论著

基于RPA-CRISPR/Cas12a技术的十二指肠钩虫核酸检测方法的建立和评价

  • 闫书宁 ,
  • 杨汉银 ,
  • 蔡玉春 ,
  • 徐斌 ,
  • 俞铖航 ,
  • 莫子冉 ,
  • 卢艳 ,
  • 杨硕 ,
  • 辛怡 ,
  • 郑彬
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  • 1 中国疾病预防控制中心寄生虫病预防控制所(国家热带病研究中心),传染病溯源预警与智能决策全国重点实验室,国家卫生健康委员会寄生虫病原与媒介生物学重点实验室,世界卫生组织热带病合作中心,科技部国家级热带病国际研究中心,上海 200025
    2 上海交通大学医学院-国家热带病研究中心全球健康学院,上海 200025
    3 内蒙古大学生命科学学院,内蒙古呼和浩特 010070
闫书宁(2000—),女,硕士研究生,从事寄生虫病监测与预警研究。E-mail:ysn3123@163.com
*郑彬(1972—),女,博士,研究员,从事寄生虫病防治研究。E-mail:zhengbin@nipd.chinacdc.cn

收稿日期: 2024-07-08

  修回日期: 2024-08-16

  网络出版日期: 2025-01-14

基金资助

中国疾病预防控制中心寄生虫病预防控制所科技创新支撑计划(TF2024008)

Establishment and assessment of nucleic acid detection method for Ancylostoma duodenale based on RPA-CRISPR/Cas12a technology

  • YAN Shuning ,
  • YANG Hanyin ,
  • CAI Yuchun ,
  • XU Bin ,
  • YU Chenghang ,
  • MO Ziran ,
  • LU Yan ,
  • YANG Shuo ,
  • XIN Yi ,
  • ZHENG Bin
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  • 1 National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Chinese Center for Tropical Diseases Research; National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; Key Laboratory on Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
    2 School of Global Health, Chinese Center for Tropical Diseases Research and Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
    3 College of Life Sciences, Inner Mongolia University, Hohhot 010070, Inner Mongolia, China

Received date: 2024-07-08

  Revised date: 2024-08-16

  Online published: 2025-01-14

Supported by

Science and Technology Innovation Support Program of the Institute of Parasitic Disease Prevention and Control, Chinese Centre for Disease Control and Prevention(TF2024008)

摘要

目的 基于重组酶聚合酶扩增(RPA)技术和簇状规则间隔短回文重复序列及其相关蛋白12a(CRISPR/Cas12a)技术,建立快速、便捷、高效检测人粪样中十二指肠钩虫的方法,以及时干预、降低疾病传播风险,提高公共卫生水平。 方法 参考十二指肠钩虫线粒体细胞色素c氧化酶亚基Ⅰ(cox1)序列,设计并筛选RPA引物和CRISPR RNA(crRNA),优化crRNA浓度、ssDNA浓度和其他反应条件,建立RPA-CRISPR/Cas12a荧光检测体系。以105、104、103、102、101、100、10-1、10-2拷贝/µl的十二指肠钩虫阳性质粒为模板,分别采用RPA法和RPA-CRISPR/Cas12a法检测最低检出限,评价该方法的敏感度。分别以十二指肠钩虫(105拷贝/µl)、美洲钩虫(20 ng/µl)、异尖线虫(30 ng/µl)、旋毛形线虫(60 ng/µl)基因组DNA为模板,采用RPA-CRISPR/Cas12a法进行检测,评价该方法的特异性。以Kato-Katz法结合半巢式PCR法结果为标准,检测42份粪样(经Kato-Katz法检测31份为钩虫阳性,11份为钩虫阴性),计算RPA-CRISPR/Cas12a法的灵敏度和特异度,Kappa值比较检测结果的一致性。 结果 建立了基于十二指肠钩虫cox1序列的RPA-CRISPR/Cas12a荧光检测体系,在优化的CRISPR/Cas12a体系中,LbCasl2a核酸酶终浓度为50 nmol/L、crRNA探针终浓度为50 nmol/L、ssDNA报告分子终浓度为100 nmol/L。该检测体系的反应条件为37 ℃ 40 min。RPA的最低检出限为102拷贝/μl,RPA-CRISPR/Cas12a法的最低检出限为10拷贝/μl,后者敏感度更高,且与美洲钩虫、异尖线虫、旋毛形线虫无交叉反应。与Kato-Katz法结合半巢式PCR法比较,RPA-CRISPR/Cas12a检测的灵敏度为19/19,特异度为91.30%(21/23),一致性较好(Kappa = 0.904 8)。 结论 该研究建立的RPA-CRISPR/Cas12a荧光检测体系具备快速、灵敏、特异的检测能力,为公共卫生监测和钩虫病防控提供了可靠技术支持。

