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Valente MJ, Streett H, Turner R, O'Brien C, Fournet V, Jansen A, Dubey JP, Rosenthal BM, Jenkins M, Khan A. Morphological and autofluorescence assessment of oocysts differentiate live from dead coccidian parasites. Int J Parasitol 2025:S0020-7519(25)00065-7. [PMID: 40209889 DOI: 10.1016/j.ijpara.2025.04.003] [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: 11/06/2024] [Revised: 03/02/2025] [Accepted: 04/03/2025] [Indexed: 04/12/2025]
Abstract
To assess and mitigate foodborne risk, regulatory agencies and produce growers require the means not merely to detect but moreover determine the viability of foodborne eukaryotic pathogens such as Cyclospora cayetanensis. Viability assessment would also aid those employing live attenuated vaccines against coccidiosis, a major problem in poultry production. Therefore, we sought to identify morphological changes differentiating viable from non-viable coccidian oocysts, employing Eimeria acervulina as a tractable model, enabling empirical validation by means of in vivo challenge infections in the natural chicken host. High resolution microscopic examinations identified granular structures that autofluoresce under UV exposure in dead oocysts, greatly intensifying overall autofluorescence in dead oocysts. We harnessed this intensification as a basis to sort live from dead oocysts using a Fluorescence-Activated Cell Sorting (FACS) cell sorter, validating their distinction by documenting infectivity in chickens using the former, and minimal shedding with the latter. Our rapid, sensitive, and robust assay holds promise for application to other species of coccidia, including those important to livestock and public health.
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Affiliation(s)
- Matthew J Valente
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hannah Streett
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Randi Turner
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Celia O'Brien
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Valsin Fournet
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Andrew Jansen
- Systematic Entomology Laboratory, Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Jitender P Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Mark Jenkins
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Asis Khan
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
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2
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McCaughan KJ, Scott Z, Rock C, Kniel KE. Evaluation of aqueous chlorine and peracetic acid sanitizers to inactivate protozoa and bacteria of concern in agricultural water. Appl Environ Microbiol 2025; 91:e0165324. [PMID: 39641604 PMCID: PMC11784247 DOI: 10.1128/aem.01653-24] [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: 08/20/2024] [Accepted: 10/28/2024] [Indexed: 12/07/2024] Open
Abstract
Agricultural water is a potential source of microbial contamination whereby Escherichia coli, Salmonella, Cryptosporidium, and Cyclospora cayetenensis can enter the food supply. To reduce this risk, effective sanitization of agricultural water may be critical to food safety. As such, it is important to investigate the effects of aqueous peracetic acid (PAA) and chlorine (Cl) on bacteria and protozoa at different treatment times and temperatures in agricultural water with respect to key water characteristics. Multiple concentrations of each sanitizer, ranging from 3 to 200 ppm, were prepared in recently collected agricultural water, the solution was brought to the desired temperature, and the target organisms were added and left for the desired contact time (5 or 10 minutes) when sodium metabisulfite was added to neutralize the sanitizers. Bacterial samples were enumerated on MacConkey or XLT4 agar. Samples with protozoa were added to mammalian cell culture (HCT-8 cells for Cryptosporidium parvum and MDBK cells for Eimeria tenella). After 48 hours, the infected cells were collected, DNA extracted and infectivity assessed by quantitative PCR (qPCR). Low and high concentrations of sanitizer were effective at eliminating bacteria with Cl being significantly (P < 0.05) more effective. The greatest reductions in E. coli and Salmonella (3.48 log and 2.5 log cfu/mL, respectively) were observed after 10 minutes of exposure to 10 ppm Cl. Concentrations of sanitizer 50 ppm and lower resulted in insignificant (P > 0.05) reductions in parasite infectivity of less than 1 log for both organisms. A 200 ppm PAA treatment reduced infectious oocyst populations by 3.8 log for C. parvum and 2.6 log for E. tenella, with Cl being significantly (P < 0.05) less effective against these organisms. IMPORTANCE This research is critical to inform decisions regarding the application and use of sanitizers in pre-harvest agricultural water settings to enhance food safety. Understanding the effectiveness of chlorine (Cl) and peracetic acid (PAA) on bacteria and protozoa will allow for the more efficient and practical use of these sanitizers, thus improving agricultural practices in ways that are beneficial to both growers and consumers.
