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Durigan M, Ewing-Peeples L, Almeria S, Balan KV, Grocholl J, Irizawa S, Mammel M. Detection of Cyclospora cayetanensis in Food and Water Samples: Optimized Protocols for Specific and Sensitive Molecular Methods from a Regulatory Agency Perspective. J Food Prot 2024; 87:100291. [PMID: 38701974 DOI: 10.1016/j.jfp.2024.100291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/29/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cyclospora cayetanensis is a coccidian parasite of the phylum Apicomplexa that causes cyclosporiasis, a human-specific gastrointestinal disease. Unlike most enteric pathogens, C. cayetanensis does not infect via direct fecal-oral transmission between humans because shed oocysts must be exposed to environmental triggers prior to becoming infectious. The development of specific and sensitive detection methods for C. cayetanensis is crucial to effectively address data gaps and provide regulatory support during outbreak investigations. In this study, new more specific molecular markers for the detection of C. cayetanensis were developed based on updated genomic databases of Apicomplexa mitochondrial sequences. Novel alternative reagents and supplies, as well as optimization protocols, were tested in spiked produce and agricultural water samples. The selected Mit1C primers and probe combined showed at least 13 mismatches to other related species. The new optimized qualitative real-time PCR assay with modifications to sample processing and replacement of discontinued items produced results comparable to the previously validated methods. In conclusion, the new optimized qualitative Mit1C real-time PCR assay demonstrated an increase in its specificity in comparison to other detection methods previously published, while it showed to be robust and as sensitive as the previously validated method at the FDA. This study has also expanded the array of PCR reagents that can be used to detect C. cayetanensis in produce and agricultural water samples and provided several improvements to the method for detection in agricultural water including replacements for discontinued items and a new dialysis filter for water filtration.
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Affiliation(s)
- Mauricio Durigan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA.
| | - Laura Ewing-Peeples
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Sonia Almeria
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - Kannan V Balan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
| | - John Grocholl
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA; Goldbelt C6, Chesapeake, VA 23320, USA
| | - Sachi Irizawa
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD 20742, USA
| | - Mark Mammel
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Virulence Assessment, Laurel, MD 20708, USA
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Jacobson DK, Peterson AC, Qvarnstrom Y, Barratt JL. Novel insights on the genetic population structure of human-infecting Cyclospora spp. and evidence for rapid subtype selection among isolates from the USA. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 4:100145. [PMID: 37841306 PMCID: PMC10569985 DOI: 10.1016/j.crpvbd.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
Human-infecting Cyclospora was recently characterized as three species, two of which (C. cayetanensis and C. ashfordi) are currently responsible for all known human infections in the USA, yet much remains unknown about the genetic structure within these two species. Here, we investigate Cyclospora genotyping data from 2018 through 2022 to ascertain if there are temporal patterns in the genetic structure of Cyclospora parasites that cause infections in US residents from year to year. First, we investigate three levels of genetic characterization: species, subpopulation, and strain, to elucidate annual trends in Cyclospora infections. Next, we determine if shifts in genetic diversity can be linked to any of the eight loci used in our Cyclospora genotyping approach. We observed fluctuations in the abundance of Cyclospora types at the species and subpopulation levels, but no significant temporal trends were identified; however, we found recurrent and sporadic strains within both C. ashfordi and C. cayetanensis. We also uncovered major shifts in the mitochondrial genotypes in both species, where there was a universal increase in abundance of a specific mitochondrial genotype that was relatively abundant in 2018 but reached near fixation (was observed in over 96% of isolates) in C. ashfordi by 2022. Similarly, this allele jumped from 29% to 82% relative abundance of isolates belonging to C. cayetanensis. Overall, our analysis uncovers previously unknown temporal-genetic patterns in US Cyclospora types from 2018 through 2022 and is an important step to presenting a clearer picture of the factors influencing cyclosporiasis outbreaks in the USA.
