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Sajeer Paramabth M, Varma M. Demystifying PCR tests, challenges, alternatives, and future: A quick review focusing on COVID and fungal infections. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:719-728. [PMID: 37485773 DOI: 10.1002/bmb.21771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
The polymerase chain reaction (PCR) technique is one of the most potent tools in molecular biology. It is extensively used for various applications ranging from medical diagnostics to forensic science and food quality testing. This technique has facilitated to survive COVID-19 pandemic by identifying the virus-infected individuals effortlessly and effectively. This review explores the principles, recent advancements, challenges, and alternatives of PCR technique in the context of COVID-19 and fungal infections. The introduction of PCR technique for anyone new to this field is the primary aim of this review and thereby equips them to understand the science of COVID-19 and related fungal infections in a simplistic manner.
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Affiliation(s)
| | - Manoj Varma
- Center for Nano Science and Engineering (CeNSE), Indian Institute of Science, Bangalore, India
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2
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Ma JY, Wang XF, Peng C, Chen XY, Xu XL, Wei W, Yang L, Cai J, Xu JF. SMART: On-Site Rapid Detection of Nucleic Acid from Plants, Animals, and Microorganisms in under 25 Minutes. BIOSENSORS 2023; 13:82. [PMID: 36671917 PMCID: PMC9855345 DOI: 10.3390/bios13010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
The rapid on-site nucleic acid detection method is urgently required in many fields. In this study, we report a portable and highly integrated device for DNA detection that combines ultrafast DNA adsorption and rapid DNA amplification. The device, known as silicon film mediated recombinase polymerase amplification (RPA) for nucleic acid detection (SMART), can detect target DNA in less than 25 min from plants, animals, and microbes. Utilizing SMART, transgenic maize was rapidly detected with high selectivity and sensitivity. The sensitivity threshold of the SMART for transgenic maize genomic DNA was 50 copies. The detection results of genuine samples containing plants, animals, and microbes by SMART were consistent with the conventional polymerase chain reaction (PCR) method, demonstrating the high robustness of SMART. Additionally, SMART does not require expensive equipment and is fast, affordable, and user-friendly, making it suited for the broad-scale on-site detection of nucleic acids.
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Affiliation(s)
- Jun-Yuan Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- College of Biological and Food Engineering, Fuyang Normal University, Fuyang 236041, China
| | - Xiao-Fu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Xiao-Yun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Xiao-Li Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Cai
- College of Biological and Food Engineering, Fuyang Normal University, Fuyang 236041, China
| | - Jun-Feng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Hangzhou 310021, China
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Çelik A, Emiralioğlu O, Yeken MZ, Çiftçi V, Özer G, Kim Y, Baloch FS, Chung YS. A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris. Front Genet 2023; 14:1136794. [PMID: 37021006 PMCID: PMC10067576 DOI: 10.3389/fgene.2023.1136794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yoonha Kim
- Laboratory of Crop Production, Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Kumar P, Rani A, Singh S, Kumar A. Recent advances on
DNA
and omics‐based technology in Food testing and authentication: A review. J Food Saf 2022. [DOI: 10.1111/jfs.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pramod Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Alka Rani
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Shalini Singh
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Anuj Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
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Microbiological quality of tempeh with different wraps: banana leaf versus plastic. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:300-307. [PMID: 35068574 PMCID: PMC8758877 DOI: 10.1007/s13197-021-05014-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023]
Abstract
Tempeh is a traditional Indonesian fermented food widely consumed and became staple food in some Indonesian diet. Commercially, tempeh is available in banana leaf or plastic wraps. The wraps are not only important for fermentation and giving final form of tempeh, but also potential source of food microbiome. This study aimed to investigate the effect of different packaging materials on the lactic acid bacteria (LAB) quantity and community composition of tempeh from three manufacturers with different production environments. Each tempeh wrapped with banana leaf or plastic during the fermentation process and then LAB from every tempeh sample were quantified using qPCR and plate count method. Terminal Restriction Fragment Length Polymorphism analysis was carried out to assign bacterial community composition from these samples. The LAB population quantity of fresh tempeh from three manufacturers were essentially similar around 10 log CFU/g. However, there is a difference in the proportion of cultured and uncultured bacteria. Principal Coordinate Analyses based on Bray-Curtis similarity matrices showed an apparent clustering pattern for tempeh samples according to tempeh manufacturers. Meanwhile, packaging materials did not significantly influence changes in bacterial community composition. The result of this work could be used for determination, authentication, and improvement of tempeh quality.
