Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

doi:10.1016/j.fochms.2023.100183

Review

. 2023 Sep 18:7:100183.

doi: 10.1016/j.fochms.2023.100183. eCollection 2023 Dec 30.

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

Nodali Ndraha¹, Hung-Yun Lin², Chen-Yow Wang¹, Hsin-I Hsiao³, Han-Jia Lin^{1

2}

Affiliations

¹ Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan.
² Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan.
³ Department of Food Science, National Taiwan Ocean University, Keelung, 202301 Taiwan.

PMID: 37767229
PMCID: PMC10520789
DOI: 10.1016/j.fochms.2023.100183

Review

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

Nodali Ndraha et al. Food Chem (Oxf). 2023.

. 2023 Sep 18:7:100183.

doi: 10.1016/j.fochms.2023.100183. eCollection 2023 Dec 30.

Authors

Nodali Ndraha¹, Hung-Yun Lin², Chen-Yow Wang¹, Hsin-I Hsiao³, Han-Jia Lin^{1

2}

Affiliations

¹ Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan.
² Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan.
³ Department of Food Science, National Taiwan Ocean University, Keelung, 202301 Taiwan.

PMID: 37767229
PMCID: PMC10520789
DOI: 10.1016/j.fochms.2023.100183

Abstract

This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.

Keywords: Foodborne pathogen; Isothermal amplification; Molecular detection method; Polymerase chain reaction; Thermo-cycle amplification.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

**Fig. 1**
A schematic representation of the PCR, NASBA, RPA/RAA, and RCA technique.

**Fig. 2**
A schematic representation of the SRCA, NASBA, SDA, and EXPAR technique.

**Fig. 3**
A schematic representation of the SPIA, HDA, and CPA technique.

**Fig. 4**
Interrelated concepts for promoting the widespread implementation of NAA-based methods in food safety areas.

See this image and copyright information in PMC

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References

1. Amore G., Boelaert F., Papanikolaou A., Rizzi V., Stoicescu A. Manual for reporting on zoonoses and zoonotic agents, within the framework of Directive 2003/99/EC, and on some other pathogenic microbiological agents for information derived from the year 2021. EFSA Supporting Publications. 2022;19 doi: 10.2903/sp.efsa.2022.EN-7130. - DOI
1. Andrews, W. H., Wang, H., Jacobson, A., Ge, B., Zhang, G., & Hammack, T. (2023). BAM Chapter 5: Salmonella. US Food & Drug Administration. https://www.fda.gov/food/laboratory-methods-food/bam-chapter-5-salmonella (accessed on August 17, 2023).
1. Bundidamorn D., Supawasit W., Trevanich S. Taqman® probe based multiplex RT-PCR for simultaneous detection of Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing Escherichia coli in foods. LWT. 2021;147 doi: 10.1016/j.lwt.2021.111696. - DOI - PMC - PubMed
1. Cai Q., Wang R., Qiao Z., Yang W. Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system. The Analyst. 2021;146:5271–5279. doi: 10.1039/d1an00717c. - DOI - PubMed
1. Cai R., Yin F., Chen H., Tian Y., Zhou N. A fluorescent aptasensor for Staphylococcus aureus based on strand displacement amplification and self-assembled DNA hexagonal structure. Microchimica Acta. 2020;187:304. doi: 10.1007/s00604-020-04293-9. - DOI - PubMed

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[1] Amore G., Boelaert F., Papanikolaou A., Rizzi V., Stoicescu A. Manual for reporting on zoonoses and zoonotic agents, within the framework of Directive 2003/99/EC, and on some other pathogenic microbiological agents for information derived from the year 2021. EFSA Supporting Publications. 2022;19 doi: 10.2903/sp.efsa.2022.EN-7130. - DOI

[2] Amore G., Boelaert F., Papanikolaou A., Rizzi V., Stoicescu A. Manual for reporting on zoonoses and zoonotic agents, within the framework of Directive 2003/99/EC, and on some other pathogenic microbiological agents for information derived from the year 2021. EFSA Supporting Publications. 2022;19 doi: 10.2903/sp.efsa.2022.EN-7130. - DOI

[3] Andrews, W. H., Wang, H., Jacobson, A., Ge, B., Zhang, G., & Hammack, T. (2023). BAM Chapter 5: Salmonella. US Food & Drug Administration. https://www.fda.gov/food/laboratory-methods-food/bam-chapter-5-salmonella (accessed on August 17, 2023).

[4] Andrews, W. H., Wang, H., Jacobson, A., Ge, B., Zhang, G., & Hammack, T. (2023). BAM Chapter 5: Salmonella. US Food & Drug Administration. https://www.fda.gov/food/laboratory-methods-food/bam-chapter-5-salmonella (accessed on August 17, 2023).

[5] Bundidamorn D., Supawasit W., Trevanich S. Taqman® probe based multiplex RT-PCR for simultaneous detection of Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing Escherichia coli in foods. LWT. 2021;147 doi: 10.1016/j.lwt.2021.111696. - DOI - PMC - PubMed

[6] Bundidamorn D., Supawasit W., Trevanich S. Taqman® probe based multiplex RT-PCR for simultaneous detection of Listeria monocytogenes, Salmonella spp. and Shiga toxin-producing Escherichia coli in foods. LWT. 2021;147 doi: 10.1016/j.lwt.2021.111696. - DOI - PMC - PubMed

[7] Cai Q., Wang R., Qiao Z., Yang W. Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system. The Analyst. 2021;146:5271–5279. doi: 10.1039/d1an00717c. - DOI - PubMed

[8] Cai Q., Wang R., Qiao Z., Yang W. Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system. The Analyst. 2021;146:5271–5279. doi: 10.1039/d1an00717c. - DOI - PubMed

[9] Cai R., Yin F., Chen H., Tian Y., Zhou N. A fluorescent aptasensor for Staphylococcus aureus based on strand displacement amplification and self-assembled DNA hexagonal structure. Microchimica Acta. 2020;187:304. doi: 10.1007/s00604-020-04293-9. - DOI - PubMed

[10] Cai R., Yin F., Chen H., Tian Y., Zhou N. A fluorescent aptasensor for Staphylococcus aureus based on strand displacement amplification and self-assembled DNA hexagonal structure. Microchimica Acta. 2020;187:304. doi: 10.1007/s00604-020-04293-9. - DOI - PubMed

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Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

Affiliations

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

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Conflict of interest statement

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