Pietsch Michael, Simon Sandra, Richter Anne, Malorny Burkhard, Uelze Laura, Hepner Sabrina, Dangel Alexandra, Sing Andreas, Huber Ingrid, Busch Ulrich, Linde Jörg, Methner Ulrich, Becker Natalie, Werner Guido, Mellmann Alexander, Fruth Angelika, Flieger Antje
Fachgebiet 11: Bakterielle darmpathogene Erreger und Legionellen und Nationales Referenzzentrum (NRZ) für Salmonellen und andere bakterielle Enteritiserreger, Robert Koch-Institut (RKI), Burgstr. 37, 38855, Wernigerode, Deutschland.
Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung (BfR), Berlin, Deutschland.
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2023 Jan;66(1):75-83. doi: 10.1007/s00103-022-03622-y. Epub 2022 Dec 22.
In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence potential of pathogens, as well as their dissemination via outbreak clusters and transmission chains within the framework of molecular epidemiology. In order to gain an overview of the available genotypic and phenotypic methods used for pathogen typing of Salmonella and Shiga toxin-producing and enterohemorrhagic Escherichia coli (STEC/EHEC) in Germany at state and federal level, along with the availability of WGS-based typing and corresponding analytical methods, a survey of laboratories was conducted.
An electronic survey of laboratories working for public health protection and consumer health protection was conducted from February to June 2020.
The results of the survey showed that many of the participating laboratories provide a wide range of phenotypic and molecular methods. Molecular typing is most commonly used for species identification of Salmonella. In many cases, WGS-based methods have already been established at federal and state institutions or are in the process of being established. The Illumina sequencing technology is the most widely used technology. The survey confirms the importance of molecular biology and whole genome typing technologies for laboratories in the diagnosis of bacterial zoonotic pathogens.
近年来，全基因组测序（WGS）结合生物信息学分析已成为评估细菌致病性/耐药潜力及亲缘关系的先进技术。因此，WGS分析是研究病原体耐药性和毒力潜力以及在分子流行病学框架内通过暴发集群和传播链进行传播的核心工具。为了全面了解德国州和联邦层面用于沙门氏菌、产志贺毒素大肠杆菌和肠出血性大肠杆菌（STEC/EHEC）病原体分型的现有基因型和表型方法，以及基于WGS的分型方法和相应分析方法的可用性，我们对实验室进行了一项调查。
2020年2月至6月，对从事公共卫生保护和消费者健康保护工作的实验室进行了电子调查。
调查结果显示，许多参与调查的实验室提供了广泛的表型和分子方法。分子分型最常用于沙门氏菌的菌种鉴定。在许多情况下，基于WGS的方法已在联邦和州机构中建立或正在建立过程中。Illumina测序技术是使用最广泛的技术。该调查证实了分子生物学和全基因组分型技术对实验室诊断细菌性人畜共患病原体的重要性。
