ArticleParasitology2019
Genotyping genetically heterogeneous
Article in Parasitology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 40 citations in OpenAlex.
- 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
- Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for GenotypingMicroorganisms · 2024Article
- Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis.Parasitology research · 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
- Novel insights on the genetic population structure of human-infectingCurrent research in parasitology & vector-borne diseases · 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
- 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
- Development of a Molecular Marker Based on the Mitochondrial Genome for Detection ofMicroorganisms · 2022Article
- Genotyping Cyclospora cayetanensis From Multiple Outbreak Clusters With An Emphasis on a Cluster Linked to Bagged Salad Mix-United States, 2020.The Journal of infectious diseases · 2022Article
- Genotyping CanadianMicroorganisms · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Sexually reproducing pathogens such as Cyclospora cayetanensis often produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness of C. cayetanensis infections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containing C. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P < 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of cyclosporiasis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.