Article(id=1216517521772036238, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1216517514570417012, articleNumber=null, orderNo=null, doi=10.19812/j.cnki.jfsq11-5956/ts.20241206006, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1733414400000, receivedDateStr=2024-12-06, revisedDate=null, revisedDateStr=null, acceptedDate=null, acceptedDateStr=null, onlineDate=1767969978993, onlineDateStr=2026-01-09, pubDate=1755187200000, pubDateStr=2025-08-15, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1767969978993, onlineIssueDateStr=2026-01-09, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1767969978993, creator=13701087609, updateTime=1767969978993, updator=13701087609, issue=Issue{id=1216517514570417012, tenantId=1146029695717560320, journalId=1149652044408987649, year='2025', volume='16', issue='15', pageStart='1', pageEnd='322', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1767969977276, creator=13701087609, updateTime=1768211590858, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1217530915467743720, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1216517514570417012, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1217530915467743721, tenantId=1146029695717560320, journalId=1149652044408987649, issueId=1216517514570417012, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=94, endPage=100, ext={EN=ArticleExt(id=1216517523227459807, articleId=1216517521772036238, tenantId=1146029695717560320, journalId=1149652044408987649, language=EN, title=Amplification-free molecular detection of pathogenic microbial contamination in food packaging based on tandem CRISPR-Cas13a, columnId=1216517518575980656, journalTitle=Journal of Food Safety & Quality, columnName=Special Topic: Application of Biosensors in Food Safety Detection, runingTitle=null, highlight=null, articleAbstract=

Objective To develop a rapid and sensitive detection technology for pathogenic microorganisms in food packaging based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 13a (Cas13a) system. Methods The method leveraged the specific recognition and signal amplification characteristics of the CRISPR-Cas13a technology. Multiple guide RNAs were designed to target different sites on pathogenic RNA, enabling a single RNA molecule to activate multiple Cas13a enzymes simultaneously. This cascade triggered trans-cleavage of RNA reporter molecules in the reaction mixture, generating a detectable fluorescent signal. The tandem design synergistically enhanced signal amplification efficiency, thereby improving detection sensitivity. Results The limits of detection of this method for pathogenic and RNA were 800 copies/mL and 18.7 pmol/L, respectively, and the detection could be completed in a short time, accurately distinguishing different pathogens. Testing food packaging samples contaminated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudvirus showed recovery rates ranging from 89.71% to 102.56%. Conclusion This study presents a rapid, cost-effective and easy-to-operate method for detecting pathogenic microbial contamination on food packaging surfaces, indicating high accuracy, offering potential application value for monitoring microbial risks in foodborne transmission pathways.

, correspAuthors=Hong GAO, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Yong ZHANG, Di-Ming HUA, Rui-Jie DENG, Hong GAO), CN=ArticleExt(id=1216517527384015209, articleId=1216517521772036238, tenantId=1146029695717560320, journalId=1149652044408987649, language=CN, title=基于串联CRISPR-Cas13a的食品包装病原微生物污染免扩增分子检测, columnId=1216517518756335730, journalTitle=食品安全质量检测学报, columnName=专题:生物传感器在食品安全检测中的应用, runingTitle=null, highlight=null, articleAbstract=目的 开发一款基于串联规律间隔成簇短回文重复序列(clustered regularly interspaced short palindromic repeats, CRISPR)和CRISPR相关蛋白13a (CRISPR-associated protein 13a, Cas13a)组成的CRISPR-Cas13a快速、灵敏的食品包装病原微生物检测技术。方法 利用CRISPR-Cas13a技术的特异识别和信号放大特性, 同时基于对病原RNA多靶点识别的串联设计, 通过一个病原RNA分子激活多个Cas13a, 反式切割反应体系中的RNA信号报告分子并伴随荧光信号产生, 协同提升信号放大效率, 从而实现对病原体的灵敏检测。结果 该方法对病原微生物及RNA的检出限分别为800 copies/mL和18.7 pmol/L, 能够在较短时间内完成病原RNA检测, 同时能够准确区分不同病原微生物。测试新型冠状病毒(severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)假病毒污染的食品包装样品显示, 方法测定的回收率在89.71%~102.56%。结论 本研究提供了一种快速、经济且操作简便的食品包装病原微生物污染检测方法, 具备较好的准确性。对食源途径风险微生物的监控具有潜在应用价值。, correspAuthors=高鸿, authorNote=null, correspAuthorsNote=
*高鸿(1973—), 男, 博士, 教授, 主要研究方向为食品质量与安全、食品营养与功能。E-mail:
, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=G2p/HzoJrY44XC/DczYpsA==, magXml=N15p8vBurm+GnOl6MO7bIA==, pdfUrl=null, pdf=hx9+WdmggpIpasQgiS5peg==, pdfFileSize=2275595, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=bQKoLUG8DjId5ZNKWbKfgQ==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=/v7rvaF0LvEzeTsAWYr8PQ==, mapNumber=null, authorCompany=null, fund=null, authors=