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Affiliation(s)
- Kyle J. McCaughan
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Zoe Scott
- Department of Environmental Science, University of Arizona, Maricopa, Arizona, USA
| | - Channah Rock
- Department of Environmental Science, University of Arizona, Maricopa, Arizona, USA
| | - Kalmia E. Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
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3
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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: 3] [Impact Index Per Article: 1.5] [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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4
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Zhou X, Wang Z, Zhu P, Gu X, He R, Xu J, Jing B, Wang L, Chen S, Xie Y. Eimeria zuernii (Eimeriidae: Coccidia): mitochondrial genome and genetic diversity in the Chinese yak. Parasit Vectors 2023; 16:312. [PMID: 37661262 PMCID: PMC10475197 DOI: 10.1186/s13071-023-05925-8] [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: 05/24/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis. METHODS We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China. RESULTS The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations. CONCLUSIONS To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130 China
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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: 13] [Impact Index Per Article: 6.5] [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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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: 4] [Impact Index Per Article: 2.0] [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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7
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Li J, Xu F, Karim MR, Zhang L. Review on Cyclosporiasis Outbreaks and Potential Molecular Markers for Tracing Back Investigations. Foodborne Pathog Dis 2022; 19:796-805. [PMID: 36450125 DOI: 10.1089/fpd.2022.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Cyclosporiasis is an emerging disease caused by Cyclospora cayetanensis, which induces protracting and relapsing gastroenteritis and has been linked to huge and complicated travel- and food-related outbreaks worldwide. Cyclosporiasis has become more common in both developing and developed countries as a result of increased global travel and the globalization of the human food supply. It is not just a burden on individual human health but also a worldwide public health problem. As a pathogen of interest, the molecular biological characteristics of C. cayetanensis have advanced significantly over the last few decades. However, only one FDA-approved molecular platform has been commercially used in the investigation of cyclosporiasis outbreaks. More potential molecular markers and genotyping of C. cayetanensis in samples based on the polymorphic region of the whole genomes might differentiate between separate case clusters and would be useful in tracing back investigations, especially during cyclosporiasis outbreak investigations. Considering that there is no effective vaccine for cyclosporosis, epidemiological investigation using effective tools is crucial for controlling cyclosporiasis by source tracking. Therefore, more and more epidemiological investigative studies for human cyclosporiasis should be promoted around the world to get a deeper understanding of its characteristics as well as management. This review focuses on major cyclosporiasis outbreaks and potential molecular markers for tracing back investigations into cyclosporiasis outbreaks.
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Affiliation(s)
- Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, China.,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, China
| | - Feifei Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Md Robiul Karim
- Department of Medicine, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, China.,International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, China
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8
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Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples. Heliyon 2022; 8:e11575. [DOI: 10.1016/j.heliyon.2022.e11575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/17/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
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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: 7] [Impact Index Per Article: 2.3] [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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10
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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: 0.3] [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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11
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Dubey JP, Khan A, Rosenthal BM. Life Cycle and Transmission of Cyclospora cayetanensis: Knowns and Unknowns. Microorganisms 2022; 10:microorganisms10010118. [PMID: 35056567 PMCID: PMC8779055 DOI: 10.3390/microorganisms10010118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Although infections with Cyclospora cayetanensis are prevalent worldwide, many aspects of this parasite’s life cycle and transmission remain unknown. Humans are the only known hosts of this parasite. Existing information on its endogenous development has been derived from histological examination of only a few biopsy specimens. Its asexual and sexual stages occur in biliary-intestinal epithelium. In histological sections, its stages are less than 10 μm, making definitive identification difficult. Asexual (schizonts) and sexual (gamonts) are located in epithelial cells. Male microgamonts have two flagella; female macrogametes contain wall-forming bodies. Oocysts are excreted in feces unsporulated. Sporulation occurs in the environment, but there are many unanswered questions concerning dissemination and survival of C. cayetanensis oocysts. Biologically and phylogenetically, C. cayetanensis closely resembles Eimeria spp. that parastize chickens; among them, E. acervulina most closely resembles C. cayetanensis in size. Here, we review known and unknown aspects of its life cycle and transmission and discuss the appropriateness of surrogates best capable of hastening progress in understanding its biology and developing mitigating strategies.
