Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli

Background: In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods: Specific peaks in the outbreak strain’s spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results: Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.

背景：2011年，德国北部暴发了大规模产志贺毒素大肠杆菌O104:H4（Shiga-Toxigenic Escherichia coli O104:H4）疫情。大量样本被送至微生物实验室开展流行病学评估，此举凸显了快速且低成本分型方法的重要性。因此，我们评估了基于基质辅助激光解吸电离飞行时间质谱（MALDI-TOF mass spectrometry）的策略在疫情菌株鉴定中的适用性。方法：通过比对疫情暴发前存档的、用于常规物种水平鉴定的质谱谱图，我们鉴定出了疫情菌株谱图中的特异性峰。采用液相色谱串联质谱（liquid chromatography tandem mass spectrometry）对这些具有区分性的峰对应的蛋白质进行鉴定，并对照公开数据库进行验证。我们以294株来源于此次疫情期间临床样本的大肠杆菌分离株为研究对象，将该分型方案与PCR基因分型方法进行了对比评估。结果：比对谱图分析发现，该疫情菌株存在两个特征性峰，质荷比分别为m/z 6711和m/z 10883。经分析，这些特征峰对应的蛋白质在已完成基因组测序的大肠杆菌菌株中检出率较低。标记峰检测法成功对293株研究分离株中的292株实现了准确分类，涵盖全部104株疫情分离株。结论：在此次大规模产志贺毒素大肠杆菌疫情中，基质辅助激光解吸电离飞行时间质谱可实现可靠的疫情菌株鉴定。本研究所采用的分型策略或可适配其他分型任务，有望作为常规病原体鉴定工作流程的一部分，助力流行病学调查工作。