张勇(1995—), 男, 博士研究生, 主要研究方向为食品安全分子检测。E-mail:

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张勇(1995—), 男, 博士研究生, 主要研究方向为食品安全分子检测。E-mail:

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Journal of Clinical Microbiology, 2020, 58(9): 1520-1535., articleTitle=Direct comparison of SARS-CoV-2 analytical limits of detection across seven molecular assays, refAbstract=null)], funds=[Fund(id=1217127913305064296, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, awardId=2022YFF1103000, language=CN, fundingSource=国家重点研发计划项目(2022YFF1103000), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1217127907349152283, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, xref=null, ext=[AuthorCompanyExt(id=1217127907353346589, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, companyId=1217127907349152283, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China), AuthorCompanyExt(id=1217127907445621276, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, companyId=1217127907349152283, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=四川大学轻工科学与工程学院, 成都 610065)])], figs=[ArticleFig(id=1217127911799309057, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Fig.1, caption=Schematic diagram of the principle of tandem CRISPR-Cas13a for detecting target RNA and the graph of fluorescence signal-to-noise ratio, figureFileSmall=UKFvzCQLhaQLsN/Jm+X5Zg==, figureFileBig=c7V7GNfBx2Xbr6K+PII6BA==, tableContent=null), ArticleFig(id=1217127911899972361, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=图1, caption=串联CRISPR-Cas13a检测靶标RNA的原理示意图及荧光信噪比图, figureFileSmall=UKFvzCQLhaQLsN/Jm+X5Zg==, figureFileBig=c7V7GNfBx2Xbr6K+PII6BA==, tableContent=null), ArticleFig(id=1217127912042578706, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Fig.2, caption=Optimization of experimental conditions and analysis of reaction efficiency (n=3), figureFileSmall=lsdSrLdvVVId2QPUEXaNzw==, figureFileBig=foMBwd1z7iDba5SNN1Sxbw==, tableContent=null), ArticleFig(id=1217127912160019226, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=图2, caption=实验条件优化与反应效率分析(n=3)

注: A. 不同结合位点数对靶标RNA的荧光响应; B. 不同Cas13a浓度对靶标RNA的荧光响应; C. 不同信号报告分子浓度对靶标RNA的荧光响应。

, figureFileSmall=lsdSrLdvVVId2QPUEXaNzw==, figureFileBig=foMBwd1z7iDba5SNN1Sxbw==, tableContent=null), ArticleFig(id=1217127912290042655, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Fig.3, caption=Effects of different concentrations of target on fluorescence response (n=3), figureFileSmall=cByEjVpJkDCAPLsVS/I1LA==, figureFileBig=DOCTo1iOtDGLH1C+uteZzg==, tableContent=null), ArticleFig(id=1217127912428454695, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=图3, caption=不同浓度靶标对荧光响应的影响(n=3)

注: A. 不同浓度靶标RNA对荧光光谱的影响; B. 靶标RNA浓度与荧光强度的关系(内部: 靶标RNA浓度与荧光强度呈线性关系); C. SARS-CoV-2假病毒浓度与荧光强度的关系。**P<0.01, 使用双尾学生t检验确定。