本文引用格式

闫书宁 , 杨汉银 , 蔡玉春 , 徐斌 , 俞铖航 , 莫子冉 , 卢艳 , 杨硕 , 辛怡 , 郑彬 . 基于RPA-CRISPR/Cas12a技术的十二指肠钩虫核酸检测方法的建立和评价[J]. 中国寄生虫学与寄生虫病杂志, 2024 , 42(6) : 748 -755 . DOI: 10.12140/j.issn.1000-7423.2024.06.009

Abstract

Objective To develop a rapid, convenient, and efficient nucleic acid method based on RPA-CRISPR/Cas12a technology for detecting Ancylostoma duodenale in human stool samples to facilitate timely intervention, reduce the risk of disease transmission, and enhance the level of public health. Methods Based on the conserved sequence of mitochondrial cytochrome c oxidase subunit Ⅰ (cox1) of A. duodenale, RPA primers and CRISPR RNA (crRNAs) were designed and screened, while the concentration of crRNA and ssDNA, along with other reaction conditions, were optimized to establish the RPA-CRISPR/Cas12a fluorescence detection system. The minimum detection limits were determined using A. duodenale plasmid samples as templates, at the concentrations of 10⁵, 10⁴, 10³, 10², 10¹, 10⁰, 10⁻¹ and 10⁻² copies/μl, employing both the RPA method and the RPA-CRISPR/Cas12a method. The specificity of the RPA-CRISPR/Cas12a method was determined using genomic DNA templates from A. duodenale (10⁵ copies/μl), Necator americanus (20 ng/µl), Anisakis (30 ng/µl), and Trichinella spiralis (60 ng/µl). To assess the sensitivity and specificity of the RPA-CRISPR/Cas12a method, Kato-Katz combined with semi-nested PCR were used as reference standards, and 42 fecal samples (31 positive and 11 negative for A. duodenale based on the Kato-Katz method) were tested. Sensitivity and specificity values for the RPA-CRISPR/Cas12a method were calculated, and the agreement between detection results was analyzed using Kappa statistics. Results A RPA-CRISPR/Cas12a fluorescence detection system targeting the A. duodenale cox1 gene sequence was developed. In the optimized CRISPR/Cas12a system, the final concentrations of LbCas12a nuclease and crRNA probe were both 50 nmol/L, while the ssDNA reporter concentration was 100 nmol/L. The reaction was performed at 37 ℃ for 40 minutes. The minimum detection limit for the RPA assay was 100 copies/μl, while the RPA-CRISPR/Cas12a system achieved a lower detection limit of 10 copies/μl, demonstrating enhanced sensitivity. The system showed no cross-reactivity with N. americanus, Anisakis, and T. spiralis. When compared with the Kato-Katz combined with semi-nested PCR, the RPA-CRISPR/Cas12a assay exhibited a sensitivity of 100% (19/19), a specificity of 91.30% (21/23), and good consistency (Kappa = 0.9048). Conclusion The RPA-CRISPR/Cas12a fluorescent detection system established in this study possesses rapid, sensitive, and specific detectability, providing reliable technical support for public health surveillance and the prevention and control of hookworm disease.

