase gene and developed as a complementary method to the TaqMan qPCR present in the U.S. FDA BAM Chapter 19b and Chapter 19c. The comparative results between the new PCR protocol and the qPCR for detection of C. cayetanensis in food and water samples provided similar results in both matrices with the same seeding level. The target region and primers in the protocol discussed in this study contain sufficient Cyclospora-specific sequence fidelity as observed by sequence comparison with other Eimeriidae species. The sequence of the PCR product appears to represent a robust target for identifying C. cayetanensis on samples from different sources. Such a sensitive method for detection of C. cayetanensis would add to the target repertoire of qPCR-based screening strategies for food and water samples.
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Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations. Microorganisms 2022; 10:microorganisms10020447. [PMID: 35208901 PMCID: PMC8879297 DOI: 10.3390/microorganisms10020447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/23/2022] Open
Abstract
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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Barratt J, Ahart L, Rice M, Houghton K, Richins T, Cama V, Arrowood M, Qvarnstrom Y, Straily A. Genotyping Cyclospora cayetanensis from multiple outbreak clusters with an emphasis on a cluster linked to bagged salad mix - United States, 2020. J Infect Dis 2021; 225:2176-2180. [PMID: 34606577 PMCID: PMC9200147 DOI: 10.1093/infdis/jiab495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Cyclosporiasis is a diarrheal illness caused by the foodborne parasite Cyclospora cayetanensis. Annually reported cases have been increasing in the United States prompting development of genotyping tools to aid cluster detection. A recently developed Cyclospora genotyping system based on 8 genetic markers was applied to clinical samples collected during the cyclosporiasis peak period of 2020, facilitating assessment of its epidemiologic utility. While the system performed well and helped inform epidemiologic investigations, inclusion of additional markers to improve cluster detection was supported. Consequently, investigations have commenced to identify additional markers to enhance performance.
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Affiliation(s)
- Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Ahart
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marion Rice
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katelyn Houghton
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Travis Richins
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Vitaliano Cama
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Arrowood
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yvonne Qvarnstrom
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anne Straily
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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