A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques

Kim, Tai-Yong; Zhu, Xiaoning; Kim, Se-Min; Lim, Jeong-A; Woo, Min-Ah; Lim, Min-Cheol; Luo, Ke

doi:10.1016/j.foodres.2023.113502

Cited by 9 publications

(3 citation statements)

References 127 publications

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“…The detection limit of this method is 10 pg per reaction for bacterial genomic DNA, and the serovar-specificity was verified by bacteriological methods [ 11 ]. Although PCR remains the gold standard for monitoring food contamination by pathogens [ 27 ], its reliance on sophisticated equipment, skilled technicians, and time-consuming processes limits its applicability in resource-limited regions. In contrast, the isothermal amplification technique presents outstanding advantages, amplifying isothermally at 22–65 °C within 30 min without specific equipment or the requirement of skilled operators [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection

Gong,

Zhang,

et al. 2024

Microorganisms

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Salmonella enterica serovar Indiana (S. Indiana) is among the most prevalent serovars of Salmonella and is closely associated with foodborne diseases worldwide. In this study, we combined a recombinase polymerase amplification (RPA) technique with clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (Cas) protein Cas12b (CRISPR/Cas12b)-based biosensing in a one-pot platform to develop a novel one-step identification method for S. Indiana infection diagnosis. The entire RPA-CRISPR/Cas12b reaction can be completed at 41 °C within 1 h without the need for specific instruments. The optimal concentrations of Cas12b and single-guide RNA (sgRNA) for the reaction were the same at 250 nM. The single-stranded DNA (ssDNA) reporter 8C-FQ (5′-/6-FAM/CCCCCCCC/BHQ1/-3′) presented the best performance in the reaction compared with the other reporters. The limit of detection (LoD) of the RPA-CRISPR/Cas12b assay was 14.4 copies per reaction. As for specificity, we successfully identified four S. Indiana strains among twenty-two Salmonella strains without any false-positive results, presenting 100% accuracy for S. Indiana, and no cross-reactions were observed in eight other pathogens. Moreover, a total of 109 chicken carcasses were classified by the S. Indiana RPA-CRISPR assay and PCR methods from three processing points, including 43 post-shedding, 35 post-evisceration, and 31 post-chilling. There were 17 S. Indiana-positive samples identified during the whole processing step, consisting of nine post-shedding, five post-evisceration, and three post-chilling. The corresponding S. Indiana-positive rates of post-shedding, post-evisceration, and post-chilling were 20.93% (9/43), 14.29% (5/35), and 9.68% (3/31), respectively. Results from the S. Indiana one-step RPA-CRISPR/Cas12b assay were totally in agreement with those obtained using a traditional culture method, demonstrating 100% agreement with no false-positive or false-negative results observed. Altogether, the RPA-CRISPR/Cas12b assay developed in this study represents a promising, accurate, and simple diagnostic tool for S. Indiana detection.

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Section: Discussionmentioning

confidence: 99%

A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection

Gong,

Zhang,

et al. 2024

Microorganisms

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“…Nanomaterials have played a huge role in the development of biosensors. 51–53 Jeon et al described a sample preparation chip embedded with a bi-porous silica nanomembrane for pathogen and nucleic acid enrichment/separation. The chip has a unique bi-porous nanostructure consisting of a macroporous layer and a small porous layer.…”

Section: Detection Of Viral Nucleic Acidsmentioning

confidence: 99%

Advances in rapid point-of-care virus testing

Zhang,

Bu,

Shu

et al. 2024

Analyst

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“…The polymerase chain reaction (PCR) serves as a direct test available for detecting M. bovis in cattle. However, PCR requires adequately trained personnel along with costly reagents and equipment [ 11 ]. Furthermore, calcium may inhibit polymerase activity by competing with magnesium ions present in milk [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

High-Performance Detection of Mycobacterium bovis in Milk Using Recombinase-Aided Amplification–Clustered Regularly Interspaced Short Palindromic Repeat–Cas13a–Lateral Flow Detection

Wang,

et al. 2024

Foods

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Mycobacterium bovis (M. bovis), the microorganism responsible for bovine tuberculosis (bTB), is transferred to people by the ingestion of unpasteurized milk and unprocessed fermented milk products obtained from animals with the infection. The identification of M. bovis in milk samples is of the utmost importance to successfully prevent zoonotic diseases and maintain food safety. This study presents a comprehensive description of a highly efficient molecular test utilizing recombinase-aided amplification (RPA)–clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) 13a–lateral flow detection (LFD) for M. bovis detection. In contrast to ELISA, RPA–CRISPR–Cas13a–LFD exhibited greater accuracy and sensitivity in the detection of M. bovis in milk, presenting a detection limit of 2 × 100 copies/μL within a 2 h time frame. The two tests exhibited a moderate level of agreement, as shown by a kappa value of 0.452 (95%CI: 0.287–0.617, p < 0.001). RPA–CRISPR–Cas13a–LFD holds significant potential as a robust platform for pathogen detection in complex samples, thereby enabling the more dependable regulation of food safety examination, epidemiology research, and medical diagnosis.

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A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques

Cited by 9 publications

References 127 publications

A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection

A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection

Advances in rapid point-of-care virus testing

High-Performance Detection of Mycobacterium bovis in Milk Using Recombinase-Aided Amplification–Clustered Regularly Interspaced Short Palindromic Repeat–Cas13a–Lateral Flow Detection

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