参考文献

[1] Hotez PJ, Bottazzi ME, Kaye PM, et al. Neglected tropical disease vaccines: hookworm, leishmaniasis, and schistosomiasis[J]. Vaccine, 2023, 41(Suppl 2): S176.
[2] Loukas A, Hotez PJ, Diemert D, et al. Hookworm infection[J]. Nat Rev Dis Pri, 2016, 2: 16088.
[3] Bethony J, Brooker S, Albonico M, et al. Soil-transmitted helminth infections: ascariasis, trichuriasis, and hookworm[J]. Lancet, 2006, 367(9521): 1521-1532.
[4] Zhu XP, Su C. Human parasitology[M]. 9th ed. Beijing: People’s Medical Publishing House, 2018: 167-172. (in Chinese)
  (诸欣平, 苏川. 人体寄生虫学[M]. 9版. 北京: 人民卫生出版社, 2018: 167-172.)
[5] National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention. Report on the national survey of important human parasitic diseases in China (2015)[M]. Beijing: People’s Medical Publishing House, 2018: 48-55. (in Chinese)
  (中国疾病预防控制中心寄生虫病预防控制所. 2015年全国人体重点寄生虫病现状调查报告[M]. 北京: 人民卫生出版社, 2018: 48-55.)
[6] Wisetmora A, Artchayasawat A, Laummaunwai P, et al. Formalin-fixed stool improves the performance of the Kato-Katz method[J]. Vet World, 2024, 17(1): 99-107.
[7] Liang JR, Xu B, Hu W, et al. Research progress of hookworm detection technology[J]. China Trop Med, 2023, 23(4): 413-419. (in Chinese)
  (梁家瑞, 徐斌, 胡薇, 等. 钩虫检测技术研究进展[J]. 中国热带医学, 2023, 23(4): 413-419.)
[8] Keller L, Patel C, Welsche S, et al. Performance of the kato-katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation[J]. Parasit Vectors, 2020, 13(1): 517.
[9] Wang YN, Chen CG. Advances in the research of recombinase polymerase amplification technology[J]. Med J Chin People’s Liberation Army, 2021, 46(5): 504-511. (in Chinese)
  (王亚楠, 陈昌国. 重组酶聚合酶扩增技术研究进展[J]. 解放军医学杂志, 2021, 46(5): 504-511.)
[10] Song HY, Wu J, Zou FC, et al. Mechanism of CRISPR/cas system and its application in parasitology[J]. China Anim Husb Vet Med, 2017, 44(1): 208-213. (in Chinese)
  (宋海洋, 吴杰, 邹丰才, 等. CRISPR/Cas系统作用机制及其在寄生虫学研究中的应用[J]. 中国畜牧兽医, 2017, 44(1): 208-213.)
[11] Li MR, Qin ZQ, Yin K, et al. Application of CRISPR/cas systems in the nucleic acid detection of pathogens: A review[J]. Chin J Schisto Control, 2023, 35(1): 98-103, 110. (in Chinese)
  (李梦茹, 秦志强, 殷堃, 等. CRISPR/Cas系统在病原体核酸检测中的应用进展[J]. 中国血吸虫病防治杂志, 2023, 35(1): 98-103, 110.)
[12] Huang MQ, Liu SH, Xu YN, et al. CRISPR/Cas12a technology combined with RPA for rapid and portable SFTSV detection[J]. Front Microbiol, 2022, 13: 754995.
[13] Yan SN, Yang S, Yang HY, et al. Application of the CRISPR/cas system in gene editing and nucleic acid detection of parasitic diseases: a review[J]. Chin J Schisto Control, 2024, 36(3): 314-320. (in Chinese)
  (闫书宁, 杨硕, 杨汉银, 等. CRISPR/Cas系统在寄生虫基因编辑与核酸检测中的应用进展[J]. 中国血吸虫病防治杂志, 2024, 36(3): 314-320.)
[14] Li XR, Zhang DC, Gan XF, et al. A cascade signal amplification based on dynamic DNA nanodevices and CRISPR/Cas12a trans-cleavage for highly sensitive microRNA sensing[J]. ACS Synth Biol, 2021, 10(6): 1481-1489.
[15] Liang JR, Xu B, Hu W, et al. Development and preliminary evaluation of a fluorescence RPA assay for the rapid detection of Necator americanus[J]. China Trop Med, 2023, 23(7): 681-685. (in Chinese)
  (梁家瑞, 徐斌, 胡薇, 等. 基于荧光重组酶聚合酶扩增技术快速检测美洲钩虫方法研究[J]. 中国热带医学, 2023, 23(7): 681-685.)
[16] de Gruijter JM, van Lieshout L, Gasser RB, et al. Polymerase chain reaction-based differential diagnosis of Ancylostoma duodenale and Necator americanus infections in humans in northern Ghana[J]. Trop Med Int Health, 2005, 10(6): 574-580.
[17] Romstad A, Gasser RB, Monti JR, et al. Differentiation of Oesophagostomum bifurcum from Necator americanus by PCR using genetic markers in spacer ribosomal DNA[J]. Mol Cell Probes, 1997, 11(3): 169-176.
[18] Jonker FAM, Calis JCJ, Phiri K, et al. Real-time PCR demonstrates Ancylostoma duodenale is a key factor in the etiology of severe Anemia and iron deficiency in Malawian pre-school children[J]. PLoS Negl Trop Dis, 2012, 6(3): e1555.
[19] Huang, Taojun, et al. Rapid, sensitive, and visual detection of Clonorchis sinensis with an RPA-CRISPR/Cas12a-based dual readout portable platform[J]. Int J Biol Macromol, 2023, 249: 125967.
[20] Verweij JJ, Pit DS, van Lieshout L, et al. Determining the prevalence of Oesophagostomum bifurcum and Necator americanus infections using specific PCR amplification of DNA from faecal samples[J]. Trop Med Int Health, 2001, 6(9): 726-731.
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