Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing

Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis

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.

Cyclospora cayetanensis: A Perspective (2020-2023) with Emphasis on Epidemiology and Detection Methods

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.

Migrating Anatidae as Sources of Environmental Contamination with Zoonotic Giardia, Cryptosporidium, Cyclospora and Microsporidia

Giardia, Cryptosporidium, Cyclospora, and microsporidia are gastrointestinal pathogens that can cause various disease symptoms in both animals and humans. Numerous studies worldwide have confirmed the presence of these eukaryotic pathogens in nesting and migrating wild geese, ducks, and swans. Migration spreads these zoonotic enteric pathogens to distant locations, which could have public health implications. Soils and water bodies (lakes, ponds, rivers and wetlands) in urban and suburban areas have been shown to be vulnerable to contamination by waterfowl droppings. This review addresses the epidemiology of these enteric pathogens in wild migratory bird species (Anatidae) and some consequences of their spread in the environment. To date, both zoonotic pathogens and genotypes restricted to avian hosts have been found in faecal samples from 21 anatid species worldwide. One of the routes of infection for these zoonotic gastrointestinal micropathogens is the indirect route. For example, shared water bodies (e.g., for drinking or recreational purposes) previously contaminated by birds during the migratory season may facilitate infections of humans through water. However, it is unclear how much wild waterfowl contribute to the transmission of giardiasis, cryptosporidiosis, cyclosporosis, and microsporidiosis in many regions through contaminated environmental sources. Comprehensive epidemiological surveillance based on molecular data on gastrointestinal pathogens is crucial to take measures to control infections in the future.

Cyclospora cayetanensis Infection in Developed Countries: Potential Endemic Foci?

Cyclospora cayetanensis infection has emerged as a significant public health concern worldwide. Developed countries are generally considered non-endemic for infection. However, sporadic cases and non-travel-related outbreaks of C. cayetanensis infections associated with domestically grown produce are becoming more common in developed countries. Cyclospora cayetanensis has been detected in fresh produce, surface water, wastewater, irrigation water, and soil in these countries, suggesting that the parasite may be more common in areas with advanced sanitation than previously thought and illustrating the potential risk for exposure and indigenous/autochthonous infections. The evidence suggests the possibility of foci of endemicity in developed countries, particularly in communities where sanitary conditions are compromised, and raises transmission issues that require further research to better define the risks for infection, how widespread C. cayetanensis may be in these areas, and to guide interventions against this infection. The main purpose of the present opinion was to evaluate the presence of cyclosporiasis in developed countries, which is a very important and ongoing issue in food safety.

Review on Cyclosporiasis Outbreaks and Potential Molecular Markers for Tracing Back Investigations

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.

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

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.

Development of a Molecular Marker Based on the Mitochondrial Genome for Detection of Cyclospora cayetanensis in Food and Water Samples

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.

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

Verification and Use of the US-FDA BAM 19b Method for Detection of Cyclospora cayetanensis in a Survey of Fresh Produce by CFIA Laboratory

To facilitate the harmonized surveillance and investigation of cyclosporiasis outbreaks in the US and Canada, we adapted and verified the US-FDA’s BAM 19b method and employed it in a national produce survey. Performance was verified by spiking 200, 10, 5 or 0 C. cayetanensis oocysts onto berries (50 ± 5 g, n = 85) and 200, 10 or 0 oocysts onto green onions (25 ± 3 g, n = 24) and leafy greens (25 ± 1 g, n = 120) and testing these samples by the BAM method on Bio-Rad CFX96. Method robustness was assessed by aging (0 or 7 days) and freezing the produce and washes prior to testing, then implementing the method for the surveillance testing of 1759 imported leafy green, herb and berry samples. Diagnostic sensitivity was 100/44% and 93/30% for berries and leafy greens spiked with 200/10 oocysts, respectively. The diagnostic and analytical specificity were 100% for all matrices and related parasites tested. The proportion positive was unaffected (p = 0.22) by age or condition of produce (7d, fresh, frozen) or wash concentrate (3d, fresh, frozen); however, the Cq values were higher (p = 0.009) for raspberries aged 7d (37.46 ± 0.29) compared to fresh (35.36 ± 0.29). C. cayetanensis was detected in berries (two), herbs (two) and leafy greens (one), representing 0.28% of the tested survey samples. These results independently verified the reported performance characteristics and robustness of the BAM method for the detection of C. cayetanensis in a variety of matrices, including under adverse sample conditions, using a unique detection platform and demonstrating its routine diagnostic use in our Canadian Food Inspection Agency (CFIA) laboratory.

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian

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.

Host Range of Cyclospora Species: Zoonotic Implication

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.

Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis

Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis.