Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping
Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping
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DOI：
10.1074/mcp.ra119.001667
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发表时间：
2020-03-01
影响因子：
7
通讯作者：
Moore, Edward R. B.
中科院分区：
文献类型：
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作者：
Karlsson, Roger;Thorsell, Annika;Moore, Edward R. B.
质谱 (MS) 和蛋白质组学可对微生物进行全面的表征和鉴定，并发现适用于传染病诊断的蛋白质生物标志物。用于诊断的生物标记物在临床中广泛应用，并且越来越多地研究肽生物标记物在临床实验室中的应用。呼吸道感染是医疗的主要原因，尽管临床评估和标准临床实验室方案非常耗时，而且往往不足以做出可靠的诊断。需要新方法，最好直接应用于临床样本（不包括培养步骤），以改进传染病的诊断，提供充分的治疗并减少抗生素的使用以及相关的抗生素耐药性的发展。这项研究应用纳米液相色谱 (LC) 与串联 MS 相结合，以及生物信息学管道和精选的高质量参考基因组序列的内部数据库，以识别物种独特的肽作为呼吸道感染 (RTI) 中常见的四种细菌病原体的潜在生物标志物：金黄色葡萄球菌；卡他莫拉氏菌；流感嗜血杆菌和肺炎链球菌。这些物种独特的肽最初是在细菌参考菌株的纯培养物中鉴定出来的，反映了四个物种的基因组变异，此外，在临床呼吸道样本中，未经事先培养，阐明了在感染的临床条件下表达的蛋白质。对于四种细菌病原体中的每一种，都提出了临床样本中最常见的候选肽生物标志物。数据可通过 ProteomeXchange 获得，标识符为 PXD014522。作为原理验证，最有前途的物种独特肽被应用于临床样本的靶向串联 MS 分析，并验证了它们与病原体鉴定（即蛋白质分型）的相关性，从而证明了它们作为用于诊断传染病的肽生物标志物候选物的潜力。
Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.