IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-63094-x.html
   My bibliography  Save this article

Sensitive pathogen DNA detection by a multi-guide RNA Cas12a assay favoring trans- versus cis-cleavage

Author

Listed:
  • Zhen Huang

    (Tulane University School of Medicine
    Tulane University School of Medicine
    Southern University of Science and Technology
    Tulane School of Medicine)

  • Zhe Song

    (Southern University of Science and Technology)

  • Jianfeng Zeng

    (Southern University of Science and Technology)

  • Xuhui Liu

    (Fudan University)

  • Mutong Fang

    (Southern University of Science and Technology)

  • Zhiyuan Wu

    (Fudan University)

  • Yao Zhao

    (Southern University of Science and Technology)

  • Yanli Chen

    (Fudan University)

  • Dan Li

    (Southern University of Science and Technology)

  • Huan Huang

    (Tulane University School of Medicine
    Fudan University)

  • Liang Fu

    (Southern University of Science and Technology)

  • Peng Xu

    (Southern University of Science and Technology)

  • Bo Ning

    (Tulane University School of Medicine
    Tulane University School of Medicine)

  • Jun Chen

    (Fudan University)

  • Ming Guan

    (Fudan University)

  • Lin Sun

    (Beijing Children’s Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health)

  • Christopher J. Lyon

    (Tulane University School of Medicine
    Tulane University School of Medicine)

  • Xiao-Yong Fan

    (Fudan University)

  • Shuihua Lu

    (Southern University of Science and Technology)

  • Tony Hu

    (Tulane University School of Medicine
    Tulane University School of Medicine)

Abstract

Most CRISPR assays lack clinical utility due to their complex workflows and limited validation. Here we present a streamlined “one-pot” asymmetric CRISPR tuberculosis assay that attenuates amplicon degradation to achieve 5 copies/μL sensitivity within 60 min and detect positive patient samples within 15 min. This assay exhibited 93%, 83%, and 93% sensitivity with adult respiratory, pediatric stool, and adult cerebral spinal fluid specimens, and detected 64% of clinically diagnosed tuberculous meningitis cases, in a cohort of 603 clinical samples. This assay achieves complete specificity and greater sensitivity (74% vs. 56%) than the most sensitive reference test with prospectively collected tongue swabs, and exhibits similar performance when adapted to a lateral flow assay format and employed to analyze self-collected tongue swabs. These results demonstrate the utility of this approach across diverse specimen types, including those suitable for use in remote and resource-limited settings, to improve access to molecular diagnostics.

Suggested Citation

  • Zhen Huang & Zhe Song & Jianfeng Zeng & Xuhui Liu & Mutong Fang & Zhiyuan Wu & Yao Zhao & Yanli Chen & Dan Li & Huan Huang & Liang Fu & Peng Xu & Bo Ning & Jun Chen & Ming Guan & Lin Sun & Christopher, 2025. "Sensitive pathogen DNA detection by a multi-guide RNA Cas12a assay favoring trans- versus cis-cleavage," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63094-x
    DOI: 10.1038/s41467-025-63094-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-63094-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-63094-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63094-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.