TY - JOUR
T1 - Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering
AU - Cheng, Wen Chih
AU - Horn, Troy
AU - Zayats, Maya
AU - Rizk, Georges
AU - Major, Samuel
AU - Zhu, Hongying
AU - Russell, Joseph
AU - Xu, Zhiguang
AU - Rothman, Richard E.
AU - Celedon, Alfredo
N1 - Funding Information:
The authors would like to thank Gregory Bowman and Karen Carroll at Johns Hopkins University for discussions that helped to improve the manuscript significantly and Nikki Parrish at Johns Hopkins Hospital for providing sputum samples. Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases and by the National Institute on Aging of the National Institutes of Health under Awards R44AI124871, R44AI122527 and R43AG056208. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-020-18574-7
DO - 10.1038/s41467-020-18574-7
M3 - Article
C2 - 32963224
AN - SCOPUS:85091277119
SN - 2041-1723
VL - 11
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 4774
ER -