Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis
Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis
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DOI：
10.1017/s0950268820001697
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发表时间：
2020-01-01
影响因子：
4.2
通讯作者：
Qvarnstrom, Yvonne
中科院分区：
文献类型：
--
作者：
Nascimento, Fernanda S.;Barratt, Joel;Qvarnstrom, Yvonne
环孢子虫病是一种由球虫寄生虫——卡耶塔环孢子虫引起的食源性疾病，近年来在美国的发病数量有所增加，2018年报告了约2300例实验室确诊病例。需要基因分型工具为流行病学调查提供信息，然而，由于环孢子虫的有性生殖周期会产生以高度遗传异质性为特征的复杂感染，对其进行基因分型已被证明具有挑战性。我们使用靶向扩增子深度测序以及一种最近描述的基于集合的距离统计方法（该方法适用于异质（混合）基因型以及具有部分基因分型数据的样本），对2018年提交给美国疾控中心的648份卡耶塔环孢子虫样本进行基因分型和聚类。通过将集合识别出的基因簇与基于常见食物暴露独立识别出的类似簇进行比较，来评估该集合的性能。将这些流行病学簇作为金标准，该集合促进基因聚类的敏感度为93.8%，特异度为99.7%。因此，我们预计这一程序将对环孢子虫病的流行病学调查起到极大的补充作用。
Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasiteCyclospora cayetanensishave 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 genotypingCyclosporahas 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 648C. cayetanensissamples 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.