Nielsen Morten Eneberg, Søgaard Kirstine Kobberøe, Karst Søren Michael, Krarup Anne Lund, Albertsen Mads, Nielsen Hans Linde
Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
Microbiol Spectr. 2025 Mar 26;13(5):e0329524. doi: 10.1128/spectrum.03295-24.
Bloodstream infections are a major cause of mortality, often leading to sepsis or septic shock. Rapid initiation of effective antimicrobial therapy is essential for survival; however, the current gold standard for identifying pathogens in bloodstream infections, blood culturing, has limitations with long turnaround time and poor sensitivity. This delay in refining empirical broad-spectrum antimicrobial treatments contributes to increased mortality and the development of antimicrobial resistance. In this study, we developed a metagenomic next-generation sequencing assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. We demonstrated proof of concept in a prospective observational clinical study including patients ( = 40) admitted to the emergency ward on suspicion of bloodstream infection. Study samples were drawn from the same venipuncture as a blood culture sample from the included patients. Nanopore metagenomic sequencing confirmed all microbiological findings in patients with positive blood cultures ( = 11) and identified pathogens relevant to the acute infection in an additional 11 patients with negative blood cultures. This proof-of-concept study demonstrates that culture-independent Nanopore metagenomic sequencing directly on blood plasma could be a feasible supplementary test for infection diagnostics in patients admitted with severe infections or sepsis. These findings support further studies on Nanopore metagenomic sequencing for sepsis diagnostics in larger cohorts to validate and expand the results from this study.IMPORTANCEThis study demonstrates the potential of Nanopore metagenomic sequencing as a rapid, culture-independent diagnostic tool for bloodstream infections, identifying pathogens missed by conventional blood cultures. The study highlights the method's promise in improving pathogen detection and warrants further validation in larger clinical studies.
血流感染是导致死亡的主要原因，常引发脓毒症或脓毒性休克。迅速启动有效的抗菌治疗对生存至关重要；然而，目前用于识别血流感染病原体的金标准——血培养，存在周转时间长和灵敏度低的局限性。这种在优化经验性广谱抗菌治疗方面的延迟导致死亡率上升和抗菌药物耐药性的产生。在本研究中，我们开发了一种宏基因组下一代测序检测方法，利用牛津纳米孔技术平台对血浆中的微生物游离DNA进行测序。我们在一项前瞻性观察性临床研究中验证了概念，该研究纳入了因疑似血流感染入住急诊病房的患者（n = 40）。研究样本与纳入患者的血培养样本取自同一静脉穿刺。纳米孔宏基因组测序证实了血培养阳性患者（n = 11）的所有微生物学结果，并在另外11例血培养阴性的患者中鉴定出与急性感染相关的病原体。这项概念验证研究表明，直接对血浆进行不依赖培养的纳米孔宏基因组测序可能是对重症感染或脓毒症患者进行感染诊断的一种可行的补充检测方法。这些发现支持在更大队列中对纳米孔宏基因组测序用于脓毒症诊断进行进一步研究，以验证和扩展本研究的结果。重要性本研究证明了纳米孔宏基因组测序作为一种快速、不依赖培养的血流感染诊断工具的潜力，可识别传统血培养遗漏的病原体。该研究突出了该方法在改善病原体检测方面的前景，并需要在更大规模的临床研究中进行进一步验证。