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12
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Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
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Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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13
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Tucker MS, O’Brien CN, Jenkins MC, Rosenthal BM. Dynamically expressed genes provide candidate viability biomarkers in a model coccidian. PLoS One 2021; 16:e0258157. [PMID: 34597342 PMCID: PMC8486141 DOI: 10.1371/journal.pone.0258157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/18/2021] [Indexed: 11/29/2022] Open
Abstract
Eimeria parasites cause enteric disease in livestock and the closely related Cyclosporacayetanensis causes human disease. Oocysts of these coccidian parasites undergo maturation (sporulation) before becoming infectious. Here, we assessed transcription in maturing oocysts of Eimeria acervulina, a widespread chicken parasite, predicted gene functions, and determined which of these genes also occur in C. cayetanensis. RNA-Sequencing yielded ~2 billion paired-end reads, 92% of which mapped to the E. acervulina genome. The ~6,900 annotated genes underwent temporally-coordinated patterns of gene expression. Fifty-three genes each contributed >1,000 transcripts per million (TPM) throughout the study interval, including cation-transporting ATPases, an oocyst wall protein, a palmitoyltransferase, membrane proteins, and hypothetical proteins. These genes were enriched for 285 gene ontology (GO) terms and 13 genes were ascribed to 17 KEGG pathways, defining housekeeping processes and functions important throughout sporulation. Expression differed in mature and immature oocysts for 40% (2,928) of all genes; of these, nearly two-thirds (1,843) increased their expression over time. Eight genes expressed most in immature oocysts, encoding proteins promoting oocyst maturation and development, were assigned to 37 GO terms and 5 KEGG pathways. Fifty-six genes underwent significant upregulation in mature oocysts, each contributing at least 1,000 TPM. Of these, 40 were annotated by 215 GO assignments and 9 were associated with 18 KEGG pathways, encoding products involved in respiration, carbon fixation, energy utilization, invasion, motility, and stress and detoxification responses. Sporulation orchestrates coordinated changes in the expression of many genes, most especially those governing metabolic activity. Establishing the long-term fate of these transcripts in sporulated oocysts and in senescent and deceased oocysts will further elucidate the biology of coccidian development, and may provide tools to assay infectiousness of parasite cohorts. Moreover, because many of these genes have homologues in C. cayetanensis, they may prove useful as biomarkers for risk.
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Affiliation(s)
- Matthew S. Tucker
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States of America
| | - Celia N. O’Brien
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States of America
| | - Mark C. Jenkins
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States of America
| | - Benjamin M. Rosenthal
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States of America
- * E-mail:
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14
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Abstract
Cyclospora is an intracellular, gastrointestinal parasite found in birds and mammals worldwide. Limited accessibility of the protozoan for experimental use, scarcity, genome heterogeneity of the isolates and narrow panel of molecular markers hamper zoonotic investigations. One of the significant limitation in zoonotic studies is the lack of precise molecular tools that would be useful in linking animal vectors as a source of human infection. Strong and convincing evidence of zoonotic features will be achieved through proper typing of Cyclospora spp. taxonomic units (e.g. species or genotypes) in animal reservoirs. The most promising method that can be employ for zoonotic surveys is next-generation sequencing.
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15
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Blake DP, Worthing K, Jenkins MC. Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities. Genes (Basel) 2020; 11:E1103. [PMID: 32967167 PMCID: PMC7564333 DOI: 10.3390/genes11091103] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.
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Affiliation(s)
- Damer P. Blake
- Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms AL9 7TA, UK
| | - Kate Worthing
- Animal Parasitic Diseases Laboratory, Building 1040, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; (K.W.); (M.C.J.)
| | - Mark C. Jenkins
- Animal Parasitic Diseases Laboratory, Building 1040, Agricultural Research Service, USDA, Beltsville, MD 20705, USA; (K.W.); (M.C.J.)
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16
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Houghton KA, Lomsadze A, Park S, Nascimento FS, Barratt J, Arrowood MJ, VanRoey E, Talundzic E, Borodovsky M, Qvarnstrom Y. Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis. ACTA ACUST UNITED AC 2020; 27:24. [PMID: 32275020 PMCID: PMC7147239 DOI: 10.1051/parasite/2020022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/02/2020] [Indexed: 01/29/2023]
Abstract
Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.
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Affiliation(s)
- Katelyn A Houghton
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Subin Park
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Fernanda S Nascimento
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Michael J Arrowood
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Erik VanRoey
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yvonne Qvarnstrom
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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17
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Cinar HN, Gopinath G, Murphy HR, Almeria S, Durigan M, Choi D, Jang A, Kim E, Kim R, Choi S, Lee J, Shin Y, Lee J, Qvarnstrom Y, Benedict TK, Bishop HS, da Silva A. Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing. Parasit Vectors 2020; 13:122. [PMID: 32143704 PMCID: PMC7060604 DOI: 10.1186/s13071-020-3997-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing. METHODS We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline. RESULTS This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study. CONCLUSIONS Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.
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Affiliation(s)
- Hediye Nese Cinar
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Gopal Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Helen R. Murphy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Sonia Almeria
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Mauricio Durigan
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Dajung Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - AhYoung Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Eunje Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - RaeYoung Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Seonju Choi
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jeongu Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yurim Shin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Jieon Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Theresa K. Benedict
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Henry S. Bishop
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Alexandre da Silva
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD USA
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18
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Nascimento FS, Barta JR, Whale J, Hofstetter JN, Casillas S, Barratt J, Talundzic E, Arrowood MJ, Qvarnstrom Y. Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis. Emerg Infect Dis 2019; 25:1314-1319. [PMID: 31211668 PMCID: PMC6590752 DOI: 10.3201/eid2507.181447] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.