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Simultaneous isolation and enumeration of virulent Vibrio cholerae and Vibrio vulnificus using an advanced MPN-PCR method. Arch Microbiol 2021; 204:5. [DOI: 10.1007/s00203-021-02613-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/28/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022]
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8
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Kokane AD, Lawrence K, Kokane SB, Gubyad MG, Misra P, Reddy MK, Ghosh DK. Development of a SYBR Green-based RT-qPCR assay for the detection of Indian citrus ringspot virus. 3 Biotech 2021; 11:359. [PMID: 34295604 DOI: 10.1007/s13205-021-02903-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022] Open
Abstract
The Indian citrus ringspot virus (ICRSV) that causes ringspot disease, especially to 'Kinnow mandarin' hampers the sustainability of crop production. Presently, the disease is not amenable for control through host resistance or the introduction of chemicals, hence raising virus-free plants is one of the most effective approaches to manage the disease. Consequently, it is necessary to develop rapid, sensitive, specific, and early diagnostic methods for disease control. In the present study, newly designed primers targeting a 164 bp region of the ICRSV coat protein gene were used to develop and optimize a SYBR Green-based quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay, for the detection of ICRSV. The RT-qPCR assay was evaluated and confirmed using viral RNA extracted from ICRSV infected plants maintained in screen house as well as field samples. The standard curves displayed a dynamic linear range across eight log units of ICRSV-cRNA copy number ranging from 9.48.1 fmol (5.709 × 109) to 0.000948 amol (5.709 × 102), with detection limit of 5.709 × 102 copies per reaction using serial tenfold diluted in vitro transcribed viral cRNA. The developed RT-qPCR is very specific to ICRSV does not react to other citrus pathogens, and approximately 100-fold more sensitive than conventional RT-PCR. Thus, this assay will be useful in laboratories, KVKs, and nurseries for the citrus budwood certification program as well as in plant quarantine stations. To our knowledge, this is the first study of the successful detection of ICRSV by RT-qPCR.
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Jin J, Duan L, Fu J, Chai F, Zhou Q, Wang Y, Shao X, Wang L, Yan M, Su X, Zhang Y, Pan J, Chen J. A real-time LAMP-based dual-sample microfluidic chip for rapid and simultaneous detection of multiple waterborne pathogenic bacteria from coastal waters. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2710-2721. [PMID: 34041513 DOI: 10.1039/d1ay00492a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Waterborne pathogens are becoming a serious worldwide health hazard; thus, the regular monitoring of epidemic pathogens is urgently required for public safety. In the present study, we developed a microfluidic chip integrated loop-mediated isothermal amplification technique (on-chip LAMP) to simultaneously detect 10 waterborne pathogenic bacteria, Campylobacter jejuni, Listeria monocytogenes, Salmonella enterica, Shigella flexneri, Staphylococcus aureus, Vibrio alginolyticus, V. cholerae, V. parahemolyticus, V. vulnificus, and Yersinia enterocolitica. This method was capable of simultaneously completing 22 genetic analyses of two specimens and achieved limits of detection ranging from 7.92 × 10-3 to 9.54 × 10-1 pg of genomic DNA of pure bacteria per reaction. The processes from sample loading to microfluidic operation were in a highly automated format, and the LAMP reaction ran to completion within 35 minutes, with a minimal volume of 22 μl per each half of a single chip. The coefficient of variation for the time-to-positive value was less than 0.1, indicating an excellent reproducibility of the dual-sample on-chip LAMP assay. The clinical sensitivity and specificity in analyses of coastal water samples were 93.1% and 98.0%, respectively, in comparison with traditional microbiological methods. Our established dual-sample on-chip LAMP assay provides an effective multiple-pathogen analysis of waterborne bacterial pathogens. This indicates that the method is applicable for on-site detection and routine monitoring of waterborne bacteria in aquatic environments.
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Affiliation(s)
- Jinglei Jin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Lijun Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Ningbo Haishu District Animal Husbandry and Veterinary Medicine Technical Management Service Station, Ningbo 315153, China
| | - Jiali Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Fangchao Chai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Qianjin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yaohua Wang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xinbin Shao
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Lei Wang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Maocang Yan
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Junhang Pan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, China
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Yadav N, Chhillar AK, Rana JS. Detection of pathogenic bacteria with special emphasis to biosensors integrated with AuNPs. SENSORS INTERNATIONAL 2020. [DOI: 10.1016/j.sintl.2020.100028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Farhoudi A, Ghajarbeygi P, Jozani RAJ, Mahmoudi R, Mardani K. Comparison of real‐time PCR and cultural method for detection of bacterial load in pasteurized milk. J Food Saf 2019. [DOI: 10.1111/jfs.12624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ayda Farhoudi
- School of Public HealthQazvin University of Medical Sciences Qazvin Iran
| | - Peyman Ghajarbeygi
- Health Products Safety Research CenterQazvin University of Medical Sciences Qazvin Iran
| | - Razi Allah Jafari Jozani
- Department of Clinical Sciences, Faculty of Veterinary MedicineUniversity of Tabriz Tabariz Iran
| | - Razzagh Mahmoudi
- Medical Microbiology Research CenterQazvin University of Medical Sciences Qazvin Iran
| | - Karim Mardani
- Department of Food Hygiene and Quality Control, Faculty of Veterinary MedicineUrmia University Urmia Iran
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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13
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Levin RE. Recent Developments in Molecular Detection of Food-Borne Disease Bacteria and GMOs. FOOD BIOTECHNOL 2015. [DOI: 10.1080/08905436.2014.996896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Law JWF, Ab Mutalib NS, Chan KG, Lee LH. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 2015; 5:770. [PMID: 25628612 PMCID: PMC4290631 DOI: 10.3389/fmicb.2014.00770] [Citation(s) in RCA: 504] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/17/2014] [Indexed: 12/11/2022] Open
Abstract
The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.
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Affiliation(s)
- Jodi Woan-Fei Law
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
- School of Science, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun RazakKuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
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15
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Real-Time PCR Quantification of Protease-Producing Bacteria in Traditional Chinese Fish Sauce. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9799-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Lin M, Jia R, Wang M, Gao X, Zhu D, Chen S, Yin Z, Wang Y, Chen X, Cheng A. The transcription analysis of duck enteritis virus UL49.5 gene using real-time quantitative reverse transcription PCR. Virus Genes 2013; 47:298-304. [PMID: 23836488 DOI: 10.1007/s11262-013-0949-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/26/2013] [Indexed: 12/25/2022]
Abstract
Duck enteritis virus (DEV) UL49.5 encoding glycoprotein N was a conserved gene. The transcription dynamic process of UL49.5 homologous genes in herpesviruses was reported. However, the transcription dynamic process of DEV UL49.5 gene has not yet been established. In this study, a real-time quantitative reverse transcription PCR (real-time qRT-PCR) assay was established to test the transcription dynamic process of DEV UL49.5 gene, and the recombinant plasmid pUCm-T/UL49.5 was constructed as the standard DNA. The samples prepared from DEV-infected (at different time points) and uninfected cell were detected and calculated. The results demonstrated that the real-time qRT-PCR assay was successfully established. The transcription product of DEV UL49.5 gene was first detected at 0.5 h post infection (p.i.), increased at 8 h p.i. and reached a peak at 60 h p.i. Our results illustrated that DEV UL49.5 gene could be regarded as a late gene. The transcription dynamic process of DEV UL49.5 gene may provide a significant clue for further studies of DEV UL49.5 gene.
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Affiliation(s)
- Meng Lin
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China,
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Sánchez A, Vázquez JA, Quinteiro J, Sotelo CG. Modeling real-time PCR kinetics: Richards reparametrized equation for quantitative estimation of European hake (Merluccius merluccius). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3488-3493. [PMID: 23484589 DOI: 10.1021/jf400136j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Real-time PCR is the most sensitive method for detection and precise quantification of specific DNA sequences, but it is not usually applied as a quantitative method in seafood. In general, benchmark techniques, mainly cycle threshold (Ct), are the routine method for quantitative estimations, but they are not the most precise approaches for a standard assay. In the present work, amplification data from European hake (Merluccius merluccius) DNA samples were accurately modeled by three sigmoid reparametrized equations, where the lag phase parameter (λc) from the Richards equation with four parameters was demonstrated to be the perfect substitute for Ct for PCR quantification. The concentrations of primers and probes were subsequently optimized by means of that selected kinetic parameter. Finally, the linear correlation among DNA concentration and λc was also confirmed.
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Affiliation(s)
- Ana Sánchez
- Grupo de Bioquı́mica de Alimentos, Instituto de Investigacións Mariñas (CSIC), Vigo, Spain.
