Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters.
Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters.
复制标题
2019年美国卡耶坦环孢子虫疫情调查及改进的环孢子虫基因分型系统对2019年环孢子虫疫情聚集性的评价
DOI：
10.1017/s0950268821002090
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发表时间：
2021-09-13
影响因子：
4.2
通讯作者：
Qvarnstrom Y
中科院分区：
文献类型：
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作者：
Barratt J;Houghton K;Richins T;Straily A;Threlkel R;Bera B;Kenneally J;Clemons B;Madison-Antenucci S;Cebelinski E;Whitney BM;Kreil KR;Cama V;Arrowood MJ;Qvarnstrom Y
环孢子虫病是一种由食源寄生虫环孢子虫（Cyclospora cayetanensis）引起的以水样腹泻为特征的疾病。美国环孢子虫病年度病例的增加促使公共卫生机构开发有助于疫情调查的基因分型工具。美国疾病控制与预防中心（CDC）的一个团队开发了一种基于深度扩增子测序和机器学习的系统，用于检测环孢子虫病的遗传相关簇，以辅助流行病学调查。2018年对该系统的评估证实了其稳健性，表明它具有足够的实用性，值得进一步评估。然而，从生物信息学的角度来看，CDC系统的早期版本存在一些局限性。即依赖专有软件、无法检测新的单倍型以及缺乏选择适当数量离散遗传簇的策略，这些都会限制该系统未来的应用潜力。我们最近引入了一些改进措施来解决这些局限性，本研究的目的是重新评估该系统的性能，以确保所引入的改变没有可观察到的负面影响。将2019年流行病学定义的环孢子虫病簇与使用CDC改进系统检测到的类似遗传簇进行比较，再次证实了其出色的敏感性（90%）和特异性（99%），并确认了其高鉴别能力。这种环孢子虫基因分型系统是稳健的，并且随着不断改进，它将构成美国全国临床样本环孢子虫基因分型网络的基础。
Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.