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19
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Cyclospora cayetanensis infection in humans: biological characteristics, clinical features, epidemiology, detection method and treatment. Parasitology 2019; 147:160-170. [PMID: 31699163 DOI: 10.1017/s0031182019001471] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclospora cayetanensis, a coccidian parasite that causes protracted and relapsing gastroenteritis, has a short recorded history. At least 54 countries have documented C. cayetanensis infections and 13 of them have recorded cyclosporiasis outbreaks. Cyclospora cayetanensis infections are commonly reported in developing countries with low-socioeconomic levels or in endemic areas, although large outbreaks have also been documented in developed countries. The overall C. cayetanensis prevalence in humans worldwide is 3.55%. Among susceptible populations, the highest prevalence has been documented in immunocompetent individuals with diarrhea. Infections are markedly seasonal, occurring in the rainy season or summer. Cyclospora cayetanensis or Cyclospora-like organisms have also been detected in food, water, soil and some other animals. Detection methods based on oocyst morphology, staining and molecular testing have been developed. Treatment with trimethoprim-sulfamethoxazole (TMP-SMX) effectively cures C. cayetanensis infection, whereas ciprofloxacin is less effective than TMP-SMX, but is suitable for patients who cannot tolerate co-trimoxazole. Here, we review the biological characteristics, clinical features, epidemiology, detection methods and treatment of C. cayetanensis in humans, and assess some risk factors for infection with this pathogen.
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20
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Almeria S, Cinar HN, Dubey JP. Cyclospora cayetanensis and Cyclosporiasis: An Update. Microorganisms 2019; 7:E317. [PMID: 31487898 PMCID: PMC6780905 DOI: 10.3390/microorganisms7090317] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022] Open
Abstract
Cyclospora cayetanensis is a coccidian parasite of humans, with a direct fecal-oral transmission cycle. It is globally distributed and an important cause of foodborne outbreaks of enteric disease in many developed countries, mostly associated with the consumption of contaminated fresh produce. Because oocysts are excreted unsporulated and need to sporulate in the environment, direct person-to-person transmission is unlikely. Infection by C. cayetanensis is remarkably seasonal worldwide, although it varies by geographical regions. Most susceptible populations are children, foreigners, and immunocompromised patients in endemic countries, while in industrialized countries, C. cayetanensis affects people of any age. The risk of infection in developed countries is associated with travel to endemic areas and the domestic consumption of contaminated food, mainly fresh produce imported from endemic regions. Water and soil contaminated with fecal matter may act as a vehicle of transmission for C. cayetanensis infection. The disease is self-limiting in most immunocompetent patients, but it may present as a severe, protracted or chronic diarrhea in some cases, and may colonize extra-intestinal organs in immunocompromised patients. Trimetoprim-sulfamethoxazole is the antibiotic of choice for the treatment of cyclosporiasis, but relapses may occur. Further research is needed to understand many unknown epidemiological aspects of this parasitic disease. Here, we summarize the biology, epidemiology, outbreaks, clinical symptoms, diagnosis, treatment, control and prevention of C. cayetanensis; additionally, we outline future research needs for this parasite.
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Affiliation(s)
- Sonia Almeria
- Department of Health and Human Services, Food and Drug Administration, Center for Food Safety and Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Hediye N Cinar
- Department of Health and Human Services, Food and Drug Administration, Center for Food Safety and Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Jitender P Dubey
- Animal Parasitic Disease Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Building 1001, BARC-East, Beltsville, MD 20705-2350, USA.
