Detection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL⁻¹ (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT’s clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood.

检测体液中微生物核酸已成为许多传染病快速诊断的首选方法。然而，耗时的基于培养的诊断在某些情况下仍然是金标准方法，例如败血症。迫切需要新的无文化方法。在这里，我们描述了单分子束缚或 SMOLT，这是一种无扩增和无纯化的分子检测，无需培养即可高灵敏度检测体液中的微生物。SMOLT 的信号是由由 1 到 7 微米长的 DNA 探针束缚的微米级珠子的置换产生的。使用稳健且快速的光学方法以亚微米精度确定数千个 DNA 探针的分子延伸。我们证明 SMOLT 可以直接检测血液中的核酸，^-1（每毫升菌落形成单位）比放大方法快三倍，具有更高的多路复用能力和更直接的方案。SMOLT 的临床效用通过开发一种多重检测方法来进一步证明，该检测方法可以直接在全血中同时检测引起败血症的念珠菌种类。