, figureFileSmall=cByEjVpJkDCAPLsVS/I1LA==, figureFileBig=DOCTo1iOtDGLH1C+uteZzg==, tableContent=null), ArticleFig(id=1217127912541700906, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Fig.4, caption=Effects of different RNA on fluorescence response of detection system (n=3), figureFileSmall=9OAAmNjT6DSDV9Q9baCstQ==, figureFileBig=uYt2rurjN+Jok6UO0AxWgw==, tableContent=null), ArticleFig(id=1217127912671724340, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=图4, caption=不同RNA对检测体系荧光响应的影响(n=3), figureFileSmall=9OAAmNjT6DSDV9Q9baCstQ==, figureFileBig=uYt2rurjN+Jok6UO0AxWgw==, tableContent=null), ArticleFig(id=1217127912793359163, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Fig.5, caption=Recovery test results of recovery test results of false virus labels on food packaging on food packaging (n=3), figureFileSmall=0x+/X21BKnzb+B9EdgUYlA==, figureFileBig=ItPx88F+5/SO73xHAxkM3g==, tableContent=null), ArticleFig(id=1217127912898216777, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=图5, caption=食品包装上假病毒加标回收检测结果(n=3), figureFileSmall=0x+/X21BKnzb+B9EdgUYlA==, figureFileBig=ItPx88F+5/SO73xHAxkM3g==, tableContent=null), ArticleFig(id=1217127913028240208, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=EN, label=Table 1, caption=

DNA template primer sequence for in vitro transcription of crRNA

, figureFileSmall=null, figureFileBig=null, tableContent=
引物名称 序列(5'-3')
T7 promoter TAATACGACTCACTATAGGG
crRNA1-DNA ACGTTTGGTGGACCCTCAGAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA2-DNA TAACCAGAATGGAGAACGCAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA3-DNA GATCAAAACAACGTCGGCCCGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA4-DNA TGCGTCTTGGTTCACCGCTCGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA5-DNA GACCTTAAATTCCCTCGAGGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA6-DNA TAGCAGTCCAGATGACCAAAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA7-DNA TACCAGACGAATTCGTGGTGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA8-DNA GAAAGATCTCAGTCCAAGATGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA9-DNA TAGGAACTGGGCCAGAAGCTGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA10-DNA TCATATGGGTTGCAACTGAGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
), ArticleFig(id=1217127913120514905, tenantId=1146029695717560320, journalId=1149652044408987649, articleId=1216517521772036238, language=CN, label=表1, caption=

用于crRNA体外转录的DNA模板引物序列

, figureFileSmall=null, figureFileBig=null, tableContent=
引物名称 序列(5'-3')
T7 promoter TAATACGACTCACTATAGGG
crRNA1-DNA ACGTTTGGTGGACCCTCAGAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA2-DNA TAACCAGAATGGAGAACGCAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA3-DNA GATCAAAACAACGTCGGCCCGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA4-DNA TGCGTCTTGGTTCACCGCTCGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA5-DNA GACCTTAAATTCCCTCGAGGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA6-DNA TAGCAGTCCAGATGACCAAAGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA7-DNA TACCAGACGAATTCGTGGTGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA8-DNA GAAAGATCTCAGTCCAAGATGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA9-DNA TAGGAACTGGGCCAGAAGCTGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
crRNA10-DNA TCATATGGGTTGCAACTGAGGTTTTAGTCCCCTTCATTTTTGGGGTGGTCTACCCTATAGTGAGTCGTATTA
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基于串联CRISPR-Cas13a的食品包装病原微生物污染免扩增分子检测
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张勇 , 华迪明 , 邓锐杰 , 高鸿 *
食品安全质量检测学报 | 专题:生物传感器在食品安全检测中的应用 2025,16(15): 94-100
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食品安全质量检测学报 | 专题:生物传感器在食品安全检测中的应用 2025, 16(15): 94-100
基于串联CRISPR-Cas13a的食品包装病原微生物污染免扩增分子检测
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张勇 , 华迪明, 邓锐杰, 高鸿*
作者信息
  • 四川大学轻工科学与工程学院, 成都 610065
  • 张勇(1995—), 男, 博士研究生, 主要研究方向为食品安全分子检测。E-mail:

通讯作者:

