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Liu X, Yuan W, Xiao H. Recent progress on DNAzyme-based biosensors for pathogen detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4917-4937. [PMID: 38984495 DOI: 10.1039/d4ay00934g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Pathogens endanger food safety, agricultural productivity, and human health. Those pathogens are spread through direct/indirect contact, airborne transmission and food/waterborne transmission, and some cause severe health consequences. As the population grows and global connections intensify, the transmission of infectious diseases expands. Traditional detection methods for pathogens still have some shortcomings, such as time-consuming procedures and high operational costs. To fulfil the demands for simple and effective detection, numerous biosensors have been developed. DNAzyme, a unique DNA structure with catalytic activity, is gradually being applied in the field of pathogen detection owing to its ease of preparation and use. In this review, we concentrated on the two main types of DNAzyme, hemin/G-quadruplex DNAzyme (HGD) and RNA-cleaving DNAzyme (RCD), explaining their research progress in pathogen detection. Furthermore, we introduced two additional novel DNAzymes, CLICK 17 DNAzyme and Supernova DNAzyme, which showed promising potential in pathogen detection. Finally, we summarize the strengths and weaknesses of these four DNAzymes and offer feasible recommendations for the development of biosensors.
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Affiliation(s)
- Xingxing Liu
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Wenxu Yuan
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
| | - Heng Xiao
- Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Department of Immunology and Microbiology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, P. R. China
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Haider A, Iqbal SZ, Bhatti IA, Alim MB, Waseem M, Iqbal M, Mousavi Khaneghah A. Food authentication, current issues, analytical techniques, and future challenges: A comprehensive review. Compr Rev Food Sci Food Saf 2024; 23:e13360. [PMID: 38741454 DOI: 10.1111/1541-4337.13360] [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: 02/05/2024] [Revised: 03/29/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024]
Abstract
Food authentication and contamination are significant concerns, especially for consumers with unique nutritional, cultural, lifestyle, and religious needs. Food authenticity involves identifying food contamination for many purposes, such as adherence to religious beliefs, safeguarding health, and consuming sanitary and organic food products. This review article examines the issues related to food authentication and food fraud in recent periods. Furthermore, the development and innovations in analytical techniques employed to authenticate various food products are comprehensively focused. Food products derived from animals are susceptible to deceptive practices, which can undermine customer confidence and pose potential health hazards due to the transmission of diseases from animals to humans. Therefore, it is necessary to employ suitable and robust analytical techniques for complex and high-risk animal-derived goods, in which molecular biomarker-based (genomics, proteomics, and metabolomics) techniques are covered. Various analytical methods have been employed to ascertain the geographical provenance of food items that exhibit rapid response times, low cost, nondestructiveness, and condensability.
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Affiliation(s)
- Ali Haider
- Food Safety and Toxicology Lab, Department of Applied Chemistry, Government College University, Faisalabad, Punjab, Pakistan
| | - Shahzad Zafar Iqbal
- Food Safety and Toxicology Lab, Department of Applied Chemistry, Government College University, Faisalabad, Punjab, Pakistan
| | - Ijaz Ahmad Bhatti
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | | | - Muhammad Waseem
- Food Safety and Toxicology Lab, Department of Applied Chemistry, Government College University, Faisalabad, Punjab, Pakistan
| | - Munawar Iqbal
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore, Pakistan
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3
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Kim TY, Zhu X, Kim SM, Lim JA, Woo MA, Lim MC, Luo K. A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques. Food Res Int 2023; 174:113502. [PMID: 37986417 DOI: 10.1016/j.foodres.2023.113502] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 11/22/2023]
Abstract
Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.
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Affiliation(s)
- Tai-Yong Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Xiaoning Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Se-Min Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Science and Technology, Jeonbuk National University, Jeonju-si, Jeollabuk-do 54896, Republic of Korea
| | - Jeong-A Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Ah Woo
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Cheol Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Biotechnology, Korea University of Science and Technology, Daejeon-si 34113, Republic of Korea.
| | - Ke Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China.
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Lee CJ, Shin W, Song M, Shin SS, Park Y, Srikulnath K, Kim DH, Han K. Comparison of digital PCR platforms using the molecular marker. Genomics Inform 2023; 21:e24. [PMID: 37704210 PMCID: PMC10326530 DOI: 10.5808/gi.23008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 07/08/2023] Open
Abstract
Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.
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Affiliation(s)
- Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan 31116, Korea
| | | | | | - Yujun Park
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Facult y of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Kyudong Han
- Department of Bio-Convergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- HuNBiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Bio-Medical Engineering Research Center, Dankook University, Cheonan 31116, Korea
- DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 31116, Korea
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Kim U, Lee SY, Oh SW. Thermophilic helicase-dependent amplification-based CRISPR/Cas12a system: Detection of stx2 in Escherichia coli O157:H7 by controlling primer dimers. Anal Chim Acta 2023; 1239:340679. [PMID: 36628706 DOI: 10.1016/j.aca.2022.340679] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND s: To overcome the limitation of polymerase chain reaction (PCR), isothermal amplification methods such as thermophilic helicase-dependent amplification (tHDA) have been developed. However, formation of primer dimer due to the single amplification temperature are major problems of tHDA. When cross-dimerization of forward and reverse primer occurred, false-positive results can be found on the lateral flow assay (LFA) which is one of the major detection methods widely used as a point of care diagnosis. Therefore, specific method of detecting only the target amplicon is required. RESULTS In this study, a tHDA-based CRISPR/Cas12a system was developed to detect low levels of Escherichia coli O157:H7 in fresh salad mix without the false-positive results produced by primer dimers. For the comparison of the effect in eliminating false-positive results by CRISPR/Cas12a system, LFA was also evaluated. The tHDA-based CRISPR/Cas12a system detected as low as 101 CFU/mL E. coli O157:H7 in bacterial pure culture. In LFA false-positive results were produced due to the primer dimer, whereas the primer dimer produced by tHDA was not detected in the CRISPR/Cas12a system. These results indicated that the CRISPR/Cas12a system eliminated the formation of primer dimer. In fresh salad mix, the tHDA-based CRISPR/Cas12a system combined with the filter concentration method detected 103 CFU/g E. coli O157:H7. CONCLUSION This study was the first to amplify stx2 of E. coli O157:H7 with tHDA as an isothermal amplification method and detected the amplicon without false-positive results by combining tHDA with CRISPR/Cas12a. Therefore, this study showed great potential for detecting low levels of E. coli O157:H7 present in fresh salad mix.
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Affiliation(s)
- Unji Kim
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea
| | - So-Young Lee
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea.
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Qu LL, Ying YL, Yu RJ, Long YT. In situ food-borne pathogen sensors in a nanoconfined space by surface enhanced Raman scattering. Mikrochim Acta 2021; 188:201. [PMID: 34041602 PMCID: PMC8154335 DOI: 10.1007/s00604-021-04864-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/13/2021] [Indexed: 01/04/2023]
Abstract
The incidence of disease arising from food-borne pathogens is increasing continuously and has become a global public health problem. Rapid and accurate identification of food-borne pathogens is essential for adopting disease intervention strategies and controlling the spread of epidemics. Surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest due to the attractive features including simplicity, rapid measurement, and high sensitivity. It can be used for rapid in situ sensing of single and multicomponent samples within the nanostructure-based confined space by providing molecular fingerprint information and has been demonstrated to be an effective detection strategy for pathogens. This article aims to review the application of SERS to the rapid sensing of food-borne pathogens in food matrices. The mechanisms and advantages of SERS, and detection strategies are briefly discussed. The latest progress on the use of SERS for rapid detection of food-borne bacteria and viruses is considered, including both the labeled and label-free detection strategies. In closing, according to the current situation regarding detection of food-borne pathogens, the review highlights the challenges faced by SERS and the prospects for new applications in food safety. In this review, the advances on the SERS detection of pathogens over the past decades have been reviewed, focusing on the improvements in sensitivity, reproducibility, specificity, and the performance of the SERS-based assay in complex analytical scenarios. ![]()
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Affiliation(s)
- Lu-Lu Qu
- School of Chemistry and Materials Science, Jiangsu Normal University, 221116, Xuzhou, People's Republic of China.
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, People's Republic of China
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7
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Lu X, Ye Y, Zhang Y, Sun X. Current research progress of mammalian cell-based biosensors on the detection of foodborne pathogens and toxins. Crit Rev Food Sci Nutr 2020; 61:3819-3835. [PMID: 32885986 DOI: 10.1080/10408398.2020.1809341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Foodborne diseases caused by pathogens and toxins are a serious threat to food safety and human health; thus, they are major concern to society. Existing conventional foodborne pathogen or toxin detection methods, including microbiological assay, nucleic acid-based assays, immunological assays, and instrumental analytical method, are time-consuming, labor-intensive and expensive. Because of the fast response and high sensitivity, cell-based biosensors are promising novel tools for food safety risk assessment and monitoring. This review focuses on the properties of mammalian cell-based biosensors and applications in the detection of foodborne pathogens (bacteria and viruses) and toxins (bacterial toxins, mycotoxins and marine toxins). We discuss mammalian cell adhesion and how it is involved in the establishment of 3D cell culture models for mammalian cell-based biosensors, as well as evaluate their limitations for commercialization and further development prospects.
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Affiliation(s)
- Xin Lu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
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8
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SAMAD ABDUL, ABBAS FERHAT, TANVEER ZUNERA, AHMAD ZAFAR, AHMAD IRSHAD, PATCHING SIMONG, NAWAZ NIGHAT, ASMAT MUHAMMADTAUSEEF, RAZIQ ABDUL, LAH ASADUL, SHEIKH IRFANSHAHZAD, NAEEM MUHAMMAD, POKRYSHKO OLENA, MUSTAFA MOHAMMADZAHID. Prevalence of Salmonella spp. in chicken meat from Quetta retail outlets and typing through multiplex PCR. ROMANIAN BIOTECHNOLOGICAL LETTERS 2019. [DOI: 10.25083/rbl/24.2/271.279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Ricke SC, Feye KM, Chaney WE, Shi Z, Pavlidis H, Yang Y. Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States. Front Microbiol 2019; 9:3280. [PMID: 30728816 PMCID: PMC6351486 DOI: 10.3389/fmicb.2018.03280] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.
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Affiliation(s)
- Steven C. Ricke
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Kristina M. Feye
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Zhaohao Shi
- Department of Food Science, Center of Food Safety, University of Arkansas, Fayetteville, AR, United States
| | | | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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10
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Rao J, Liao J, Bu Y, Wang Y, Hu X, Long G, Huang M, Zhong L, Yang X, Liao F. Ampholytic ion-exchange materials coated with small zwitterions for high-efficacy purification of ionizable soluble biomacromolecules. Int J Biol Macromol 2018; 120:2234-2241. [PMID: 30092309 DOI: 10.1016/j.ijbiomac.2018.08.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/02/2018] [Accepted: 08/05/2018] [Indexed: 01/17/2023]
Abstract
For the purification of soluble proteins and nucleic acids through ion-exchange, the ampholytic ion-exchange materials (AIEMs) were designed, which possessed both short aliphatic carboxyl and short aliphatic amines/imidazole at optimized ratios on solid supports coated with high density of small zwitterions; under optimized conditions, the soluble ionizable biomacromolecules were adsorbed on those AIEMs via electrostatic attractions and eluted effectively through electrostatic repulsions. As the proof-of-concept, magnetic submicron particles bearing short aliphatic carboxyl and the coats of small zwitterion served as the starting solid supports, which were conjugated with lysine alone, or with lysine plus glycine or N,N‑dimethylethylenediamine, to yield magnetic AIEMs whose surfaces possessed zero net charges at different pH. Such magnetic AIEMs exhibited ideal efficacy to release acid red 13 as an anion at the elution pH optimized for strong electrostatic repulsions; those magnetic AIEMs were proven absorbing under optimized conditions for the purification of soluble proteins stable at pH close to their isoelectric points and solid-phase extraction of nucleic acids in applicable biological mixtures. Therefore, the designed AIEMs are promising for the high-efficacy purification of ionizable soluble biomacromolecules.
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Affiliation(s)
- Jingjing Rao
- College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Juan Liao
- Yongchuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Youquan Bu
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yitao Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaolei Hu
- College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Gaobo Long
- Chongqing Bolanying Biotechnology Co. Ltd., Xiyong, Shapingba, Chongqing 401332, China
| | - Mingtong Huang
- Chongqing Bolanying Biotechnology Co. Ltd., Xiyong, Shapingba, Chongqing 401332, China
| | - Luhui Zhong
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 401135, China
| | - Xiaolan Yang
- College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Fei Liao
- College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 401135, China.
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11
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Juvonen R, Satokari R, Mallison K, Haikara A. Detection of Spoilage Bacteria in Beer by Polymerase Chain Reaction. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-57-0099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Riikka Juvonen
- Technical Research Centre of Finland, Biotechnology and Food Research, P.O. Box 1500, FIN-02044 VTT, Finland
| | - Reetta Satokari
- Technical Research Centre of Finland, Biotechnology and Food Research, P.O. Box 1500, FIN-02044 VTT, Finland
| | - Kirstie Mallison
- University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, England
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12
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Seedy FRE, Samy AA, Salam HSH, Khairy EA, Koraney AA. Polymerase chain reaction detection of genes responsible for multiple antibiotic resistance Staphylococcus aureus isolated from food of animal origin in Egypt. Vet World 2017; 10:1205-1211. [PMID: 29184366 PMCID: PMC5682265 DOI: 10.14202/vetworld.2017.1205-1211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/11/2017] [Indexed: 01/04/2023] Open
Abstract
Aim: The aim of our study was polymerase chain reaction (PCR) detection of the genes responsible for the multiple antibiotic resistance S. aureus isolated from food of animal origin in Egypt. Materials and Methods: A total of 125 samples were randomly collected from milk, meat, and their products from Giza and Beni-Suef Governorates markets. The S. aureus isolates were subjected to antimicrobial sensitivity tests using four antibacterial disks (Oxoid), and then the polymerase chain reaction (PCR) was performed for detection of antibiotic resistance genes. Results: Out of 125 samples, 19 S. aureus isolates were detected. All detected isolates were multiple drug resistance (MDR). The penicillin-, erythromycin-, kanamycin-, and tetracycline-resistant isolates were examined by PCR for resistance genes blaZ, (msrA, ermB, and ermC), aac(6’)aph (2”), and tetK. The isolates harbored these resistance genes with percentage of 100% (100%, 0%, and 100%), 62.5%, and 100%, respectively. Conclusion: Contaminated foods of animal origin may represent a source of MDR S. aureus that can be a major threat to public health.
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Affiliation(s)
- Fawzy R El Seedy
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - A A Samy
- Department of Microbiology and Immunology, National Research Center, Cairo, Egypt
| | - Hala S H Salam
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Eman A Khairy
- Department of Microbiology and Immunology, National Research Center, Cairo, Egypt
| | - Aya A Koraney
- Department of Microbiology and Immunology, National Research Center, Cairo, Egypt
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13
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Rosimin AA, Kim MJ, Joo IS, Suh SH, Kim KS. Simultaneous detection of pathogenic Listeria including atypical Listeria innocua in vegetables by a quadruplex PCR method. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2016.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Shin H, Kim M, Yoon E, Kang G, Kim S, Song A, Kim J. Isothermal target and probe amplification assay for the real-time rapid detection of Staphylococcus aureus. J Food Prot 2015; 78:723-7. [PMID: 25836397 DOI: 10.4315/0362-028x.jfp-14-193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Staphylococcus aureus, the species most commonly associated with staphylococcal food poisoning, is one of the most prevalent causes of foodborne disease in Korea and other parts of the world, with much damage inflicted to the health of individuals and economic losses estimated at $120 million. To reduce food poisoning outbreaks by implementing prevention methods, rapid detection of S. aureus in foods is essential. Various types of detection methods for S. aureus are available. Although each method has advantages and disadvantages, high levels of sensitivity and specificity are key aspects of a robust detection method. Here, we describe a novel real-time isothermal target and probe amplification (iTPA) method that allows the rapid and simultaneous amplification of target DNA (the S. aureus nuc gene) and a fluorescence resonance energy transfer-based signal probe under isothermal conditions at 61 °C or detection of S. aureus in real time. The assay was able to specifically detect all 91 S. aureus strains tested without nonspecific detection of 51 non-S. aureus strains. The real-time iTPA assay detected S. aureus at an initial level of 10(1) CFU in overnight cultures of preenriched food samples (kiwi dressing, soybean milk, and custard cream). The advantage of this detection system is that it does not require a thermal cycler, reducing the cost of the real-time PCR and its footprint. Combined with a miniaturized fluorescence detector, this system can be developed into a simplified quantitative hand-held real-time device, which is often required. The iTPA assay was highly reliable and therefore may be used as a rapid and sensitive means of identifying S. aureus in foods.
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Affiliation(s)
- Hyewon Shin
- Food Research and Development Center, Samsung Welstory, Inc., 2442-1 Yonggu-daero, Giheunggu, YongIn-si, Gyeonggi-do, South Korea
| | - Minhwan Kim
- DxGene, Inc., 306 Ace Technotower 5th, 197-22 Guro-3-dong, Guro-gu, Seoul, South Korea
| | - Eunju Yoon
- Department of Food Science and Nutrition, Dong-A University, 550 Nakdong-daero, Sahagu, Busan, South Korea
| | - Gyoungwon Kang
- Food Research and Development Center, Samsung Welstory, Inc., 2442-1 Yonggu-daero, Giheunggu, YongIn-si, Gyeonggi-do, South Korea
| | - Seungyu Kim
- DxGene, Inc., 306 Ace Technotower 5th, 197-22 Guro-3-dong, Guro-gu, Seoul, South Korea
| | - Aelee Song
- Food Research and Development Center, Samsung Welstory, Inc., 2442-1 Yonggu-daero, Giheunggu, YongIn-si, Gyeonggi-do, South Korea
| | - Jeongsoon Kim
- Food Research and Development Center, Samsung Welstory, Inc., 2442-1 Yonggu-daero, Giheunggu, YongIn-si, Gyeonggi-do, South Korea.
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15
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Radhika M, Saugata M, Murali H, Batra H. A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species. Braz J Microbiol 2014; 45:667-76. [PMID: 25242957 PMCID: PMC4166298 DOI: 10.1590/s1517-83822014005000041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 09/09/2013] [Indexed: 12/19/2022] Open
Abstract
Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.
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Affiliation(s)
- M. Radhika
- Microbiology DivisionDefence Food Research LaboratorySiddharthanagar, MysoreKarnatakaIndiaMicrobiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, India
| | - Majumder Saugata
- Microbiology DivisionDefence Food Research LaboratorySiddharthanagar, MysoreKarnatakaIndiaMicrobiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, India
| | - H.S. Murali
- Microbiology DivisionDefence Food Research LaboratorySiddharthanagar, MysoreKarnatakaIndiaMicrobiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, India
| | - H.V. Batra
- Microbiology DivisionDefence Food Research LaboratorySiddharthanagar, MysoreKarnatakaIndiaMicrobiology Division, Defence Food Research Laboratory, Siddharthanagar, Mysore, Karnataka, India
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16
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AlMasoud N, Xu Y, Nicolaou N, Goodacre R. Optimization of matrix assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) for the characterization of Bacillus and Brevibacillus species. Anal Chim Acta 2014; 840:49-57. [PMID: 25086893 PMCID: PMC4223412 DOI: 10.1016/j.aca.2014.06.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/16/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
Optimization of MALDI-TOF-MS for characterizing Bacillus and Brevibacillus species. Development of a suitable chemometric workflow for processing raw MALDI-TOF-MS data. Classification of 7 species from bacteria achieved high accuracy (∼90%). Allowed to dry at room temperature (ca. 22 °C) for 1 h.
Over the past few decades there has been an increased interest in using various analytical techniques for detecting and identifying microorganisms. More recently there has been an explosion in the application of matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) for bacterial characterization, and here we optimize this approach in order to generate reproducible MS data from bacteria belonging to the genera Bacillus and Brevibacillus. Unfortunately MALDI-TOF-MS generates large amounts of data and is prone to instrumental drift. To overcome these challenges we have developed a preprocessing pipeline that includes baseline correction, peak alignment followed by peak picking that in combination significantly reduces the dimensionality of the MS spectra and corrects for instrument drift. Following this two different prediction models were used which are based on support vector machines and these generated satisfactory prediction accuracies of approximately 90%.
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Affiliation(s)
- Najla AlMasoud
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicoletta Nicolaou
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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17
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O'Sullivan DJ, Giblin L, McSweeney PLH, Sheehan JJ, Cotter PD. Nucleic acid-based approaches to investigate microbial-related cheese quality defects. Front Microbiol 2013; 4:1. [PMID: 23346082 PMCID: PMC3549567 DOI: 10.3389/fmicb.2013.00001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/02/2013] [Indexed: 01/14/2023] Open
Abstract
The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.
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Affiliation(s)
- Daniel J. O'Sullivan
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
- School of Food and Nutritional Sciences, University College CorkCork, Ireland
| | - Linda Giblin
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
| | | | | | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
- Alimentary Pharmabiotic Centre, University College CorkCork, Ireland
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18
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El-Hadedy D, Abu El-Nour S. Identification of Staphylococcus aureus and Escherichia coli isolated from Egyptian food by conventional and molecular methods. J Genet Eng Biotechnol 2012. [DOI: 10.1016/j.jgeb.2012.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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López-Campos G, Martínez-Suárez JV, Aguado-Urda M, López-Alonso V. Detection, Identification, and Analysis of Foodborne Pathogens. SPRINGERBRIEFS IN FOOD, HEALTH, AND NUTRITION 2012. [DOI: 10.1007/978-1-4614-3250-0_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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20
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Prevalence of toxicogenic bacteria in some foods and detection of Bacillus cereus and Staphylococcus aureus enterotoxin genes using multiplex PCR. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0293-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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21
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Jeyasekaran G, Raj KT, Shakila RJ, Thangarani AJ, Sukumar DR. Detection of Salmonella enterica serovars in shrimps in eight hours by multiplex PCR assay. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0250-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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22
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Kim HW, Kim JH, Rhim SR, Lee KA, Kim CJ, Paik HD. A Multiplex PCR Assay for the Detection of Food-borne Pathogens in Meat Products. Korean J Food Sci Anim Resour 2010. [DOI: 10.5851/kosfa.2010.30.4.590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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23
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Jeyasekaran G, Raj KT, Shakila RJ, Thangarani AJ, Sukumar D, Jailani VAK. Rapid detection of Salmonella enterica serovars by multiplex PCR. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0538-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Jadeja R, Janes ME, Simonson JG. Immunomagnetic separation of Vibrio vulnificus with antiflagellar monoclonal antibody. J Food Prot 2010; 73:1288-93. [PMID: 20615341 DOI: 10.4315/0362-028x-73.7.1288] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Raw oysters are primary vectors for Vibrio vulnificus infections, and a rapid detection method for V. vulnificus in raw oysters before distribution would be an indispensable tool for the seafood industry. One approach to improving the recovery and detection of V. vulnificus without sacrificing assay time is through the use of immunomagnetic separation (IMS). The aim of this study was to develop and optimize an IMS protocol using anti-H (antiflagellar) antibody for determining the level of V. vulnificus in phosphate-buffered saline (PBS) suspensions and spiked oyster homogenate. Six monoclonal antibodies were produced by immunizing mice at 2-week intervals by injection of 50 microg of purified V. vulnificus ATCC 27562 flagellin. Antibodies that exhibited high anti-H titers were coated onto Cowan I Staphylococcus aureus cells and sheep anti-mouse immunoglobulin G immunomagnetic beads. The two reagents were used to determine the species specificity of the selected antibodies, which positively identified and coagglutinated 70 isolates identified genetically as V. vulnificus and did not react with 40 Vibrio parahaemolyticus isolates or nine other Vibrio species. The IMS protocol was optimized for PBS and oyster homogenate spiked with three different strains of V. vulnificus. IMS with V. vulnificus-spiked PBS yielded binding of 19 to 57%, and IMS with spiked oyster homogenate carried out at two V. vulnificus levels exhibited binding of 25 to 57%. The IMS protocol for V. vulnificus could be used to concentrate and detect V. vulnificus in seawater and shellfish homogenate.
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Affiliation(s)
- R Jadeja
- Department of Food Science, Agricultural Center, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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25
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González A, Suski J, Ferrús MA. Rapid and accurate detection of Arcobacter contamination in commercial chicken products and wastewater samples by real-time polymerase chain reaction. Foodborne Pathog Dis 2010; 7:327-38. [PMID: 19899959 DOI: 10.1089/fpd.2009.0368] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An SYBR Green real-time polymerase chain reaction (PCR) assay was developed for Arcobacter detection in food and wastewater samples. The assay was applied to 36 chicken and 33 wastewater samples, and the results were compared with those obtained for conventional PCR, multiplex PCR, and culture isolation. Isolates were identified by multiplex PCR and restriction fragment length polymorphism analysis of PCR-amplified DNA fragment, and typed by randomly amplified polymorphic DNA. Arcobacter sp. was detected in 25 of the 26 chicken carcasses (96%) and in 4 of the 10 liver samples (40%) by real-time PCR. Twenty-five chicken samples were positive also by conventional PCR, but in most of them the detection was only possible after 48-h enrichment. Arcobacter butzleri was the most frequently detected species. Twenty-four Arcobacter isolates were obtained from chicken samples, where A. butzleri is the only identified species. All the wastewater samples (100%) were positive for Arcobacter sp. by real-time PCR without enrichment. A. butzleri and Arcobacter cryaerophilus were detected by multiplex PCR. Fifteen samples were found to be positive by culture. Thirty-six isolates were obtained; all of them were identified as A. butzleri by multiplex PCR. However, by PCR-restriction fragment length polymorphism, 34 were identified as A. butzleri, 1 as A. cryaerophilus, and another 1 as Arcobacter skirrowii. A great genetic heterogeneity was observed by randomly amplified polymorphic DNA-PCR profiling. The real-time PCR assay developed in this work showed better detection levels than conventional PCR, together with shorter times of testing samples. Therefore, it could be used as a rapid and accurate instrument for monitoring Arcobacter contamination levels in food and water samples.
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Affiliation(s)
- Ana González
- Department of Biotechnology, Polytechnic University of Valencia, Valencia, Spain
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26
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Martín M, Martínez N, del Rio B, Ladero V, Fernández M, Alvarez M. A novel real-time polymerase chain reaction-based method for the detection and quantification of lactose-fermenting Enterobacteriaceae in the dairy and other food industries. J Dairy Sci 2010; 93:860-7. [DOI: 10.3168/jds.2009-2481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Accepted: 11/25/2009] [Indexed: 11/19/2022]
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27
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FARAJNIA S, HASSAN M, HALLAJ NEZHADI S, MOHAMMADNEJAD L, MILANI M, LOTFIPOUR F. DETERMINATION OF INDICATOR BACTERIA IN PHARMACEUTICAL SAMPLES BY MULTIPLEX PCR. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1745-4581.2009.00154.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Jarquin R, Hanning I, Ahn S, Ricke SC. Development of rapid detection and genetic characterization of salmonella in poultry breeder feeds. SENSORS (BASEL, SWITZERLAND) 2009; 9:5308-23. [PMID: 22346699 PMCID: PMC3274138 DOI: 10.3390/s90705308] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 06/21/2009] [Accepted: 06/25/2009] [Indexed: 11/17/2022]
Abstract
Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered.
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Affiliation(s)
- Robin Jarquin
- Dept. of Poultry Science, University of Arkansas, Fayetteville, AR 72704, USA; E-Mail:
- Research and Development, Cobb-Vantress Incorporated, P.O. BOX 1030, Siloam Springs, AR 72761, USA
| | - Irene Hanning
- Dept. of Food Science, University of Arkansas, Fayetteville, AR 72704, USA; E-Mail:
| | - Soohyoun Ahn
- Food Science and Technology Program, Arkansas State University, State University, AR 72467, USA; E-Mail:
| | - Steven C. Ricke
- Dept. of Poultry Science, University of Arkansas, Fayetteville, AR 72704, USA; E-Mail:
- Dept. of Food Science, University of Arkansas, Fayetteville, AR 72704, USA; E-Mail:
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29
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Tomás D, Rodrigo A, Hernández M, Ferrús MA. Validation of Real-Time PCR and Enzyme-Linked Fluorescent Assay-Based Methods for Detection of Salmonella spp. in Chicken Feces Samples. FOOD ANAL METHOD 2009. [DOI: 10.1007/s12161-009-9082-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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ZHU DONGSHENG, ZHOU MIN, FAN YILING, SHI XIANMING. IDENTIFICATION OF NEW TARGET SEQUENCES FOR PCR DETECTION OFVIBRIO PARAHAEMOLYTICUSBY GENOME COMPARISON. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1745-4581.2009.00158.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Identification of Pseudomonas aeruginosa by a duplex real-time polymerase chain reaction assay targeting the ecfX and the gyrB genes. Diagn Microbiol Infect Dis 2008; 63:127-31. [PMID: 19026507 DOI: 10.1016/j.diagmicrobio.2008.09.018] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 09/23/2008] [Accepted: 09/30/2008] [Indexed: 11/20/2022]
Abstract
Phenotypic identification of Gram-negative bacteria from respiratory specimens of patients with cystic fibrosis carries a high risk of misidentification. Molecular identification techniques that use single-gene targets are also susceptible to error, including cross-reaction issues with other Gram-negative organisms. In this study, we have designed a Pseudomonas aeruginosa duplex real-time polymerase chain reaction (PCR) (PAduplex) assay targeting the ecfX and the gyrB genes. The PAduplex was evaluated against a panel of 91 clinical and environmental isolates that were presumptively identified as P. aeruginosa. The results were compared with those obtained using a commercial biochemical identification kit and several other P. aeruginosa PCR assays. The results showed that the PAduplex assay is highly suitable for routine identification of P. aeruginosa isolates from clinical or environmental samples. The 2-target format provides simultaneous confirmation of P. aeruginosa identity where both the ecfX and gyrB PCR reactions are positive and may also reduce the potential for false negatives caused by sequence variation in primer or probe targets.
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32
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Detection of indicator pathogens from pharmaceutical finished products and raw materials using multiplex PCR and comparison with conventional microbiological methods. J Ind Microbiol Biotechnol 2008; 35:1007-18. [DOI: 10.1007/s10295-008-0376-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 05/14/2008] [Indexed: 10/22/2022]
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Riyaz-Ul-Hassan S, Verma V, Qazi GN. Evaluation of three different molecular markers for the detection of Staphylococcus aureus by polymerase chain reaction. Food Microbiol 2008; 25:452-9. [PMID: 18355670 DOI: 10.1016/j.fm.2008.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 01/17/2008] [Accepted: 01/22/2008] [Indexed: 11/16/2022]
Abstract
The aim of this study was to target three genes of Staphylococcus aureus-fmhA (coding for a factor of unknown function), catalase and femA (coding for a factor essential for methicillin resistance) to establish and validate a PCR assay for the detection of this pathogen. Two pairs of primers were designed for fmhA and one pair each for catalase and femA genes. The PCR assays were standardized and found to give specific amplicons under similar reaction parameters. Target specificity of the primers was confirmed by DNA sequencing of the amplicons. While the initial inclusivity and exclusivity test reactions were in agreement in case of three of the primer pairs, one pair based on fmhA gene produced a non-specific product with a template DNA used in exclusivity test reactions. Forty-five strains of S. aureus were subjected to these PCR assays for their evaluation. Three among the four pairs of primers, one against each gene detected all the 45 strains precisely whereas one of the PCR assays using primers targeting the fmhA gene did not generate the specific amplicon with several of the strains. Seven unidentified strains of Gram-positive cocci subjected to these PCR assays produced negative results for each culture. Six of the strains were identified as Staphylococcus haemolyticus and one strain as Staphylococcus arlettae by 16S ribosomal gene analyses. All the three assay systems showed a detection limit of 100 cells per 20mul reaction assay. For validation of these assay systems, 80 coded samples of 11% skimmed milk spiked with different pathogens were received from NICED (National Institute of Cholera and Enteric Diseases), Kolkata and subjected to these PCR assays. All the three assays could detect S. aureus correctly in two of the samples. Amongst 150 raw milk samples, 36 (24%) were found positive for S. aureus. We conclude that fmhA, catalase and femA genes are conserved in S. aureus and, therefore, could be used as specific targets for its detection and identification by PCR. The protocols developed herein could be used for rapid and specific detection of this pathogen in food, clinical and environmental samples, especially milk.
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Affiliation(s)
- Syed Riyaz-Ul-Hassan
- Biotechnology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi 180001, India.
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34
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Bhagwat AA, Patel J, Chua T, Chan A, Cruz SR, Aguilar GAG. Detection of Salmonella species in foodstuffs. Methods Mol Biol 2008; 429:33-43. [PMID: 18695957 DOI: 10.1007/978-1-60327-040-3_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Conventional methods to detect Salmonella spp. in foodstuffs may take up to 1 wk. Methods for pathogen detection are required. Real-time detection of Salmonella spp. will broaden our ability to screen large number of samples in a short time. This chapter describes a step-by-step procedure using an oligonucleotide probe that becomes fluorescent upon hybridization to the target DNA (Molecular Beacon; MB) in a real-time polymerase chain reaction (PCR) assay. The capability of the assay to detect Salmonella species from artificially inoculated fresh- and fresh-cut produce as well as ready-to-eat meats is demonstrated. The method uses internal positive and negative controls which enable researchers to detect false-negative PCR results. The procedure uses the buffered peptone water for the enrichment of Salmonella spp. and successfully detects the pathogen at low level of contamination (2-4 cells/25 g) in <24 h.
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Affiliation(s)
- Arvind A Bhagwat
- Produce Quality and Safety Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, USA
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35
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Luan XY, Chen JX, Zhang XH, Jia JT, Sun FR, Li Y. Comparison of different primers for rapid detection of Vibrio parahaemolyticus using the polymerase chain reaction. Lett Appl Microbiol 2007; 44:242-7. [PMID: 17309499 DOI: 10.1111/j.1472-765x.2006.02074.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AIMS The aim of this study was to compare different primers for rapid and effective detection of Vibrio parahaemolyticus by polymerase chain reaction (PCR). METHODS AND RESULTS A total of four pairs of primers, three previously published and one based on a newly developed V. parahaemolyticus metalloprotease (vpm) gene, have been assayed for PCR detection of V. parahaemolyticus. They have been tested for specificity and sensitivity on a total of 101 strains including reference and environment isolates belonging to V. parahaemolyticus and other species in Vibrio. Of the four sets of primers tested, the one designed on the basis of the metalloprotease gene (675 bp) gave optimal results with bacterial strains examined as they only amplified the specific fragment in strains that had been genetically and biochemically assessed as V. parahaemolyticus and the limit of detection was 4 pg of purified target DNA. CONCLUSIONS The primers designed on the metalloprotease gene gave optimal results for specific, sensitive and rapid detection of V. parahaemolyticus by PCR. SIGNIFICANCE AND IMPACT OF THE STUDY PCR amplification with the optimal primer set VPM1/VPM2 could facilitate the rapid diagnosis and surveillance of potentially pathogenic strains of V. parahaemolyticus and reduce food-borne illness.
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Affiliation(s)
- X-Y Luan
- Department of Marine Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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36
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PARAMESWARAN SANGEETHA, GUYER ROBERTB, KNABEL STEPHENJ. SIMPLE oPSU BROTH-BAX® PCR-PICOGREEN® SYSTEM FOR RAPID DETECTION OFLISTERIA MONOCYTOGENESIN PASTEURIZED MILK AND HOT DOGS. J Food Saf 2007. [DOI: 10.1111/j.1745-4565.2003.tb00367.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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González A, Botella S, Montes RM, Moreno Y, Ferrús MA. Direct detection and identification of Arcobacter species by multiplex PCR in chicken and wastewater samples from Spain. J Food Prot 2007; 70:341-7. [PMID: 17340867 DOI: 10.4315/0362-028x-70.2.341] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Twenty-two chicken livers, 10 chicken carcasses, and 15 wastewater samples were processed and analyzed for Arcobacter by PCR and traditional culture methods. Samples were enriched for 24 and 48 h, incubated at 30 degrees C under aerobic conditions, and streaked on blood selective media. To determine the best isolation conditions, 20 samples also were processed under microaerophilic conditions at 37 degrees C. Simple and multiplex PCR assays were used directly with enrichment broths and isolated strains. Seventeen Arcobacter strains were isolated from chicken samples, and A. butzleri was the only Arcobacter species identified. The direct PCR assay revealed that 29 of the 32 chicken samples were contaminated with Arcobacter. A. butzleri was the most frequently detected species, although Arcobacter cryaerophilus also was present in some of the samples and Arcobacter skirrowii occasionally was detected. All the wastewater samples were positive by PCR assay for Arcobacter after 24 h of enrichment. A. butzleri and A. cryaerophilus were detected with the multiplex PCR assay. Fourteen Arcobacter strains were isolated from 10 of the 15 water samples analyzed; 7 were identified as A. butzleri and the remaining 7 were A. cryaerophilus. Both for chicken and water samples, Arcobacter detection rate for PCR amplification was higher than for culture isolation. These results indicate the high prevalence of Arcobacter in chicken and wastewater and the inadequacy of available cultural methods for its detection. The species-specific multiplex PCR assay is a rapid method for assessing Arcobacter contamination in chicken and wastewater samples and is a viable alternative to biochemical identification of isolated strains.
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Affiliation(s)
- A González
- Departamento de Biotecnología, Universidad Politècnica, Camino de Vera 14, 46022 Valencia, Spain
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38
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Amagliani G, Omiccioli E, Campo A, Bruce IJ, Brandi G, Magnani M. Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples. J Appl Microbiol 2006; 100:375-83. [PMID: 16430514 DOI: 10.1111/j.1365-2672.2005.02761.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AIMS A rapid and sensitive method for Listeria monocytogenes direct detection from milk was developed. It is based on a magnetic capture hybridization procedure for selective DNA purification, followed by PCR identification. A comparison with two similar commercial systems from Dynal (Dynabeads) was carried out. METHODS AND RESULTS The technique used previously developed nanoparticles modified with a 21-mer oligonucleotide. This sequence, sharing homology with all the L. monocytogenes strains, was selected on hlyA gene and located outside the desired specific PCR site to avoid cross-contaminations. Capture probe properties, in term of spacer length and purification, were determined to obtain the highest hybridization efficiency. Its specificity was tested in hybridization experiments with nontarget bacterial species. Any inhibitory effect of the nanoparticles on PCR was also examined. The amplification performed with the purified DNA could reliably identify a 10 CFU ml(-1) contamination rate. CONCLUSIONS The optimized purification method showed a high specificity and sensitivity, with a detection level one log more sensitive than PCR carried out with nucleic acids obtained using commercial nanoparticles. SIGNIFICANCE AND IMPACT OF THE STUDY The method, avoiding pre-enrichment, provides a rapid alternative to conventional microbiological detection methods. Furthermore, it is suitable for automation and can be proposed for the screening of a large number of samples.
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Affiliation(s)
- G Amagliani
- Centro di Biotecnologie, Università degli Studi di Urbino, Fano, Italy
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39
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Alarcón B, Vicedo B, Aznar R. PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food. J Appl Microbiol 2006; 100:352-64. [PMID: 16430512 DOI: 10.1111/j.1365-2672.2005.02768.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the specificity of nuc targeted primers for PCR detection of Staphylococcus aureus in different food matrices and to establish a RTQ-PCR procedure suitable for the routine detection and quantification of this pathogen in food. METHODS AND RESULTS Specificity of nuc targeted primers (Pri1-Pri2 and the newly designed RTQ-PCR primers) was tested on a total of 157 strains of genetically confirmed identity, including reference and food isolates. PCR detection on artificially inoculated beef samples by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) showed a sensitivity value around 10(3) CFU g(-1). The two RTQ-PCR systems, incorporating SYBR-Green I and TaqMan, respectively, applied in the present work improved the sensitivity of conventional PCR by lowering the detection level to 10 and 100 cells, respectively. Out of 164 naturally contaminated foods tested for the presence of Staph. aureus, 74 were positive by conventional PCR and 69 by the traditional culture method with a high degree of result agreement between both methodologies (93.3%). CONCLUSIONS PCR approaches, using nuc targeted primers, have proved specific and combined with growth techniques may improve detection of Staph. aureus in different types of food. SIGNIFICANCE AND IMPACT OF THE STUDY The SYBR-Green I real-time PCR approach established allows the sensitive, automated and quantitative detection of Staph. aureus for routine analysis at a reasonable cost.
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Affiliation(s)
- B Alarcón
- Departamento de Microbiología y Ecología, Universitat de València, Spain
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40
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RODRÍGUEZ-LÁZARO DAVID, HERNÁNDEZ MARTA, D'AGOSTINO MARTIN, COOK NIGEL. APPLICATION OF NUCLEIC ACID SEQUENCE-BASED AMPLIFICATION FOR THE DETECTION OF VIABLE FOODBORNE PATHOGENS: PROGRESS AND CHALLENGES. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1745-4581.2006.00048.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Espinoza-Medina IE, Rodríguez-Leyva FJ, Vargas-Arispuro I, Islas-Osuna MA, Acedo-Félix E, Martínez-Téllez MA. PCR identification of Salmonella: potential contamination sources from production and postharvest handling of cantaloupes. J Food Prot 2006; 69:1422-5. [PMID: 16786866 DOI: 10.4315/0362-028x-69.6.1422] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella is one of the most frequently reported etiological agents in outbreaks of foodborne diseases associated with the consumption of cantaloupes. Sensitive and reliable methods for detecting and identifying foodborne microorganisms are needed. The PCR can be used to amplify specific DNA fragments and thus to detect and identify pathogenic bacteria. In this study, a PCR method was used to evaluate the incidence of Salmonella at cantaloupe production, harvest, and packaging steps, and the results were compared with those of the standard method for detection of Salmonella in foods (Mexican NOM-114-SSA1-1994). Salmonella was detected by both standard and PCR methods in 23.5% of the irrigation water samples but only by the PCR method in 9.1% of the groundwater samples, 4.8% of the chlorinated water samples, 16.7% of samples from the hands of packing workers, 20.6% of samples from the packed cantaloupes, and 25.7% of samples from the in-field cantaloupes. With the standard method, Salmonella was found in 8.3% of the crop soil samples. Statistical analysis indicated a significant difference in sensitivity (P < 0.05) between the two methods; the PCR method was 4.3 times more sensitive than the standard method. Salmonella was found at seven of the eight pointsevaluated during the production and postharvest handling of cantaloupe melons.
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Affiliation(s)
- I E Espinoza-Medina
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., A.P. 1735, 83000 Hermosillo, Sonora, México
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42
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Herrera FC, Santos JA, Otero A, García-López ML. Occurrence of Plesiomonas shigelloides in displayed portions of saltwater fish determined by a PCR assay based on the hugA gene. Int J Food Microbiol 2006; 108:233-8. [PMID: 16481056 DOI: 10.1016/j.ijfoodmicro.2005.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 10/18/2005] [Accepted: 12/11/2005] [Indexed: 11/17/2022]
Abstract
PCR primers were designed and used to amplify a 435-bp fragment from the Plesiomonas shigelloides hugA gene. The PCR assay combined with a non-selective enrichment step proved to be a reliable procedure for P. shigelloides detection in fish meat. The incidence of this bacterium was investigated in 52 lots of pre-packed saltwater fish portions (conger, swordfish, sole, grouper, whiting and halibut) displayed at two hypermarkets by a conventional two-step procedure and the PCR assay. Using the former, P. shigelloides was isolated from three lots of grouper fillets and one lot of halibut fillets. When PCR was performed with non-selective enriched cultures of fish portions, amplification products were obtained from samples that were positive by the culturing method and from eight additional lots of grouper fillets that gave negative results with the conventional procedure. After a secondary enrichment in tetrathionate broth without iodine, all PCR-positive non-selective enrichments yielded P. shigelloides colonies. Overall, P. shigelloides was found in 23% of the examined lots of marine fish (11 of grouper and one of halibut).
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Affiliation(s)
- Fanny C Herrera
- Department of Food Hygiene and Food Technology, University of León, 24071-León, Spain
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43
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Heyndrickx M, Rijpens N, Herman L. Molecular Detection and Typing of Foodborne Bacterial Pathogens: A Review. Appl Microbiol 2005. [DOI: 10.1007/0-306-46888-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Pinto B, Chenoll E, Aznar R. Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques. Syst Appl Microbiol 2005; 28:340-52. [PMID: 15997707 DOI: 10.1016/j.syapm.2005.01.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The possibility of using PCR for rapid identification of food-borne Staphylococcus aureus isolates was evaluated as an alternative to the API-Staph system. A total of 158 strains, 15 S. aureus, 12 other staphylococcal species, and 131 isolates recovered from 164 food samples were studied. They were phenotypically characterized by API-Staph profiles and tested for PCR amplification with specific primers directed to thermonuclease (nuc) and enterotoxin (sea to see) genes. Disagreement between the PCR results and API-Staph identification was further assessed by the analysis of randomly amplified polymorphic DNA (RAPD) profiles obtained with three universal primers (M13, T3, and T7) and 16S rDNA sequencing. Forty out of 131 isolates (31%) tested positive for PCR enterotoxin. Of these, 14 (11%) were positive for sea, 22 (17%) for sec, one (0.8%) for sed, and three (2.2%) for sea and sec. No amplification corresponding to seb nor see was obtained. Cluster analysis based on RAPD profiles revealed that most of the sec positive food isolates grouped together in three clusters. Cluster analysis combining the three RAPD fingerprints (M 13, T3, and T7), PCR-enterotoxin genotype and API-Staph profiles, grouped the nuc PCR positive isolates together with S. aureus reference strains and the nuc PCR negative isolates with reference strains of other staphylococcal species. The only nuc PCR positive food isolate that remained unclustered was a sed positive strain identified by 16S rDNA sequence as S. simulans. The high concordance between S. aureus and nuc PCR positive strains (99%) corroborates the specificity of the primers used and the suitability of nuc PCR for rapid identification of S. aureus in routine food analysis.
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Affiliation(s)
- Beatriz Pinto
- Departamento de Microbiologta y Ecologia, Universitat de Valencia, Spain
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45
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Arvik T, Henick-Kling T, Gafner J. Automated genotyping of Saccharomyces cerevisiae using the RiboPrinter®. Int J Food Microbiol 2005; 104:35-41. [PMID: 16109451 DOI: 10.1016/j.ijfoodmicro.2004.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 12/20/2004] [Accepted: 12/22/2004] [Indexed: 10/25/2022]
Abstract
This research note addresses the development of an automated molecular typing system for yeast. Specifically, our objectives were to generate specific probes for genotyping yeast with an automated fingerprinting system. We have adapted the RiboPrinter microbial characterization system for use with Saccharomyces cerevisiae yeast using alternative probes based on specific multi-copy gene families. Manual construction and labeling of probes proved successful in initial experiments. Results indicate that this method could be applied to food or clinical environments if the appropriate probes are developed.
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Affiliation(s)
- Torey Arvik
- Cornell University/New York State Agricultural Experiment Station, Department of Food Science and Technology, Food Science Laboratory Building, Geneva, New York 14456, USA.
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46
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Naravaneni R, Jamil K. Rapid detection of food-borne pathogens by using molecular techniques. J Med Microbiol 2005; 54:51-54. [PMID: 15591255 DOI: 10.1099/jmm.0.45687-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Traditional methods of identification of food-borne pathogens, which cause disease in humans, are time-consuming and laborious, so there is a need for the development of innovative methods for the rapid identification of food-borne pathogens. Recent advances in molecular cloning and recombinant DNA techniques have revolutionized the detection of pathogens in foods. In this study the development of a PCR-based technique for the rapid identification of the food-borne pathogens Salmonella and Escherichia coli was undertaken. Suitable primers were designed based on specific gene fimA of Salmonella and gene afa of pathogenic E. coli for amplification. Agarose gel electrophoresis and subsequent staining with ethidium bromide were used for the identification of PCR products. The size of the amplified product was 120 bp as shown by comparison with marker DNA. These studies have established that fimA and afa primers were specific for detecting Salmonella and pathogenic E. coli, respectively, in the environmental samples. Thus a rapid, sensitive and reliable technique for the detection of Salmonella and pathogenic E. coli was developed.
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Affiliation(s)
- Rambabu Naravaneni
- Department of Genetics, Bhagwan Mahavir Hospital and Research Centre, Masab tank, Hyderabad, Andhra Pradesh, India-500 004
| | - Kaiser Jamil
- Department of Genetics, Bhagwan Mahavir Hospital and Research Centre, Masab tank, Hyderabad, Andhra Pradesh, India-500 004
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Fitzmaurice J, Duffy G, Kilbride B, Sheridan JJ, Carroll C, Maher M. Comparison of a membrane surface adhesion recovery method with an IMS method for use in a polymerase chain reaction method to detect Escherichia coli O157:H7 in minced beef. J Microbiol Methods 2004; 59:243-52. [PMID: 15369860 DOI: 10.1016/j.mimet.2004.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Revised: 07/12/2004] [Accepted: 07/13/2004] [Indexed: 11/26/2022]
Abstract
In this study, enrichment procedures and two recovery methods, a membrane surface adhesion technique and an immunomagnetic separation (IMS), were compared for use in conjunction with a multiplex polymerase chain reaction (PCR) method with a view to describing a fast (24 h) and economical test for detection of Escherichia coli O157:H7 in meat samples. The study showed no significant difference between three different enrichment media (BHI, E. coli (E.C.) broth+novobiocin, modified tryptone soya broth (mTSB)+novobiocin) or two incubation temperatures (37 or 41.5 degrees C) for growth of E. coli O157:H7 in minced beef. Minced beef samples inoculated with E. coli O157:H7 at 40 cfu g(-1) were incubated at 37 degrees C for 16 h in E.C. broth+novobiocin reaching numbers of (log(10)7.82-8.70). E. coli O157:H7 were recovered by attachment to polycarbonate membranes immersed in the enriched cultures for 15 min or by immunomagnetic separation. Subsequent treatment of recovered membranes or IMS beads with lysis buffer and phenol/chloroform/isoamyl alcohol was used to extract the DNA from the extracted E. coli O157:H7 cells. The results show when E. coli O157:H7 was present at high levels in the enriched meat sample (log(10)9.6-7.5 cfu ml(-1); >16-h enrichment), the membrane and IMS techniques recovered similar levels of the pathogen and the microorganism was detectable by PCR using both methods. At lower levels of E. coli O157:H7 (log(10)6.4), only the IMS method could recover the pathogen but at levels below this neither method could recover sufficient numbers of the pathogens to allow detection. The conclusion of the study is that with sufficient enrichment time (16 h) the membrane surface adhesion membrane extraction method used in combination with multiplex PCR has the potential for a rapid and economical detection method.
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Affiliation(s)
- J Fitzmaurice
- The National Diagnostics Centre, BioResearch Ireland, National University of Ireland, Galway, Ireland
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48
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Morin NJ, Gong Z, Li XF. Reverse Transcription-Multiplex PCR Assay for Simultaneous Detection of Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella Typhi. Clin Chem 2004; 50:2037-44. [PMID: 15364889 DOI: 10.1373/clinchem.2004.036814] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Background: Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella Typhi are pathogenic bacteria that can be found in contaminated water supplies throughout the world. No currently available assays can simultaneously detect and identify all three pathogens. Our aim was to develop a rapid and reliable technique for simultaneous detection of these pathogens.
Methods: Four unique genes were chosen as the targets of detection. Forward and reverse primers were designed to specifically amplify different sizes of these target genes: a 239-bp region of the E. coli O157 lipopolysaccharide (LPS) gene (rfbE); a 179-bp region of the H7 flagellin gene (fliC); a 419-bp region of the V. cholerae O1 LPS gene (rfbE); and a 329-bp region of Salmonella Typhi LPS gene (tyv). To ensure the detection of only viable replicating bacteria, RNA was extracted for analysis. After reverse transcription, cDNAs were simultaneously amplified in a single tube by multiplex PCR. The multiplex PCR products were analyzed by gel electrophoresis. To characterize the assay we analyzed, in a blinded fashion, seven unknown RNA samples containing various combinations of total RNA from these bacteria as well as clinical isolates.
Results: All seven unknown RNA samples were correctly identified. The assay was able to detect and identify as few as 30 cells of E. coli O157:H7 and Salmonella Typhi in clinical isolates, and the presence of other bacteria did not interfere with the analysis.
Conclusion: An assay combining reverse transcription with single-tube multiplex PCR was successfully developed and validated for simultaneous detection of viable E. coli O157:H7, V. cholerae O1, and Salmonella Typhi.
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Affiliation(s)
- Nicole J Morin
- Environmental Health Sciences, Department of Public Health Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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Garcı́a-Cañas V, González R, Cifuentes A. The combined use of molecular techniques and capillary electrophoresis in food analysis. Trends Analyt Chem 2004. [DOI: 10.1016/j.trac.2004.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Abstract
AIMS To investigate the usefulness of a straightforward filtration method for the isolation of Escherichia coli O157:H7 contaminants from milk for PCR detection. METHODS AND RESULTS Escherichia coli O157:H7 is grown in milk and enriched in Luria-Bertani (LB) medium. Samples are filtered through a 0.45-microm pore membrane. The membrane is immersed in 200-microl lysis buffer and incubated at 95 degrees C for 10 min to release bacterial DNA for subsequent PCR detection. Under current conditions, the overall duration from filtration to PCR-ready DNA generation is <20 min, and the detection level for PCR was as low as 10 CFU of bacteria in 1 ml of milk. CONCLUSION Bacterial contaminants of milk can be concentrated and isolated by a simple, one-step filtration and their DNA can be released for subsequent PCR detection by heating the filter membrane at 95 degrees C for 10 min. SIGNIFICANCE AND IMPACT OF THE STUDY The simplicity of this method allows inexpensive, high throughput automation that meets the demands of modern food hygiene monitoring.
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Affiliation(s)
- S-J Wu
- Department of Life Sciences, National Central University, Jung-da Road, Jhong-li City, Taiwan.
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