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A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples

Author

Listed:
  • Wentao Chen

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Hao Luo

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Lihong Zeng

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Yuying Pan

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Jonathan B. Parr

    (University of North Carolina)

  • Yinbo Jiang

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Clark H. Cunningham

    (University of North Carolina)

  • Kelly L. Hawley

    (Connecticut Children’s
    UConn Health
    UConn Health)

  • Justin D. Radolf

    (UConn Health
    UConn Health
    UConn Health
    UConn Health)

  • Wujian Ke

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Jiangli Ou

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Jianjiang Yang

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Bin Yang

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

  • Heping Zheng

    (Southern Medical University
    Guangzhou Key Laboratory for Sexually Transmitted Diseases Control)

Abstract

The performance of commonly used assays for diagnosis of syphilis varies considerably depending on stage of infection and sample type. In response to the need for improved syphilis diagnostics, we develop assays that pair PCR pre-amplification of the tpp47 gene of Treponema pallidum subsp. pallidum with CRISPR-LwCas13a. The PCR-LwCas13a assay achieves an order of magnitude better analytical sensitivity than real-time PCR with equivalent specificity. When applied to a panel of 216 biological specimens, including 135 clinically confirmed primary and secondary syphilis samples, the PCR-LwCas13a assay demonstrates 93.3% clinical sensitivity and 100% specificity, outperforming tpp47 real-time PCR and rabbit-infectivity testing. We further adapt this approach to distinguish Treponema pallidum subsp. pallidum lineages and identify genetic markers of macrolide resistance. Our study demonstrates the potential of CRISPR-based approaches to improve diagnosis and epidemiological surveillance of syphilis.

Suggested Citation

  • Wentao Chen & Hao Luo & Lihong Zeng & Yuying Pan & Jonathan B. Parr & Yinbo Jiang & Clark H. Cunningham & Kelly L. Hawley & Justin D. Radolf & Wujian Ke & Jiangli Ou & Jianjiang Yang & Bin Yang & Hepi, 2022. "A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32250-y
    DOI: 10.1038/s41467-022-32250-y
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    References listed on IDEAS

    as
    1. Mathew A. Beale & Michael Marks & Sharon K. Sahi & Lauren C. Tantalo & Achyuta V. Nori & Patrick French & Sheila A. Lukehart & Christina M. Marra & Nicholas R. Thomson, 2019. "Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    2. Simant Dube & Jian Qin & Ramesh Ramakrishnan, 2008. "Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device," PLOS ONE, Public Library of Science, vol. 3(8), pages 1-9, August.
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    Cited by:

    1. Yuqian Guo & Yaofeng Zhou & Hong Duan & Derong Xu & Min Wei & Yuhao Wu & Ying Xiong & Xirui Chen & Siyuan Wang & Daofeng Liu & Xiaolin Huang & Hongbo Xin & Yonghua Xiong & Ben Zhong Tang, 2024. "CRISPR/Cas-mediated “one to more” lighting-up nucleic acid detection using aggregation-induced emission luminogens," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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