*高鸿(1973—), 男, 博士, 教授, 主要研究方向为食品质量与安全、食品营养与功能。E-mail:
Amplification-free molecular detection of pathogenic microbial contamination in food packaging based on tandem CRISPR-Cas13a
Yong ZHANG , Di-Ming HUA, Rui-Jie DENG, Hong GAO*
Affiliations
  • College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
出版时间: 2025-08-15 doi: 10.19812/j.cnki.jfsq11-5956/ts.20241206006
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目的 开发一款基于串联规律间隔成簇短回文重复序列(clustered regularly interspaced short palindromic repeats, CRISPR)和CRISPR相关蛋白13a (CRISPR-associated protein 13a, Cas13a)组成的CRISPR-Cas13a快速、灵敏的食品包装病原微生物检测技术。方法 利用CRISPR-Cas13a技术的特异识别和信号放大特性, 同时基于对病原RNA多靶点识别的串联设计, 通过一个病原RNA分子激活多个Cas13a, 反式切割反应体系中的RNA信号报告分子并伴随荧光信号产生, 协同提升信号放大效率, 从而实现对病原体的灵敏检测。结果 该方法对病原微生物及RNA的检出限分别为800 copies/mL和18.7 pmol/L, 能够在较短时间内完成病原RNA检测, 同时能够准确区分不同病原微生物。测试新型冠状病毒(severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)假病毒污染的食品包装样品显示, 方法测定的回收率在89.71%~102.56%。结论 本研究提供了一种快速、经济且操作简便的食品包装病原微生物污染检测方法, 具备较好的准确性。对食源途径风险微生物的监控具有潜在应用价值。
病原微生物  /  规律间隔成簇短回文重复序列相关蛋白13a  /  免扩增检测  /  食品包装  /  食品安全

Objective To develop a rapid and sensitive detection technology for pathogenic microorganisms in food packaging based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 13a (Cas13a) system. Methods The method leveraged the specific recognition and signal amplification characteristics of the CRISPR-Cas13a technology. Multiple guide RNAs were designed to target different sites on pathogenic RNA, enabling a single RNA molecule to activate multiple Cas13a enzymes simultaneously. This cascade triggered trans-cleavage of RNA reporter molecules in the reaction mixture, generating a detectable fluorescent signal. The tandem design synergistically enhanced signal amplification efficiency, thereby improving detection sensitivity. Results The limits of detection of this method for pathogenic and RNA were 800 copies/mL and 18.7 pmol/L, respectively, and the detection could be completed in a short time, accurately distinguishing different pathogens. Testing food packaging samples contaminated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudvirus showed recovery rates ranging from 89.71% to 102.56%. Conclusion This study presents a rapid, cost-effective and easy-to-operate method for detecting pathogenic microbial contamination on food packaging surfaces, indicating high accuracy, offering potential application value for monitoring microbial risks in foodborne transmission pathways.

