1
|
Yang Y, Hu Y, Yang C, Shi W, Jin S, Hua C, Jiang K. Development and validation of a novel multiplex digital PCR assay for identification of pathogens in cerebrospinal fluid of children with bacterial meningitis. Clin Chim Acta 2024; 554:117787. [PMID: 38246212 DOI: 10.1016/j.cca.2024.117787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
BACKGROUND AND AIMS Identifying the pathogens of bacterial meningitis (BM) is crucial for its diagnosis and treatment. The aim of this study is to develop and validate a novel method for detecting pathogens in cerebrospinal fluid (CSF) of children with BM using a digital polymerase chain reaction (dPCR) assay. MATERIALS AND METHODS A novel multiplex dPCR assay method has been developed and validated. The diagnostic performance of the dPCR assay was compared with that of synchronous CSF culture, and the factors affecting its performance were analyzed. RESULTS A total of 69 children with BM were enrolled prospectively. The sensitivity of the dPCR assay was 94.44 %, specificity was 100 %, coincidence rate was 98.55 %, Kappa value was 0.959, and net reclassification improvement was 61.11 %. Compared with the CSF culture assay, the dPCR assay had higher sensitivity in different bacterial groups. Multiple factors affected its performance, including previous use of antibiotics, sampling time, BM complications, and levels of inflammatory biomarkers in CSF and blood (all P < 0.05). Patients who required intensive care and died had a higher bacterial DNA loads identified by dPCR assay (both P < 0.05). CONCLUSION This novel assay has better pathogen detection ability than CSF culture. Its performance was influenced by sampling time, previous use of antibiotics, and disease severity.
Collapse
Affiliation(s)
- Ying Yang
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Yiting Hu
- Department of Child Psychology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Cheng Yang
- Clinical Laboratory Center, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Wen Shi
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China.
| | - Sufeng Jin
- Clinical Laboratory Center, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Chunzhen Hua
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| | - Kewen Jiang
- Department of Child Psychology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
| |
Collapse
|
2
|
Kabiraz MP, Majumdar PR, Mahmud MC, Bhowmik S, Ali A. Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review. Heliyon 2023; 9:e15482. [PMID: 37151686 PMCID: PMC10161726 DOI: 10.1016/j.heliyon.2023.e15482] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.
Collapse
Affiliation(s)
- Meera Probha Kabiraz
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Priyanka Rani Majumdar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - M.M. Chayan Mahmud
- CASS Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, 221 Burwood Highway, VIC, 3125, Australia
| | - Shuva Bhowmik
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author. Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand.
| | - Azam Ali
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author.
| |
Collapse
|
3
|
Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis. WATER 2021. [DOI: 10.3390/w13243551] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.
Collapse
|
4
|
Rapid Detection of Escherichia coli O157:H7 by Loop-Mediated Isothermal Amplification Coupled with a Lateral Flow Assay Targeting the z3276 Genetic Marker. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02172-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
5
|
Jia XX, Li S, Han DP, Chen RP, Yao ZY, Ning BA, Gao ZX, Fan ZC. Development and perspectives of rapid detection technology in food and environment. Crit Rev Food Sci Nutr 2021; 62:4706-4725. [PMID: 33523717 DOI: 10.1080/10408398.2021.1878101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Food safety become a hot issue currently with globalization of food trade and food supply chains. Chemical pollution, microbial contamination and adulteration in food have attracted more attention worldwide. Contamination with antibiotics, estrogens and heavy metals in water environment and soil environment have also turn into an enormous threat to food safety. Traditional small-scale, long-term detection technologies have been unable to meet the current needs. In the monitoring process, rapid, convenient, accurate analysis and detection technologies have become the future development trend. We critically synthesizing the current knowledge of various rapid detection technology, and briefly touched upon the problem which still exist in research process. The review showed that the application of novel materials promotes the development of rapid detection technology, high-throughput and portability would be popular study directions in the future. Of course, the ultimate aim of the research is how to industrialization these technologies and apply to the market.
Collapse
Affiliation(s)
- Xue-Xia Jia
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China.,State Key Laboratory of Food Nutrition and Safety, China International Scientific & Technological Cooperation Base for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Shuang Li
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Dian-Peng Han
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Rui-Peng Chen
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Zi-Yi Yao
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Bao-An Ning
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Zhi-Xian Gao
- Institute of Environmental and Operational Medicine, Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin, P.R. China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, China International Scientific & Technological Cooperation Base for Health Biotechnology, College of Food Engineering and Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| |
Collapse
|
6
|
Qi X, Xu H, Liu W, Guo A. Development of a rapid
FLISA
detection of
Salmonella
spp. based on
CdTe
/
ZnS
quantum dots. J Food Saf 2020. [DOI: 10.1111/jfs.12830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiaobao Qi
- Key Laboratory of Environment Correlative Dietology, Ministry of Education Huazhong Agricultural University Wuhan People's Republic of China
| | - Huanhuan Xu
- National Research and Development Center for Egg Processing Huazhong Agriculture University Wuhan People's Republic of China
| | - Wukang Liu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education Huazhong Agricultural University Wuhan People's Republic of China
| | - Ailing Guo
- Key Laboratory of Environment Correlative Dietology, Ministry of Education Huazhong Agricultural University Wuhan People's Republic of China
- National Research and Development Center for Egg Processing Huazhong Agriculture University Wuhan People's Republic of China
| |
Collapse
|
7
|
Pissuwan D, Gazzana C, Mongkolsuk S, Cortie MB. Single and multiple detections of foodborne pathogens by gold nanoparticle assays. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1584. [PMID: 31532914 DOI: 10.1002/wnan.1584] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022]
Abstract
A late detection of pathogenic microorganisms in food and drinking water has a high potential to cause adverse health impacts in those who have ingested the pathogens. For this reason there is intense interest in developing precise, rapid and sensitive assays that can detect multiple foodborne pathogens. Such assays would be valuable components in the campaign to minimize foodborne illness. Here, we discuss the emerging types of assays based on gold nanoparticles (GNPs) for rapidly diagnosing single or multiple foodborne pathogen infections. Colorimetric and lateral flow assays based on GNPs may be read by the human eye. Refractometric sensors based on a shift in the position of a plasmon resonance absorption peak can be read by the new generation of inexpensive optical spectrometers. Surface-enhanced Raman spectroscopy and the quartz microbalance require slightly more sophisticated equipment but can be very sensitive. A wide range of electrochemical techniques are also under development. Given the range of options provided by GNPs, we confidently expect that some, or all, of these technologies will eventually enter routine use for detecting pathogens in food. This article is categorized under: Diagnostic Tools > Biosensing.
Collapse
Affiliation(s)
- Dakrong Pissuwan
- Materials Science and Engineering Program, Faculty of Science, Mahidol University, Bangkok, Thailand.,Nanobiotechnology and Nanobiomaterials Research Laboratory, School of Materials Science and Innovation, Faculty of Science, Mahidol University, Bangkok, Thailand.,School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| | - Camilla Gazzana
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| | - Skorn Mongkolsuk
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Michael B Cortie
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| |
Collapse
|
8
|
Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| |
Collapse
|
9
|
Liu Z, Yao C, Yang C, Wang Y, Wan S, Huang J. Development of DNAzyme-based PCR signal cascade amplification for visual detection of Listeria monocytogenes in food. Anal Biochem 2018; 553:7-11. [PMID: 29777679 DOI: 10.1016/j.ab.2018.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 01/04/2023]
Abstract
Listeria monocytogenes is an important foodborne pathogen, and it can cause severe diseases. Rapid detection of L. monocytogenes is crucial to control this pathogen. A simple and robust strategy based on the cascade of PCR and G-quadruplex DNAzyme catalyzed reaction was used to detect L. monocytogenes. In the presence of hemin and the aptamer formed during PCR, the catalytic horseradish peroxidase-mimicking G-quadruplex DNAzymes allow the colorimetric responses of target DNA from L. monocytogenes. This assay can detect genomic DNA of L. monocytogenes specifically with as low as 50 pg/reaction with the naked eye. Through 20 pork samples assay, visual detection assay had the same results as conventional detection methods, and had a good performance. This is a powerful demonstration of the ability of G-quadruplex DNAzyme to be used for PCR-based assay with significant advantages of high sensitivity, low cost and simple manipulation over existing approaches and offers the opportunity for application in pathogen detection.
Collapse
Affiliation(s)
- Zhanmin Liu
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
| | - Chenhui Yao
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Cuiyun Yang
- Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200135, PR China
| | - Yanming Wang
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Sibao Wan
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Junyi Huang
- School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| |
Collapse
|
10
|
Verification and large scale clinical evaluation of a national standard protocol for Salmonella spp ./Shigella spp. screening using real-time PCR combined with guided culture. J Microbiol Methods 2018; 145:14-19. [DOI: 10.1016/j.mimet.2017.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/12/2017] [Accepted: 12/17/2017] [Indexed: 11/17/2022]
|
11
|
Cheung SF, Yee MF, Le NK, Gomes EA, Afrasiabi Z, Kamei DT. A Combined Aqueous Two-Phase System and Spot-Test Platform for the Rapid Detection of Escherichia coli O157:H7 in Milk. SLAS Technol 2017; 23:57-63. [DOI: 10.1177/2472630317731892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Foodborne illnesses are a public health concern in the United States and worldwide. Recent outbreaks of Escherichia coli O157:H7 have brought to light the need for improved ways to detect foodborne pathogens and minimize serious outbreaks. Unfortunately, current methods for the detection of foodborne pathogens are time intensive and complex. In this study, we designed a spot immunoassay that uses a UCON-potassium phosphate salt aqueous two-phase system (ATPS) for the preconcentration of O157:H7. This platform was tested with samples of O157:H7 spiked in phosphate-buffered saline and milk. The ATPS was found to improve the detection limit of the spot test, yielding detection at 106 cfu/mL within 30 min. This is the first known application of ATPSs to spot immunoassays. Moreover, detection was successfully achieved without upstream processing or dilution of the sample prior to testing, thereby further simplifying the detection process. This technology’s ease of use, sensitivity, and short time to result highlight its potential to advance the spot test as a viable diagnostic tool for foodborne pathogens.
Collapse
Affiliation(s)
- Sherine F. Cheung
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Matthew F. Yee
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Nguyen K. Le
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Elizabeth A. Gomes
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Zahra Afrasiabi
- Department of Life and Physical Sciences, Lincoln University, Jefferson City, MO, USA
- Math and Sciences, Soka University of America, Aliso Viejo, CA, USA
| | - Daniel T. Kamei
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| |
Collapse
|
12
|
Kim TH, Hwang HJ, Kim JH. Development of a Novel, Rapid Multiplex Polymerase Chain Reaction Assay for the Detection and Differentiation of Salmonella enterica Serovars Enteritidis and Typhimurium Using Ultra-Fast Convection Polymerase Chain Reaction. Foodborne Pathog Dis 2017; 14:580-586. [PMID: 28696782 DOI: 10.1089/fpd.2017.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica serovars Enteritidis and Typhimurium are the most common causative agents of human nontyphoidal salmonellosis. The rapid detection and timely treatment of salmonellosis are important to increase the curative ratio and prevent spreading of the disease. In this study, we developed a rapid multiplex convection polymerase chain reaction (PCR) method to detect Salmonella spp. and differentiate Salmonella Enteritidis and Salmonella Typhimurium. We used the invA gene for Salmonella spp. detection. Salmonella Enteritidis-specific primers and Salmonella Typhimurium-specific primers were designed using the insertion element (IE) and spy genes, respectively. The primer set for Salmonella spp. detection clearly detected both Salmonella Enteritidis and Salmonella Typhimurium after a 21-min amplification reaction. Serovar-specific primer sets for Salmonella Enteritidis and Salmonella Typhimurium specifically detected each target species in a 21-min amplification reaction. We were able to detect Salmonella spp. at a single copy level in the singleplex mode. The limits of detection for Salmonella Enteritidis and Salmonella Typhimurium were 30 copies in both the singleplex and multiplex modes. The PCR run time could be reduced to 10.5 min/15 cycles. The multiplex convection PCR method developed in this study could detect the Salmonella spp. Salmonella Enteritidis and Salmonella Typhimurium in artificially contaminated milk with as few as 100 colony-forming unit/mL after 4-h enrichment. The PCR assay developed in this study provides a rapid, specific, and sensitive method for the detection of Salmonella spp. and the differentiation of Salmonella Enteritidis and Salmonella Typhimurium.
Collapse
Affiliation(s)
- Tae-Hoon Kim
- 1 Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University , Seoul, Korea
| | | | - Jeong Hee Kim
- 1 Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University , Seoul, Korea.,3 Department of Oral Biochemistry and Molecular Biology, School of Dentistry, Kyung Hee University , Seoul, Korea
| |
Collapse
|