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Affiliation(s)
- David K. Jacobson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna C. Peterson
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel L.N. Barratt
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
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3
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Magdy Mohamed Abdelaziz Barakat S, Sallehuddin R, Yuhaniz SS, R. Khairuddin RF, Mahmood Y. Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges. PeerJ Comput Sci 2023; 9:e1180. [PMID: 37547391 PMCID: PMC10403225 DOI: 10.7717/peerj-cs.1180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/27/2023] [Indexed: 08/08/2023]
Abstract
Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization. Results Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach. Conclusion We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
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Affiliation(s)
| | - Roselina Sallehuddin
- Computer Science, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Siti Sophiayati Yuhaniz
- Advanced Informatics Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Kuala Lumpur, Kuala Lumpur, Malaysia
| | | | - Yasir Mahmood
- Faculty of Information Technology, The University of Lahore, Lahore, Lahore, Pakistan
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4
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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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5
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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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6
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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:microorganisms10101977. [PMID: 36296256 PMCID: PMC9608778 DOI: 10.3390/microorganisms10101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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7
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Development of a Molecular Marker Based on the Mitochondrial Genome for Detection of Cyclospora cayetanensis in Food and Water Samples. Microorganisms 2022; 10:microorganisms10091762. [PMID: 36144364 PMCID: PMC9504131 DOI: 10.3390/microorganisms10091762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
Cyclospora cayetanensis is a coccidian parasite that causes diarrheal illness outbreaks worldwide. The development of new laboratory methods for detection of C. cayetanensis is of critical importance because of the high potential for environmental samples to be contaminated with a myriad of microorganisms, adversely impacting the specificity when testing samples from various sources using a single molecular assay. In this study, a new sequencing-based method was designed targeting a specific fragment of C. cayetanensis cytochrome oxidase gene and developed as a complementary method to the TaqMan qPCR present in the U.S. FDA BAM Chapter 19b and Chapter 19c. The comparative results between the new PCR protocol and the qPCR for detection of C. cayetanensis in food and water samples provided similar results in both matrices with the same seeding level. The target region and primers in the protocol discussed in this study contain sufficient Cyclospora-specific sequence fidelity as observed by sequence comparison with other Eimeriidae species. The sequence of the PCR product appears to represent a robust target for identifying C. cayetanensis on samples from different sources. Such a sensitive method for detection of C. cayetanensis would add to the target repertoire of qPCR-based screening strategies for food and water samples.
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8
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Guo R, Papanicolaou A, Fritz ML. Validation of reference-assisted assembly using existing and novel Heliothine genomes. Genomics 2022; 114:110441. [PMID: 35931274 DOI: 10.1016/j.ygeno.2022.110441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran family with few genomic resources. We then examined the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa and applied it to our Heliothine genomes. Our work demonstrates that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. We conclude by discussing both the potential and pitfalls of reference-assisted assembly according to the intended downstream assembly application.
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Affiliation(s)
- Rong Guo
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia.
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA.
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9
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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: 3.0] [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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10
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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: 1.7] [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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11
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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: 18] [Impact Index Per Article: 4.5] [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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12
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Padovani de Souza K, Setubal JC, Ponce de Leon F de Carvalho AC, Oliveira G, Chateau A, Alves R. Machine learning meets genome assembly. Brief Bioinform 2020; 20:2116-2129. [PMID: 30137230 DOI: 10.1093/bib/bby072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/11/2018] [Accepted: 07/22/2018] [Indexed: 12/23/2022] Open
Abstract
MOTIVATION With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequencing projects remain unsolved. Among them is the task of assembling DNA fragments from previously unsequenced organisms, which is classified as an NP-hard (nondeterministic polynomial time hard) problem, for which no efficient computational solution with reasonable execution time exists. However, several tools that produce approximate solutions have been used with results that have facilitated scientific discoveries, although there is ample room for improvement. As with other NP-hard problems, machine learning algorithms have been one of the approaches used in recent years in an attempt to find better solutions to the DNA fragment assembly problem, although still at a low scale. RESULTS This paper presents a broad review of pioneering literature comprising artificial intelligence-based DNA assemblers-particularly the ones that use machine learning-to provide an overview of state-of-the-art approaches and to serve as a starting point for further study in this field.
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Affiliation(s)
| | - João Carlos Setubal
- University of São Paulo, Brazil.,Department of Computer Science, University of São Paulo, Brazil
| | | | | | - Annie Chateau
- Vale Technology Institute-Sustainable Development, Brazil
| | - Ronnie Alves
- Federal University of Pará, Brazil.,University of Montpellier, LIRMM, France
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13
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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: 2.8] [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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14
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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: 4.0] [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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15
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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: 75] [Impact Index Per Article: 15.0] [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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16
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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: 40] [Impact Index Per Article: 8.0] [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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17
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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: 1.8] [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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