pathogenic microorganisms  /  clustered regularly interspaced short palindromic repeats-associated protein 13a  /  amplification-free detection  /  food packaging  /  food safety
张勇, 华迪明, 邓锐杰, 高鸿. 基于串联CRISPR-Cas13a的食品包装病原微生物污染免扩增分子检测. 食品安全质量检测学报, 2025 , 16 (15) : 94 -100 . DOI: 10.19812/j.cnki.jfsq11-5956/ts.20241206006
Yong ZHANG, Di-Ming HUA, Rui-Jie DENG, Hong GAO. Amplification-free molecular detection of pathogenic microbial contamination in food packaging based on tandem CRISPR-Cas13a[J]. Journal of Food Safety & Quality, 2025 , 16 (15) : 94 -100 . DOI: 10.19812/j.cnki.jfsq11-5956/ts.20241206006
食品包装易受到病原微生物污染, 成为潜在的食品安全隐患[1-2]。病原微生物不仅广泛存在于环境中, 而且由于其快速传播的特性, 可能在运输、存储和销售过程中污染食品包装, 进而对消费者的健康构成威胁[3-4]。食品包装等环境中的病原微生物污染问题已被多次报道, 引发了公众对食品安全的担忧[5-6]。在中国的部分冷链运输过程中, 已检测到病原微生物, 而美国和欧洲的研究也发现类似情况[7-10]。这些复杂样本中病原微生物浓度通常较低, 且背景干扰较大, 进一步增加了检测的难度[11-12]。随着消费者对食品安全要求的不断提高, 如何有效监控和检测食品包装表面潜在的微生物污染已成为亟待解决的问题[13-14]。因此, 迫切需要开发快速、灵敏、经济且操作简便的检测技术, 以确保食品包装的安全性[15-17]
核酸检测技术因其高灵敏度和特异性, 已成为病原微生物分子诊断的“金标准”[18-20]。典型的核酸检测包括逆转录-聚合酶链反应(reverse transcription-polymerase chain reaction, RT-PCR)或等温扩增技术(如环介导等温扩增)来检测病原微生物RNA, 并结合实时荧光监测进行病原微生物定量[21-22]。然而, 现有核酸检测技术在环境样本中的应用仍面临一些挑战: 一方面, 传统检测方法依赖于复杂的化学修饰和昂贵的仪器设备, 这限制了其在资源有限环境中的广泛应用; 另一方面, 逆转录步骤的高误差率也影响了检测的可靠性[23-24]。此外, 这些方法在处理复杂背景干扰较大的环境样本时, 常常难以实现快速和高灵敏度的检测, 尤其是在病原微生物浓度较低的情况下[25]
近年来, 规律间隔成簇短回文重复序列(clustered regularly interspaced short palindromic repeats, CRISPR)和CRISPR相关蛋白(CRISPR-associated protein, Cas)组成的CRISPR-Cas系统的应用显著提高了核酸检测的灵敏度和特异性[26-27]。特别是CRISPR-Cas13a技术, 已被证明能够通过特异识别RNA靶标并释放荧光信号, 实现对病原微生物的快速检测[27]。与传统的RT-PCR方法相比, CRISPR-Cas13a技术具有更高的灵敏度和特异性, 并且不依赖于复杂的扩增步骤, 降低了操作的难度和成本[28-29]。然而, 尽管CRISPR-Cas13a系统在多种应用中已取得重要进展, 但现有研究多集中于单一靶标的检测, 而对于复杂样本中的多重靶标识别和信号放大仍存在一定局限[30-31]。因此本研究基于CRISPR-Cas13a技术的特异识别和信号放大特性, 开发了一种无需核酸扩增的多个串联CRISPR-Cas13a方法, 用于灵敏检测食品包装中的病原微生物污染, 也为食品安全风险监控提供了新的研究思路和技术支持。
Cas13a质粒(#172488, 美国Addgene公司); LB肉汤培养基、二硫苏糖醇(dithiothreitol, DTT)、卡那霉素、氯霉素、异丙基-β-D-硫代半乳糖苷(isopropyl β-D-1-thiogalactopyranoside, IPTG)[分析纯, 生工生物工程(上海)股份有限公司]; 双蒸水(double distilled water, ddH2O)(分析纯, 美国康宁公司); PCR预混液[分析纯, 东洋纺(上海)生物科技有限公司]; NaCl、KCl、4-羟乙基哌嗪乙磺酸(n-2-hydroxyethylpiperazine- n-2-ethane sulfonic acid, HEPES)、咪唑、甘油(分析纯, 美国Sigma公司); T7 RNA聚合酶(20 U/μL)、核苷三磷酸(nucleoside triphosphate, NTP)混合物(25 mmol/L)(美国赛默飞世尔科技公司); 病毒样品释放剂(MFSP-CoV2-10, 北京聚合美生物科技有限公司); U5 reporter[分析纯, 序列: FAM-5'-UUUUU-3'-BHQ1), 宝生物工程(大连)有限公司]。
