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 genotyp...

Full description

Saved in:
Bibliographic Details
Published in:Epidemiology and infection 2020-01, Vol.148, p.e172-e172, Article e172
Main Authors: Nascimento, Fernanda S., Barratt, Joel, Houghton, Katelyn, Plucinski, Mateusz, Kelley, Julia, Casillas, Shannon, Bennett, Carolyne (Cody), Snider, Cathy, Tuladhar, Rashmi, Zhang, Jenny, Clemons, Brooke, Madison-Antenucci, Susan, Russell, Alexis, Cebelinski, Elizabeth, Haan, Jisun, Robinson, Trisha, Arrowood, Michael J., Talundzic, Eldin, Bradbury, Richard S., Qvarnstrom, Yvonne
Format: Article
Language:English
Subjects:
Clustering
Cyclosporiasis
Deoxyribonucleic acid
Disease control
DNA
Epidemics
Epidemiology
Feces
Food
Foodborne diseases
Genotypes
Genotyping
Haplotypes
Heterogeneity
Medical laboratories
Methods
Microscopy
Original Paper
Parasites
Parasitic diseases
Polyvinyl alcohol
Reproductive cycle
Statistical methods
Statistics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0950-2688
1469-4409
DOI:10.1017/S0950268820001697