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21
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Wang X, Wang J, Liu J, Liu A, He X, Xu J, Li Z, Zhao S, Li Y, Yin H, Luo J, Guan G. Comparative analysis of apicoplast genomes of Babesia infective to small ruminants in China. Parasit Vectors 2019; 12:312. [PMID: 31234937 PMCID: PMC6591869 DOI: 10.1186/s13071-019-3581-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 06/19/2019] [Indexed: 02/08/2023] Open
Abstract
Background Babesiosis is an economically important disease caused by tick-borne apicomplexan protists of the genus Babesia. Most apicomplexan parasites, including Babesia, have a plastid-derived organelle termed an apicoplast, which is involved in critical metabolic pathways such as fatty acid, iron-sulphur, haem and isoprenoid biosynthesis. Apicoplast genomic data can provide significant information for understanding and exploring the biological features, taxonomic and evolutionary relationships of apicomplexan parasites, and identify targets for anti-parasitic drugs. However, there are limited data on the apicoplast genomes of Babesia species infective to small ruminants. Methods PCR primers were designed based on the previously reported apicoplast genome sequences of Babesia motasi Lintan and Babesia sp. Xinjiang using Illumina technology. The overlapped apicoplast genomic fragments of six ovine Babesia isolates were amplified and sequenced using the Sanger dideoxy chain-termination method. The full-length sequences of the apicoplast genomes were assembled and annotated using bioinformatics software. The gene contents and order of apicoplast genomes obtained in this study were defined and compared with those of other apicomplexan parasites. Phylogenetic trees were constructed on the concatenated amino acid sequences of 13 gene products using MEGA v.6.06. Results The results showed that the six ovine Babesia apicoplast genomes consisted of circular DNA. The genome sizes were 29,916–30,846 bp with 78.7–81.0% A + T content, 29–31 open reading frames (ORF) and 23–24 transport RNAs. The ORFs encoded four DNA-directed RNA polymerase subunits (rpoB, rpoCl, rpoC2a and rpoC2b), 13 ribosomal proteins, one elongation factor TU (tufA), two ATP-dependent Clp proteases (ClpC) and 7–11 hypothetical proteins. Babesia sp. has three more genes than Babesia motasi (rpl5, rps8 and rpoB). Phylogenetic analysis showed that Babesia sp. is located in a separate clade. Babesia motasi Lintan/Tianzhu and B. motasi Ningxian/Hebei were divided into two subclades. Conclusions To our knowledge, this study is the first to elucidate the whole apicoplast genomic structural features of six Babesia isolates infective to small ruminants in China using Sanger sequencing. The data provide useful information confirming the taxonomic relationships of these parasites and identifying targets for anti-apicomplexan parasite drugs. Electronic supplementary material The online version of this article (10.1186/s13071-019-3581-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoxing Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Xin He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jianlin Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Zhi Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Shuaiyang Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.
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22
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Human cyclosporiasis. THE LANCET. INFECTIOUS DISEASES 2019; 19:e226-e236. [PMID: 30885589 DOI: 10.1016/s1473-3099(18)30789-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 01/10/2023]
Abstract
Cyclospora species are socioeconomically important protistan pathogens. Cyclospora cayetanensis is usually transmitted via food or water to a human host via the faecal-oral route and can cause the gastrointestinal disease cyclosporiasis, which can be complicated by extra-intestinal disorders, particularly in immune-compromised people. Although more than 2 million children die each year from diarrhoeal diseases worldwide, it is not known to what extent cyclosporiasis is involved. Few epidemiological data are available on Cyclospora as a water-borne and food-borne pathogen in both underprivileged communities and developed countries. To gain an improved understanding of human cyclosporiasis, this Review describes the background of Cyclospora, summarises salient aspects of the pathogenesis, epidemiology, diagnosis, treatment, and control of cyclosporiasis, and explores what is known about its prevalence and geographical distribution. The findings show that the effect on human health of cyclosporiasis is likely underestimated, and recommendations are made about areas of future research and the prevention and control of this disease within an international collaborative context.
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23
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Smith DR. Evolution: A Plant Plastid Genome that Has Forsaken Guanine and Cytosine. Curr Biol 2019; 29:R99-R101. [PMID: 30721685 DOI: 10.1016/j.cub.2018.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The plastid genomes of the non-photosynthetic plants Balanophora reflexa and B. laxiflora are among the most GC-biased genomes observed to date. A new study shows that ∼80% of the plastid-derived proteome is represented by only six amino acids, and several genes are in excess of 95% AT.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada.
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24
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Guo Y, Wang Y, Wang X, Zhang L, Ortega Y, Feng Y. Mitochondrial genome sequence variation as a useful marker for assessing genetic heterogeneity among Cyclospora cayetanensis isolates and source-tracking. Parasit Vectors 2019; 12:47. [PMID: 30665345 PMCID: PMC6341762 DOI: 10.1186/s13071-019-3294-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/07/2019] [Indexed: 08/30/2023] Open
Abstract
Background Cyclospora cayetanensis is an important enteric pathogen, causing diarrhea and food-borne cyclosporiasis outbreaks. For effective outbreak identification and investigation, it is essential to rapidly assess the genetic heterogeneity of C. cayetanensis specimens from cluster cases and identify the likely occurrence of outbreaks. Methods In this study, we developed a quantitative PCR (qPCR) targeting the polymorphic link region between copies of the mitochondrial genome of C. cayetanensis, and evaluated the genetic heterogeneity among 36 specimens from six countries using melt curve, gel electrophoresis, and sequence analyses of the qPCR products. Results All specimens were amplified successfully in the qPCR and produced melt peaks with different Tm values in the melt curve analysis. In gel electrophoresis of the qPCR products, the specimens yielded bands of variable sizes. Nine genotypes were identified by DNA sequencing of the qPCR products. Geographical segregation of genotypes was observed among specimens analyzed, which could be useful in geographical source-tracking. Conclusions The length and nucleotide sequence variations in the mitochondrial genome marker allow rapid assessment of the genetic heterogeneity among C. cayetanensis specimens by melt curve, gel electrophoresis, or DNA sequence analysis of qPCR products. The sequence data generated could be helpful in the initial source-tracking of the pathogen.