用于crRNA体外转录的DNA模板购自擎科生物工程股份有限公司, 其中引物序列详见表1
ProFlex恒温孵育仪(美国赛默飞世尔科技公司); ZQZY-AF8大量组合式全温振荡培养箱(上海知楚仪器有限公司); CL5R大容量低速冷冻离心机(湘仪离心机仪器有限公司); SCIENTZ-IID超声波细胞破碎仪(宁波新芝生物科技股份有限公司); GMJ-50L立式高压蒸汽灭菌锅(上海申安医疗器械有限公司); HiTrap Ni-NTA柱(美国GE Healthcare公司); 50 kDa超滤装置(美国MILLIPORE公司); Unique AutoPure蛋白纯化仪(苏州英赛斯智能科技有限公司); Synergy H1荧光微孔板读取仪、Take3附件(美国BioTek公司)。
将Cas13a质粒转化至TSsetta DE3感受态细胞中, 并接种至LB培养基中, 于37 ℃振荡培养。当培养物600 nm波长处的光密度(optical density at 600 nm wavelength, OD600)达到0.6~0.8后, 加入终浓度为500 μmol/L的IPTG以诱导蛋白表达。诱导后, 将培养温度降低至16 ℃, 继续培养16 h。收集诱导后的细胞, 使用裂解缓冲液(50 mmol/L HEPES, pH 7.0, 500 mmol/L KCl, 10%甘油)重悬并裂解细胞。将裂解产物在4 °C、10000 r/min条件下离心30 min, 收集上清液。将上清液与HiTrap Ni-NTA柱于16 ℃下孵育30 min后, 用含1 mol/L KCl及25 mmol/L咪唑的裂解缓冲液洗涤3次。随后, 通过咪唑梯度(50、200、200、500 mmol/L)洗脱蛋白, 并收集各级洗脱液。将收集的含蛋白洗脱液经50 kDa超滤装置浓缩至1 mL以内。随后使用Unique AutoPure蛋白纯化仪系统, 将浓缩后的蛋白液依次通过阳离子交换柱和分子筛柱进行进一步纯化。最终, 通过Synergy H1荧光微孔板读取仪及Take3附件测定总蛋白浓度。
将4 μL DNA模板(10 μmol/L)、4 μL T7 promoter (10 μmol/L)、4 μL T7 RNA聚合酶缓冲液和25.5 μL H2O混合, 于90 ℃退火5 min后, 在室温下平衡30 min。向平衡好的混合物中加入0.5 μL T7 RNA聚合酶(20 U/μL)和2 μL NTP混合物(每种核苷酸: 腺嘌呤核苷三磷酸、鸟嘌呤核苷三磷酸、‌胞嘧啶核苷三磷酸和尿嘧啶核苷三磷酸的浓度均为10 mmol/L), 在37 ℃下反应过夜以获得crRNA的转录产物。最终通过Synergy H1及Take3附件测定crRNA浓度。
利用病毒样品释放剂从病原微生物中提取RNA基因, 或通过体外转录获得RNA基因。将40 μL反应体系用于病原微生物RNA检测, 其中包括: 4 μL 靶标RNA样品、4 μL U5 reporter (4 μmol/L)、4 μL crRNA (10 μL)、0.2 μL LbuCas13a (10 μmol/L)、4 μL 10×Cas13a缓冲液、20 mmol/L HEPES (pH 6.8)、50 mmol/L KCl、5 mmol/L MgCl2、100 μg/mL牛血清白蛋白(bovine serum albumin, BSA)、0.01%聚乙二醇单辛基苯基醚(Igepal CA630)、2% (V/V)甘油、以及23.8 μL H2O。混合物在37 ℃孵育30 min后, 被用来进行荧光分析以检测病原微生物RNA。荧光分析时使用Synergy H1, 激发波长设置为480 nm, 发射波长范围设置为510~600 nm。
为了验证该方法对于靶标RNA[新型冠状病毒N基因(severe acute respiratory syndrome coronavirus 2 n gene, SARS-CoV-2 N gene)]的检测特异性, 选择了新型冠状病毒E基因(severe acute respiratory syndrome coronavirus 2 e gene, SARS-CoV-2 E gene)、中东呼吸综合征冠状病毒N基因(middle east respiratory syndrome n gene, MERS N gene)和核糖核酸酶P (ribonuclease P, Rnase P)作为干扰与靶标RNA的输出荧光进行对比测试。选择性测试共选择了3个浓度, 分别为20、50、100 pmol/L。荧光检测参照1.3.3步骤。
