Identification of Shiga-Toxigenic Escherichia coli outbreak isolates by a novel data analysis tool after matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e. g. for outbreak investigations, is often hampered by the complexity of data analysis. We have analysed publicly available MALDI-TOF mass spectra from a large outbreak of Shiga-Toxigenic Escherichia coli in northern Germany using a general purpose software tool for the analysis of complex biological data. The software was challenged with depauperate spectra and reduced learning group sizes to mimic poor spectrum quality and scarcity of reference spectra at the onset of an outbreak. With high quality formic acid extraction spectra, the software’s built in classifier accurately identified outbreak related strains using as few as 10 reference spectra (99.8% sensitivity, 98.0% specificity). Selective variation of processing parameters showed impaired marker peak detection and reduced classification accuracy in samples with high background noise or artificially reduced peak counts. However, the software consistently identified mass signals suitable for a highly reliable marker peak based classification approach (100% sensitivity, 99.5% specificity) even from low quality direct deposition spectra. The study demonstrates that general purpose data analysis tools can effectively be used for the analysis of bacterial mass spectra.

细菌与真菌病原体的快速可靠鉴定，在传染病防控及暴发病原追踪工作中具有重要意义。基于脱氧核糖核酸（DNA）的检测方法是流行病学调查的金标准，但该类方法成本相对较高且耗时较长。基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）是一种快速、可靠且具备成本效益的技术，目前已常规用于鉴定临床相关的人类病原体。该技术已应用于亚种分化与分型工作，但在流行病学任务（如暴发调查）中的应用常受限于数据分析的复杂性。本研究采用一款用于复杂生物数据分析的通用软件工具，对德国北部一起大规模产志贺毒素大肠杆菌（Shiga-Toxigenic Escherichia coli）暴发事件中的公开MALDI-TOF质谱数据进行了分析。本研究通过引入谱峰稀疏的质谱谱图并缩小训练集规模，以模拟暴发初期谱图质量欠佳、参考谱图稀缺的场景，对该软件进行性能测试。当使用甲酸提取法获取的高质量质谱谱图时，该软件内置的分类器仅需10条参考谱图即可准确识别暴发相关菌株（灵敏度99.8%，特异度98.0%）。对处理参数进行选择性调整后发现，在背景噪音较高或人工削减峰数的样本中，该软件的标记峰检测能力受损，分类准确率也有所下降。但即便使用质量欠佳的直接沉积法质谱谱图，该软件仍能稳定识别出适用于高可靠性标记峰分类方法的质谱信号（灵敏度100%，特异度99.5%）。本研究证明，通用数据分析工具可有效应用于细菌质谱谱图的分析工作。