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Affiliation(s)
- Yaqiong Guo
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yuanfei Wang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiaolan Wang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Ynes Ortega
- College of Agricultural and Environmental Sciences, University of Georgia, Griffin, Georgia, 30223, USA
| | - Yaoyu Feng
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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25
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Su HJ, Barkman TJ, Hao W, Jones SS, Naumann J, Skippington E, Wafula EK, Hu JM, Palmer JD, dePamphilis CW. Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc Natl Acad Sci U S A 2019; 116:934-943. [PMID: 30598433 PMCID: PMC6338844 DOI: 10.1073/pnas.1816822116] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
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Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, 100 Taipei, Taiwan
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Samuel S Jones
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
| | - Julia Naumann
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | | | - Eric K Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 106 Taipei, Taiwan
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Claude W dePamphilis
- Department of Biology, Pennsylvania State University, University Park, PA 16802;
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802
- Graduate Program in Plant Biology, Pennsylvania State University, University Park, PA 16802
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26
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Qvarnstrom Y, Wei-Pridgeon Y, Van Roey E, Park S, Srinivasamoorthy G, Nascimento FS, Moss DM, Talundzic E, Arrowood MJ. Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing. Gut Pathog 2018; 10:45. [PMID: 30337964 PMCID: PMC6182803 DOI: 10.1186/s13099-018-0272-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Cyclospora cayetanensis is a food-borne intestinal human parasite that causes outbreaks of diarrhea. There is a need for efficient laboratory methods for strain-level characterization to assist in outbreak investigations. By using next generation sequencing, genomic sequences can be obtained and compared to identify potential genotyping markers. However, there is no method available to propagate this parasite in the laboratory. Therefore, genomic DNA must be extracted from oocysts purified from human stool. The objective of this study was to apply optimized methods to purify C. cayetanensis oocysts and extract DNA in order to obtain high-quality whole genome sequences with minimum contamination of DNA from other organisms. Results Oocysts from 21 human stool specimens were separated from other stool components using discontinuous density gradient centrifugation and purified further by flow cytometry. Genomic DNA was used to construct Ovation Ultralow libraries for Illumina sequencing. MiSeq sequencing reads were taxonomically profiled for contamination, de novo assembled, and mapped to a draft genome available in GenBank to assess the quality of the resulting genomic sequences. Following all purification steps, the majority (81-99%) of sequencing reads were from C. cayetanensis. They could be assembled into draft genomes of around 45 MB in length with GC-content of 52%. Conclusions Density gradients performed in the presence of a detergent followed by flow cytometry sorting of oocysts yielded sufficient genomic DNA largely free from contamination and suitable for whole genome sequencing of C. cayetanensis. The methods described here will facilitate the accumulation of genomic sequences from various samples, which is a prerequisite for the development of typing tools to aid in outbreak investigations.
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Affiliation(s)
- Yvonne Qvarnstrom
- 1Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Yuping Wei-Pridgeon
- 1Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA.,IHRC Inc, Atlanta, GA USA
| | - Erik Van Roey
- 1Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Subin Park
- 1Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | - Fernanda S Nascimento
- 1Parasitic Disease Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Delynn M Moss
- 4Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Enteric and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Eldin Talundzic
- 5Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Michael J Arrowood
- 4Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Enteric and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
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27
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Gopinath GR, Cinar HN, Murphy HR, Durigan M, Almeria M, Tall BD, DaSilva AJ. A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes. Gut Pathog 2018; 10:15. [PMID: 29643938 PMCID: PMC5891936 DOI: 10.1186/s13099-018-0242-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 04/01/2018] [Indexed: 11/10/2022] Open
Abstract
Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations.
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Affiliation(s)
- G R Gopinath
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - H N Cinar
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - H R Murphy
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - M Durigan
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - M Almeria
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - B D Tall
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - A J DaSilva
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
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28
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Guo Y, Roellig DM, Li N, Tang K, Frace M, Ortega Y, Arrowood MJ, Feng Y, Qvarnstrom Y, Wang L, Moss DM, Zhang L, Xiao L. Multilocus Sequence Typing Tool for Cyclospora cayetanensis. Emerg Infect Dis 2018; 22:1464-7. [PMID: 27433881 PMCID: PMC4982147 DOI: 10.3201/eid2208.150696] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Because the lack of typing tools for Cyclospora cayetanensis has hampered outbreak investigations, we sequenced its genome and developed a genotyping tool. We observed 2 to 10 geographically segregated sequence types at each of 5 selected loci. This new tool could be useful for case linkage and infection/contamination source tracking.