在食品包装表面(直径约3 cm的区域)喷洒200 μL含500、1000、2000和5000 copies SARS-CoV-2假病毒的溶液, 模拟SARS-CoV-2病毒的污染。随后使用300 μL洗涤缓冲液收集食品包装表面的SARS-CoV-2假病毒, 随后利用病毒样品释放剂提取RNA, 同时将相同浓度的SARS-CoV-2假病毒的溶液直接利用病毒样品释放剂提取RNA。将提取出来的RNA按照1.3.3步骤进行荧光检测, 并计算RNA浓度。将用本方法检测所得回收的靶标RNA浓度除以对应真实添加的靶标RNA浓度, 从而获得检测回收率。
本研究涉及的所有试验均重复测定3次, 采用Microsoft Excel 2019软件进行数据处理及平均值和标准偏差等相关运算, 采用OriginPro 8.0和Microsoft Power Point 2019软件进行绘图。
本研究利用了CRISPR-Cas13a系统的特异识别与信号放大特性, 通过病原RNA多靶点识别的串联设计, 实现对目标RNA的高灵敏检测。检测原理如图1所示, Cas13a通过crRNA特异性结合靶标RNA序列, 激活Cas13a的核酸酶活性, 进而切割体系中的RNA信号报告分子, 导致荧光信号的释放。信号报告分子是将荧光基团和荧光淬灭基团偶连起来的短RNA序列, 这些报告分子在未被切割时保持背景荧光信号。Cas13a在与crRNA配对, 并精确识别靶标RNA后, 其核酸酶活性被激活, 进而切割信号报告分子。此过程中, 报告分子中包含的荧光基团和淬灭基团之间的距离会发生变化, 导致荧光信号的释放。该系统的核心创新在于多靶点串联设计: 当靶标RNA分子存在时, 多个Cas13a被同时激活, 这导致一系列连续的反式切割反应, 显著放大了荧光信号的强度。这种反应链条效应有效提高了检测的灵敏度, 可以捕捉到极低浓度的靶标RNA分子。而在靶标RNA缺失的情况下, 报告分子未经切割, 荧光信号始终维持在背景水平, 从而确保了检测的特异性和准确性。实验表明, 使用单个位点时信噪比为4.3, 而采用10个位点设计时, 信噪比提升至10.7, 验证了多靶点设计在信号放大和非扩增检测中的显著优势。
作为串联CRISPR-Cas13a检测的关键条件, 结合位点数、Cas13a浓度和信号报告分子的浓度被本研究进行了系统优化。研究发现, 增加结合位点数显著增强了靶标RNA存在时的荧光信号, 而在靶标RNA缺失时, 荧光信号几乎无明显变化(如图2A)。随着结合位点数的增加, 靶标RNA响应的信噪比从4.3上升至9.1。然而, 由于结合位点数的增加需要更多种类的转录crRNA, 导致检测成本显著提升。综合考虑检测效果与成本因素, 最终选择10个位点用于靶标RNA检测。在优化Cas13a浓度时, 设定不同浓度梯度的Cas13a蛋白对靶标RNA进行检测(如图2B)。结果表明, 当Cas13a浓度为100 nmol/L时, 信噪比达到最大值, 表现出最佳检测效果。信号报告分子的浓度同样是影响实验结果的关键因素。通过比较5种终浓度(100、200、400、800、1000 nmol/L)的信号报告分子, 发现当信号报告分子浓度为400 nmol/L时, 能够产生最高的信号响应(如图2C)。因此, 在综合考虑灵敏性和检测效率的前提下, 最终选择400 nmol/L的信号报告分子作为最优浓度。
在最优实验条件下, 采用不同摩尔浓度梯度的靶标RNA标准溶液(0、1、10、20、30、40、60、80和100 pmol/L), 建立了用于靶标RNA定量分析的标准曲线。如图3A所示, 随着靶标RNA浓度的增加, 荧光强度逐步增强。在靶标RNA浓度为20~80 pmol/L的范围内, 荧光强度与靶标RNA浓度呈现良好的线性关系, 标准曲线方程为Y=196.05X-2215.2, r2=0.9953, 其中XY分别代表靶标RNA浓度和荧光强度。经计算, 检出限(limit of detection, LOD)为18.7 pmol/L(如图3B)。为了进一步测试该方法的实际检测能力, 使用含SARS-CoV-2假病毒的RNA提取液。如图3C所示, 与未添加SARS-CoV-2假病毒的背景组相比, SARS-CoV-2假病毒浓度为800 copies/mL的实验组已经出现了显著性差异。该检测能力优于大部分国际卫生组织和相关研究机构对于SARS-CoV-2 LOD的要求(1000 copies/mL左右)[32]。上述结果表明, 该方法可作为一种快速、有效的靶标RNA定量分析工具。值得注意的是, 本方法通过一步混读传感策略即可完成靶标RNA的检测, 无需涉及烦琐的分离步骤。因此, 该方法在病原微生物的现场监测中展现出广阔的应用前景。
