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Multiplexed food-borne pathogen detection using an argonaute-mediated digital sensor based on a magnetic-bead-assisted imaging transcoding system

Nature Food volume 6, pages 170–181 (2025)Cite this article

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Abstract

Accurate, sensitive and multiplexed detection of food-borne pathogens is crucial for assessing food safety risks. Here we present a digital DNA-amplification-free nucleic acid detection assay to achieve multiplexed and ultrasensitive detection of three food-borne pathogens. We used mesophilic Clostridium butyricum argonaute and magnetic beads in a digital carrier system (d-MAGIC). Clostridium butyricum argonaute, with its two-guide accurate cleavage activity, precisely targets and cleaves fluorescence-quencher reporters corresponding to different bacteria through a two-step process. The system uses fluorescence-encoded magnetic beads as programmable multi-probes, allowing the simultaneous detection of multiple pathogens and easy data interpretation via artificial intelligence. The method showed a wide detection range (101 to 107 CFU ml−1) and a low limit of detection of 6 CFU ml−1 for food-borne pathogens without DNA amplification. Digital nucleic acid testing using d-MAGIC can become a next-generation strategy for accurate and convenient pathogen detection.

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Fig. 1: Scheme of the Ago-protein-mediated digital nucleic acid biosensor based on a programmable MB-assisted imaging transcoding system.
Fig. 2: Characterization of CbAgo and MB–TA–SA conjugates.
Fig. 3: Programmable MB-assisted imaging transcoding system.
Fig. 4: Single food-borne pathogen detection using d-MAGIC.
Fig. 5: Multiplexed detection of three food-borne pathogens.
Fig. 6: Real sample analysis by d-MAGIC (triangle) and qPCR (circle) for detecting food-borne pathogens.

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Data availability

Source data are provided with this paper.

Code availability

The related code is available via GitHub at https://github.com/Wang-Qinyu/Panda/tree/main.

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Acknowledgements

We thank the National Natural Science Foundation of China (32172293), the National Key Research and Development Program of China (2022YFF0607900) and the Open Project of Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-Derived Food for State Market Regulation (number KF-202201) for financial support.

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Author notes

  1. These authors contributed equally: Zhipan Wang, Xinrui Cheng.

Authors and Affiliations

  1. College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China

    Zhipan Wang, Xinrui Cheng, Aimin Ma & Yiping Chen

  2. Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-Derived Food for State Market Regulation, Wuhan, China

    Feng Jiang

  3. State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, China

    Yiping Chen

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  1. Zhipan Wang
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  2. Xinrui Cheng
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Contributions

Z.W. and Y.C. conceptualized the research. Z.W. and X.C. planned and performed the research. Z.W. assisted in testing the code. Z.W. analysed the data. Z.W. wrote the original draft. A.M., F.J. and Y.C. reviewed and edited the paper.

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Correspondence to Yiping Chen.

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Nature Food thanks Seyed Mohammad Taghi Gharibzahedi, Sang-Soon Kim and Fengge Song for their contribution to the peer review of this work.

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Wang, Z., Cheng, X., Ma, A. et al. Multiplexed food-borne pathogen detection using an argonaute-mediated digital sensor based on a magnetic-bead-assisted imaging transcoding system. Nat Food 6, 170–181 (2025). https://doi.org/10.1038/s43016-024-01082-y

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