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29
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Characterization of two complete Isospora mitochondrial genomes from passerine birds: Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner. Vet Parasitol 2017; 237:137-142. [DOI: 10.1016/j.vetpar.2017.01.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 01/23/2017] [Accepted: 01/31/2017] [Indexed: 01/08/2023]
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30
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Cinar HN, Qvarnstrom Y, Wei-Pridgeon Y, Li W, Nascimento FS, Arrowood MJ, Murphy HR, Jang A, Kim E, Kim R, da Silva A, Gopinath GR. Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions. Parasit Vectors 2016; 9:611. [PMID: 27899155 PMCID: PMC5129617 DOI: 10.1186/s13071-016-1896-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis. The apicoplast of C. cayetanensis, a relict non-photosynthetic plastid with an independent genome, provides an attractive target to discover sequence polymorphisms useful as genetic markers for detection and trace back analysis of the parasite. Distinct differences in the apicoplast genomes of C. cayetanensis could be useful in designing advanced molecular methods for rapid detection and, subtyping and geographical source attribution, which would aid outbreak investigations and surveillance studies. METHODS To obtain the genome sequence of the C. cayetanensis apicoplast, we sequenced the C. cayetanensis genomic DNA extracted from clinical stool samples, assembled and annotated a 34,146 bp-long circular sequence, and used this sequence as a reference genome in this study. We compared the genome and the predicted proteome to the data available from other apicomplexan parasites. To initialize the search for genetic markers, we mapped the raw sequence reads from an additional 11 distinct clinical stool samples originating from Nepal, New York, Texas, and Indonesia to the apicoplast reference genome. RESULTS We identified several high quality single nucleotide polymorphisms (SNPs) and small insertion/deletions spanning the apicoplast genome supported by extensive sequencing reads data, and a 30 bp sequence repeat at the terminal spacer region in a Nepalese sample. The predicted proteome consists of 29 core apicomplexan peptides found in most of the apicomplexans. Cluster analysis of these C. cayetanensis apicoplast genomes revealed a familiar pattern of tight grouping with Eimeria and Toxoplasma, separated from distant species such as Plasmodium and Babesia. CONCLUSIONS SNPs and sequence repeats identified in this study may be useful as genetic markers for identification and differentiation of C. cayetanensis isolates found and could facilitate outbreak investigations.
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Affiliation(s)
- Hediye Nese Cinar
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yuping Wei-Pridgeon
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wen Li
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Fernanda S Nascimento
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael J Arrowood
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Helen R Murphy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - AhYoung Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Eunje Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - RaeYoung Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Alexandre da Silva
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Gopal R Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
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31
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Wang T, Guan G, Korhonen PK, Koehler AV, Hall RS, Young ND, Yin H, Gasser RB. The apicoplast genomes of two taxonomic units of Babesia from sheep. Vet Parasitol 2016; 233:123-128. [PMID: 27916258 DOI: 10.1016/j.vetpar.2016.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
Abstract
The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp. Lintan [Bl] and Babesia sp. Xinjiang [Bx]) from sheep were sequenced, assembled and annotated using a massive parallel sequencing-based approach. Then, the gene content and gene order in these ap genomes (∼30.7kb in size) were defined and compared, and the genetic differences were assessed. In addition, a phylogenetic analysis of ap genomic data sets was carried out to assess the relationships of these taxonomic units with other apicomplexan parasites for which complete ap genomic data sets were publicly available. The results showed that the ap genomes of Bl and Bx encode 59 and 57 genes, respectively, including 2 ribosomal RNA genes, 25 transfer RNA genes and 30-32 protein-encoding genes, being similar in content to those of Babesia bovis and B. orientalis. Ap gene regions that might serve as markers for future epidemiological and population genetic studies of Babesia species were identified. Using sequence data for a subset of six protein-encoding genes, a close relationship of Bl and Bx with Babesia bovis from cattle and B. orientalis from water buffalo was inferred. Although the focus of the present study was on Babesia, we propose that the present sequencing-bioinformatic approach should be applicable to organellar genomes of a wide range of apicomplexans of veterinary importance.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China; Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anson V Koehler
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S Hall
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China.
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia.
