ArticleEpidemiology and infection2020
Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis.
Article in Epidemiology and infection, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Molecular and morphologic characterization of Trichuris trichiura infecting free-roaming African vervets (Chlorocebus aethiops sabaeus) on the Caribbean Island of St. Kitts.PLoS neglected tropical diseases · 2026Article
- Assessing the sequencing success and analytical specificity of a targeted amplicon deep sequencing workflow for genotyping the foodborne parasiteJournal of clinical microbiology · 2025Article
- Cyclospora Genotypic Variations and Associated Epidemiologic Characteristics, United States, 2018-2021.Emerging infectious diseases · 2025Article
- Sources and Prevalence of Cyclospora cayetanensis in Southeastern U.S. Growing Environments.Journal of food protection · 2024Article
- Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for GenotypingMicroorganisms · 2024Article
- Editorial: Impact and control of food- and waterborne protozoan parasites.Frontiers in microbiology · 2024Article
- Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis.Parasitology research · 2023Article
- The limit of detection of the BioFire® FilmArray® gastrointestinal panel for the foodborne parasite Cyclospora cayetanensis.Diagnostic microbiology and infectious disease · 2023Article
- Article
- Retrospective evaluation of an integrated molecular-epidemiological approach to cyclosporiasis outbreak investigations - United States, 2021.Epidemiology and infection · 2023Article
- Epidemiologic Utility of a Framework for Partition Number Selection When Dissecting Hierarchically Clustered Genetic Data Evaluated on the Intestinal Parasite Cyclospora cayetanensis.American journal of epidemiology · 2023Article
- Genetic characterization ofInternational journal for parasitology. Parasites and wildlife · 2023Article
- Article
- An improved framework for detecting discrete epidemiologically meaningful partitions in hierarchically clustered genetic data.Bioinformatics advances · 2023Article
- Optimizing hierarchical tree dissection parameters using historic epidemiologic data as 'ground truth'.PloS one · 2023Article
- Development of a targeted amplicon sequencing method for genotypingFrontiers in microbiology · 2023Article
- Novel insights on the genetic population structure of human-infectingCurrent research in parasitology & vector-borne diseases · 2023Article
- Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST datasets.Molecular phylogenetics and evolution · 2022Article
- Targeted next generation sequencing ofHeliyon · 2022Article
- Hastening Progress inMicroorganisms · 2022Article
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20 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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