Lüth Stefanie, Fuchs Jannika, Deneke Carlus
Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
Chemical and Veterinary Investigation Office (CVUA) Karlsruhe, Weißenburger Str. 3, 76187 Karlsruhe, Germany.
Microb Genom. 2025 May;11(5). doi: 10.1099/mgen.0.001389.
Whole-genome sequencing (WGS) has become the key approach for molecular surveillance of . Genome comparison analysis can reveal transmission routes that cannot be found with classic epidemiology. A widespread standard for use in genome comparison analysis involves data from short-read sequencing, generated on Illumina or Ion Torrent devices. To date, little is known about the compatibility of data from both platforms. This knowledge is essential when it comes to the central analysis of data, for example, in the case of outbreaks. We used WGS data from 47 . isolates of the strain collection of the German National Reference Laboratory for , generated on either Illumina or Ion Torrent devices, to analyse the impact of the sequencing technology on downstream analyses. In our study, only the assembler SPAdes delivered qualitatively comparable results. In the gene-based core genome multilocus sequence typing (cgMLST), the same-strain allele discrepancy between the platforms was 14.5 alleles on average, which is well above the threshold of 7 alleles routinely used for cluster detection in . An application of a strict frameshift filter in cgMLST analysis could push the mean discrepancy below this threshold but reduced discriminatory power. The impact of the platform on the read-based single nucleotide polymorphism analysis was lower than that on the cgMLST. Overall, it was possible to improve compatibility in various ways, but perfect compatibility could not be achieved.
全基因组测序（WGS）已成为[具体疾病名称未给出]分子监测的关键方法。基因组比较分析能够揭示经典流行病学无法发现的传播途径。用于基因组比较分析的一个广泛标准涉及来自Illumina或Ion Torrent设备上短读长测序产生的数据。迄今为止，对于这两个平台数据的兼容性了解甚少。在进行数据核心分析时，例如在疫情爆发的情况下，这方面的知识至关重要。我们使用了来自德国国家[具体疾病名称未给出]参考实验室菌株库的47株[具体疾病名称未给出]分离株的WGS数据，这些数据由Illumina或Ion Torrent设备生成，以分析测序技术对下游分析的影响。在我们的研究中，只有SPAdes组装软件给出了质量上可比的结果。在基于基因的核心基因组多位点序列分型（cgMLST）中，两个平台之间同菌株等位基因差异平均为14.5个等位基因，远高于[具体疾病名称未给出]中用于聚类检测的常规阈值7个等位基因。在cgMLST分析中应用严格的移码过滤器可将平均差异推至该阈值以下，但会降低鉴别能力。平台对基于读段的单核苷酸多态性分析的影响低于对cgMLST的影响。总体而言，有可能通过多种方式提高兼容性，但无法实现完美兼容。
