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Ndraha N, Lin HY, Wang CY, Hsiao HI, Lin HJ. Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100183. [PMID: 37767229 PMCID: PMC10520789 DOI: 10.1016/j.fochms.2023.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
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.
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Affiliation(s)
- Nodali Ndraha
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hung-Yun Lin
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Chen-Yow Wang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
| | - Hsin-I Hsiao
- Department of Food Science, National Taiwan Ocean University, Keelung, 202301 Taiwan
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
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Liu R, Ali S, Huang D, Zhang Y, Lü P, Chen Q. A Sensitive Nucleic Acid Detection Platform for Foodborne Pathogens Based on CRISPR-Cas13a System Combined with Polymerase Chain Reaction. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zhao M, Wang X, Wang K, Li Y, Wang Y, Zhou P, Wang L, Zhu W. Recombinant polymerase amplification combined with lateral flow strips for the detection of deep-seated Candida krusei infections. Front Cell Infect Microbiol 2022; 12:958858. [PMID: 36004333 PMCID: PMC9394440 DOI: 10.3389/fcimb.2022.958858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
The incidence of Candida infections in intensive care units (ICU) has significantly increased in recent years, and these infections have become one of the most serious complications threatening the lives of ICU patients. The proportion of non-Candida albicans infections, such as Candida krusei and Candida glabrata infections, which are resistant to fluconazole, is increasing each year. Early identification of the strains causing Candida infections is important for the timely implementation of targeted treatments to save patients’ lives. However, the current methods of direct microscopy, culture, and histopathology, as well as other diagnostic methods, have many shortcomings, such as their low sensitivity and long assay times; therefore, they cannot meet the needs for early clinical diagnosis. Recombinant polymerase amplification (RPA) is a promising isothermal amplification technique that can be performed without sophisticated instruments and equipment, and is suitable for use in resource-poor areas. RPA combined with lateral flow strips (LFS) can be used to rapidly amplify and visualize target genes within 20 min. In this study, RPA-LFS was used to amplify the internal transcribed spacer 2 (ITS2) region of C. krusei. The primer-probe design was optimized by introduction of base mismatches (probe modification of five bases) to obtain a specific and sensitive primer-probe combination for the detection of clinical specimens. Thirty-five common clinical pathogens were tested with RPA-LFS to determine the specificity of the detection system. The RPA-LFS system specifically detected C. krusei without cross-reaction with other fungi or bacteria. A gradient dilution of the template was tested to explore the lower limit of detection and sensitivity of the assay. The sensitivity was 10 CFU/50 µL per reaction, without interference from genomic DNA of other species. The RPA-LFS and qPCR assays were performed on 189 clinical specimens to evaluate the detection performance of the RPA-LFS system. Seventy-six specimens were identified as C. krusei, indicating a detection rate of 40.2%. The results were consistent with those of qPCR and conventional culture methods. The RPA-LFS system established in our study provides a reliable molecular diagnostic method for the detection of C. krusei, thus meeting the urgent need for rapid, specific, sensitive, and portable clinical field testing.
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Affiliation(s)
- Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xizhen Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Kun Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yuanyuan Li
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yan Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Ping Zhou
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Lei Wang
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
| | - Wenjun Zhu
- Department of Medicine Laboratory, The Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Ping Zhou, ; Lei Wang, ; Wenjun Zhu,
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Wang K, Huo L, Li Y, Zhu L, Wang Y, Wang L. Establishment of a rapid diagnosis method for Candida glabrata based on the ITS2 gene using recombinase polymerase amplification combined with lateral flow strips. Front Cell Infect Microbiol 2022; 12:953302. [PMID: 35967865 PMCID: PMC9366737 DOI: 10.3389/fcimb.2022.953302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Candida glabrata is the second or third most common Candida-associated species isolated from hospital-acquired infections, surpassing even C. albicans in some hospitals. With the rapid progression of the disease course of C. glabrata infections, there is an urgent need for a rapid and sensitive on-site assay for clinical diagnosis. Isothermal amplification is a recently developed method for rapid nucleic acid detection that is being increasingly used for on-site detection, especially recombinase polymerase amplification (RPA). RPA combined with lateral flow strips (LFS) can rapidly amplify and visually detect the target gene within 20 min. The whole detection process can be controlled within 30–60 min by rapid sample pre-treatment. In this study, RPA-LFS was used to amplify the internal transcribed spacer region 2 gene of C. glabrata. The primer–probe design was optimized by introducing base mismatches (probe modification of one base) to obtain a highly specific and sensitive primer–probe combination for clinical sample detection. RPA-LFS was performed on 23 common clinical pathogens to determine the specificity of the assay system. The RPA-LFS system specifically detected C. glabrata without cross-reaction with other fungi or bacteria. Gradient dilutions of the template were tested to explore the lower limit of detection of this detection system and to determine the sensitivity of the assay. The sensitivity was 10 CFU/µL, without interference from genomic DNA of other species. The RPA-LFS and qPCR assays were performed on 227 clinical samples to evaluate the detection performance of the RPA-LFS system. Eighty-five samples were identified as C. glabrata, representing a detection rate of 37.5%. The results were consistent with qPCR and conventional culture methods. The collective findings indicate a reliable molecular diagnostic method for the detection of C. glabrata, and to meet the urgent need for rapid, specific, sensitive, and portable clinical field-testing.
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Affiliation(s)
- Kun Wang
- Department of Medicine Laboratory, Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Li Huo
- Department of Medicine Laboratory, Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Yuanyuan Li
- Department of Medicine Laboratory, Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
| | - Lihua Zhu
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Lihua Zhu, ; Yan Wang, ; Lei Wang,
| | - Yan Wang
- Department of Medicine Laboratory, Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- *Correspondence: Lihua Zhu, ; Yan Wang, ; Lei Wang,
| | - Lei Wang
- Department of Medicine Laboratory, Second People’s Hospital of Lianyungang (Cancer Hospital of Lianyungang), Lianyungang, China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- *Correspondence: Lihua Zhu, ; Yan Wang, ; Lei Wang,
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Yuan N, Yang H, Zhang Y, Xu H, Lu X, Xu H, Zhang W. Development of real‐time fluorescence saltatory rolling circle amplification for rapid detection of
Vibrio parahaemolyticus
in seafood. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ning Yuan
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Haoyu Yang
- Department of Sports Work Hebei Agricultural University Baoding 071001 China
| | - Yunzhe Zhang
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
| | - Hancong Xu
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
| | - Xin Lu
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Hui Xu
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Wei Zhang
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
- College of Life Sciences Hebei Agricultural University Baoding 071001 China
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