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Liu S, Wang L, Zheng H, Xu Z, Roellig DM, Li N, Frace MA, Tang K, Arrowood MJ, Moss DM, Zhang L, Feng Y, Xiao L. Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. BMC Genomics 2016; 17:316. [PMID: 27129308 PMCID: PMC4851813 DOI: 10.1186/s12864-016-2632-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/20/2016] [Indexed: 01/24/2023] Open
Abstract
Background Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of C. cayetanensis and inferred its metabolism and invasion components based on comparative genomic analysis. Results The genome organization, metabolic capabilities and potential invasion mechanism of C. cayetanensis are very similar to those of Eimeria tenella. Propanoyl-CoA degradation, GPI anchor biosynthesis, and N-glycosylation are some apparent metabolic differences between C. cayetanensis and E. tenella. Unlike Eimeria spp., there are no active LTR-retrotransposons identified in C. cayetanensis. The similar repertoire of host cell invasion-related proteins possessed by all coccidia suggests that C. cayetanensis has an invasion process similar to the one in T. gondii and E. tenella. However, the significant reduction in the number of identifiable rhoptry protein kinases, phosphatases and serine protease inhibitors indicates that monoxenous coccidia, especially C. cayetanensis, have limited capabilities or use a different system to regulate host cell nuclear activities. C. cayetanensis does not possess any cluster of genes encoding the TA4-type SAG surface antigens seen in E. tenella, and may use a different family of surface antigens in initial host cell interactions. Conclusions Our findings indicate that C. cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. Amino acid metabolism and post-translation modifications of proteins are some major differences between C. cayetanensis and other apicomplexans. The whole genome sequence data of C. cayetanensis improve our understanding of the biology and evolution of this major foodborne pathogen and facilitate the development of intervention measures and advanced diagnostic tools. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2632-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiyou Liu
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Lin Wang
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Huajun Zheng
- Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, 250 Bibo Road, Shanghai, 201203, China
| | - Zhixiao Xu
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Dawn M Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Na Li
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Michael A Frace
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Kevin Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Michael J Arrowood
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Delynn M Moss
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yaoyu Feng
- State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Lihua Xiao
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
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Zverkov OA, Seliverstov AV, Lyubetsky VA. Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch. Life (Basel) 2016; 6:E7. [PMID: 26840333 PMCID: PMC4810238 DOI: 10.3390/life6010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/20/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed.
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Affiliation(s)
- Oleg Anatolyevich Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
| | - Alexandr Vladislavovich Seliverstov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
| | - Vassily Alexandrovich Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
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34
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Characterization and annotation of Babesia orientalis apicoplast genome. Parasit Vectors 2015; 8:543. [PMID: 26474853 PMCID: PMC4609131 DOI: 10.1186/s13071-015-1158-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/08/2015] [Indexed: 11/30/2022] Open
Abstract
Background Babesia orientalis is an obligate intraerythrocytic protozoan parasite of the buffalo (Bubalus bubalis, Linnaeus, 1758) transmitted by the tick Rhipicephalus heamaphysaloides. It is the causative agent of water buffalo babesiosis, one of the most important pathogens of water buffalo in central and southern China. As a member of the phylum Apicomplexa, B. orientalis possesses a relatively independent and alga originated organelle the apicoplast. Apicoplasts in other apicomplexa parasites are involved in the biosynthesis of haem, fatty acids, iron-sulphur clusters and isoprenoids. Some of these metabolic pathways were shown to be essential for parasite survival, therefore can serve as potential drug targets. Methods 30 pairs of primers were designed based on the full genome sequence of B. orientalis (unpublished data) and by aligning reported apicoplast genomes of Babesia bovis and Theileria parva. Conventional PCRs was performed to obtain overlapped fragments to cover the whole apicoplast genome. Then the apicoplast genome of B.orientalis was sequenced, assembled and aligned with reported apicoplast genomes of B. bovis and T. parva. The obtained apicoplast genome was annotated by using Artemis and comparing with published apicomplexan apicoplast genomes. The SSU and LSU nucleotide sequences generated were used in a phylogenetic analysis using the maximum likelihood implemented in MAGE 6.0. Results We have obtained and analyzed the complete genome sequence of the B. orientalis apicoplast. It consisted of a 33.2 kb circular DNA (78.9 % A + T). The apicoplast genome unidirectionally encodes one large and one small subunit ribosomal RNAs, 24 tRNA genes, 4 DNA-dependent RNA polymerase beta subunits (rpoB, rpoC1, rpoC2a and rpoC2b), 17 ribosomal proteins, one EF-Tu elongation factor, 2 Clp protease chaperones, and 14 hypothetical proteins. In addition, it includes two copies of the clpC gene. The structure and organization of the B. orientalis apicoplast genome are most similar to those of the B. bovis apicoplast. Conclusions This is the first report of the complete sequence of the B. orientalis apicoplast genome. This information should be useful in the development of safe and efficient treatment against buffalo babesiosis. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1158-x) contains supplementary material, which is available to authorized users.
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