为验证本方法在病原微生物检测中的特异性选择能力, 本研究设计了针对SARS-CoV-2 E gene、MERS N gene以及SARS-CoV-2核酸检测的内源性内参Rnase P的检测实验, 并测试了在3种不同浓度(20、50、100 pmol/L)下的荧光响应强度, 以进一步评估其检测选择性和抗干扰能力。实验结果如图4所示, 在相同浓度条件下, 靶标RNA (SARS-CoV-2 N gene)引起的特征荧光信号显著高于其他干扰物质所导致的荧光信号。具体而言, 对于SARS-CoV-2 E gene检测, 其荧光信号变化幅度明显超越了MERS N gene及内参Rnase P的荧光响应值, 干扰影响被有效抑制。这表明, 本方法能够准确区分靶标RNA与其他干扰核酸, 展现出卓越的特异性检测能力。此外, 不同浓度实验中, 靶标RNA的荧光信号变化幅度随着浓度的增加而呈现良好的正相关性, 而干扰物质的信号变化幅度无明显规律性或增强趋势。这一结果清晰地表明, 该检测方法对靶标RNA具有卓越的选择性特异性。同时, 这也进一步证明该方法在分析复杂实际样品方面具有广泛的应用潜力。
为评估本方法在实际环境中检测病原微生物的可行性, 本研究综合考虑食品包装病原微生物污染的特性。食品包装表面由于其材质复杂、易受环境影响, 相较于其他环境, 其病原微生物污染不仅更难监测, 还对疾病的传播存在更高的潜在风险。因此, 本研究选择食品包装表面的SARS-CoV-2假病毒作为测试对象, 模拟病毒污染并开展实际样本的回收率实验。在食品包装表面喷洒含有不同浓度SARS-CoV-2假病毒的溶液, 适当涂布后使用洗涤缓冲液回收病毒样本, 并结合RNA提取和荧光检测进行回收率计算。实验结果(如图5所示)显示, 本方法在不同病毒浓度下的检测回收率范围为89.71%~102.56%, 证明了其在复杂环境样本中对靶标RNA检测的高效性与可靠性。同时, 本方法具有检测迅速、无需核酸扩增和操作简单等优势, 为病原微生物的现场快速检测提供了一种高效、便捷且可行的技术手段。综上, 结合实验验证结果, 本研究表明该方法可广泛应用于食品包装等复杂环境中的病原微生物监测。
综上所述, 本研究基于CRISPR-Cas13a技术的特异性靶标识别和信号放大特性, 设计并开发了一种无需核酸扩增的多个串联CRISPR-Cas13a方法, 用于快速检测食品包装中的病原微生物污染。该方法具有以下优势: (1)操作简便, 无需核酸扩增, 检测步骤显著缩短, 能够在较短时间内完成检测; (2)通过串联设计显著提高信号放大效率, 具备高灵敏度(LOD为800 copies/mL)和高特异性, 可准确区分不同病原微生物; (3)利用荧光信号输出, 无需复杂仪器设备或昂贵试剂, 降低了检测成本; (4)回收率在89.71%~102.56%之间, 验证了该方法在复杂食品包装样本中的良好准确性和可靠性。
尽管本方法具有较高的灵敏度和特异性, 但其在实际应用中仍然面临一些局限性。首先, 样品预处理过程中需要提取病原微生物的RNA, 这一过程可能影响检测成本及检测效率。其次, 特异性和灵敏度可能受到样本中杂质、RNA降解或其他外源性因素的影响, 从而影响最终结果的准确性。因此, 未来的研究应进一步优化RNA提取步骤, 降低试剂成本并提高提取效率, 同时在多种环境条件下验证该方法的稳定性和可靠性。
本研究为食品包装病原微生物的快速检测提供了一种高效、经济的新策略, 具有广泛的应用潜力。特别是在冷链物流、食品加工厂等高风险环境中, 快速而简便的检测方法可以显著提高食品安全监测效率, 及时发现污染源, 避免食品安全事故的发生。例如, 冷链物流环节中的食品包装经常与多个接触面接触, 容易成为病原微生物的传播载体, 因此快速检测方法能有效保障消费者的食品安全。未来的研究可进一步优化该方法, 提升对更广泛病原微生物的检测能力, 并探索其在其他食品相关样本中的应用, 如蔬菜、水果和加工食品等, 以进一步推动食品安全监测技术的发展。
  • 国家重点研发计划项目(2022YFF1103000)
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doi: 10.19812/j.cnki.jfsq11-5956/ts.20241206006
  • 接收时间:2024-12-06
  • 首发时间:2026-01-09
  • 出版时间:2025-08-15
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  • 收稿日期:2024-12-06
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国家重点研发计划项目(2022YFF1103000)
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    四川大学轻工科学与工程学院, 成都 610065

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*高鸿(1973—), 男, 博士, 教授, 主要研究方向为食品质量与安全、食品营养与功能。E-mail:
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Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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