Di Lorenzo Alessio, Mangone Iolanda, Colangeli Patrizia, Cioci Daniela, Curini Valentina, Vincifori Giacomo, Mercante Maria Teresa, Di Pasquale Adriano, Iannetti Simona
Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Campo Boario, 64100 Teramo, Abruzzo, Italy.
One Health. 2023 Jun;16:100471. doi: 10.1016/j.onehlt.2022.100471. Epub 2022 Dec 7.
The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.
意大利实验动物卫生研究所(IZSs)是处理家畜和野生动物传染病病因及发病机制的公共卫生机构。在2019年冠状病毒病疫情期间,意大利卫生部指定IZSs对人类样本进行检测严重急性呼吸综合征冠状病毒2(SARS-CoV-2)的诊断测试。特别是,阿布鲁佐和莫利塞实验动物卫生研究所(IZS-泰拉莫)通过实时逆转录聚合酶链反应检测鼻咽拭子参与了SARS-CoV-2的诊断。在“同一健康”框架下,基于跨学科、实验室及时性、人类样本中SARS-CoV-2 RNA检测试验的认证以及敏感数据的保密管理,活动和基础设施根据新的优先事项进行了重组。实验室信息系统——SILAB——通过一个用于管理人类源数据的“同一健康”模块得以实施,配备了自动登记信息的工具以提高数据质量。此外,正式在IZS-泰拉莫成立的“微生物病原体全基因组测序国家参考中心——数据库和生物信息学分析”——GENPAT,开发了生物信息学工作流程和带有特设监测工具的信息技术仪表板,以支持基于宏基因组学的SARS-CoV-2监测,提供分子测序分析以快速截获该地区传播的变异株。本文描述了通过改编和整合SILAB和GENPAT工具开发的“同一健康”系统,以支持意大利南部阿布鲁佐地区在新冠疫情期间的监测。所开发的仪表板使卫生当局能够观察SARS-CoV-2在该地区的传播情况,并通过将时空信息与宏基因组学相结合,为在市镇层面识别变异株的新兴时空聚集提供早期证据。“同一健康”模块的实施旨在易于建模并适用于其他疾病的管理以及未来假设的大流行性质事件。