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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barratt JLN, Lane M, Talundzic E, Richins T, Robertson G, Formenti F, Pritt B, Verocai G, Nascimento de Souza J, Soares NM, Traub R, Buonfrate D, Bradbury RS. Correction: A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing. PLoS Negl Trop Dis 2021; 15:e0009538. [PMID: 34143780 PMCID: PMC8213129 DOI: 10.1371/journal.pntd.0009538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Barratt JLN, Lane M, Talundzic E, Richins T, Robertson G, Formenti F, Pritt B, Verocai G, Nascimento de Souza J, Mato Soares N, Traub R, Buonfrate D, Bradbury RS. A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing. PLoS Negl Trop Dis 2019; 13:e0007609. [PMID: 31525192 PMCID: PMC6762204 DOI: 10.1371/journal.pntd.0007609] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/26/2019] [Accepted: 07/06/2019] [Indexed: 01/21/2023] Open
Abstract
Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allows a truly global understanding of the population genetic structure of the Strongyloides species infecting humans, non-human primates, and domestic dogs. Strongyloidiasis is a neglected tropical disease caused by the human infective worms (nematodes) Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Little is known about the genetic diversity of these nematodes and the possibility of geographically isolated genetic types is a particularly interesting research question, given the unique life cycle of these worms which includes both sexual and asexual stages. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using next-generation sequencing, we analyzed three Strongyloides DNA fragments from these specimens; two fragments of the 18S gene and one from the cytochrome c oxidase subunit 1 (cox1) gene. Using this approach, we discovered some unique S. stercoralis and S. fuelleborni genotypes, and identified a previously unknown S. fuelleborni infecting humans within Australia. We compared our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in public databases and identified several patterns relating to the global distribution of certain genotypes. This knowledge could allow us to infer the origin of human Strongyloides infections in the future, and assess the role certain animals (non-human primates and dogs) might play in the transmission of Strongyloides to humans.
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Affiliation(s)
- Joel L. N. Barratt
- Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Associated Universities, Oak Ridge, Tennessee, United States of America
| | - Meredith Lane
- Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Synergy America Inc., Atlanta, Georgia, United States of America
| | - Emir Talundzic
- Franklin College of Arts and Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Travis Richins
- Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Gemma Robertson
- Forensic and Scientific Services, Health Support Queensland, Brisbane, Queensland, Australia
| | - Fabio Formenti
- Department of Infectious–Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Bobbi Pritt
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Guilherme Verocai
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States of America
| | | | - Neci Mato Soares
- Faculdade de Farmacia, Universidade Federal da Bahia, Bahia, Brazil
| | - Rebecca Traub
- Faculty of Veterinary Science, University of Melbourne, Victoria, Australia
| | - Dora Buonfrate
- Department of Infectious–Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Richard S. Bradbury
- Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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