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18
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Nakano M, Niwa M, Nishimura N. Specific and sensitive detection of Alcaligenes species from an agricultural environment. Microbiol Immunol 2013; 57:240-5. [PMID: 23489084 DOI: 10.1111/1348-0421.12026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/05/2012] [Accepted: 12/26/2012] [Indexed: 11/28/2022]
Abstract
A quantitative real-time PCR assay to specifically detect and quantify the genus Alcaligenes in samples from the agricultural environment, such as vegetables and farming soils, was developed. The minimum detection sensitivity was 106 fg of pure culture DNA, corresponding to DNA extracted from two cells of Alcaligenes faecalis. To evaluate the detection limit of A. faecalis, serially diluted genomic DNA from this organism was mixed with DNA extracted from soil and vegetables and then a standard curve was constructed. It was found that Alcaligenes species are present in the plant phytosphere at levels 10(2)-10(4) times lower than those in soil. The approach presented here will be useful for tracking or quantifying species of the genus Alcaligenes in the agricultural environment.
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Affiliation(s)
- Miyo Nakano
- Department of Translational Medical Science and Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
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19
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Ferrario C, Ricci G, Borgo F, Fortina MG. Species-specific DNA probe and development of a quantitative PCR assay for the detection of Morganella morganii. Lett Appl Microbiol 2012; 54:292-8. [PMID: 22251367 DOI: 10.1111/j.1472-765x.2012.03206.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To develop a SYBR Green quantitative PCR assay (qPCR) for the specific detection of Morganella morganii, a fish pathogen responsible for the Histamine Fish Poisoning. METHODS AND RESULTS A new primer set, amplifying a 179-bp fragment of the 16S rRNA gene, was selected for specificity, and 14 M. morganii strains and 32 non-Morganella strains were evaluated. The melting temperature of 84°C was consistently specific for the amplicon. Two standard curves were constructed: the minimum detection sensitivity was 0·563 pg of pure DNA, corresponding to DNA extracted from nine cells of M. morganii. The qPCR assay was evaluated in experiments with seeded fish samples, and the regression coefficient values were calculated. CONCLUSIONS A highly specific and rapid assay was developed for the detection of M. morganii in tuna fish samples. SIGNIFICANCE AND IMPACT OF THE STUDY This method represents the first study about the quantification of pathogenic M. morganii in fish products. This approach can be utilized to prevent the presence of this undesirable species in the food chain.
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Affiliation(s)
- C Ferrario
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli Studi di Milano, Milan, Italy
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20
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qPCR as a powerful tool for microbial food spoilage quantification: Significance for food quality. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Wu Y, Cheng A, Wang M, Zhang S, Zhu D, Jia R, Luo Q, Chen Z, Chen X. Establishment of real-time quantitative reverse transcription polymerase chain reaction assay for transcriptional analysis of duck enteritis virus UL55 gene. Virol J 2011; 8:266. [PMID: 21631934 PMCID: PMC3120788 DOI: 10.1186/1743-422x-8-266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/01/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Real-time quantitative reverse transcription polymerase chain reaction assay (qRT-PCR) has become the benchmark for detection and quantification of target gene expression level and been utilized increasingly in detection of viral load and therapy monitoring. The dynamic transcription variation of duck enteritis virus UL55 gene during the life cycle of duck enteritis virus in infected cells has not been reported yet. RESULTS The newly identified duck enteritis virus UL55 gene was amplified and cloned into pMD18-T vector after digestion to generate a recombinant plasmid pMD18-T/UL55 for the establishment of qRT-PCR as standard DNA. The results of agarose gel electrophoresis and melting curve analysis demonstrated the primers we designed for qRT-PCR were specific and available. We used β-actin as a reference gene for normalization and established two standard curves based on pMD18-T/UL55 and pMD18-T/β-actin successfully. Based on that, the transcriptional analysis of DEV UL55 gene was performed, and the result suggested the expression of UL55 mRNA was at a low level from 0 to 8 h post-infection(p.i.), then accumulated quickly since 12 h p.i. and peaked at 36 h p.i., it can be detected till 60 h p.i.. Nucleic acid inhibition test was carried out for analyzing a temporal regulation condition of DEV UL55 gene, result revealed that it was sensitive to ganciclovir. Synthesis procedures of DEV UL55 gene can be inhibited by ganciclovir. CONCLUSIONS The method we established in this paper can provide quantitative values reflecting the amounts of measured mRNA in samples. It's available for detection and quantification, also can be used in DEV diagnosis. The DEV UL55 gene was produced most abundantly during the late phase of replication in DEV-infected cells and the transcription of it depended on the synthesized DNA. DEV UL55 gene is a γ2 gene which occurs last and have a strict requirement for viral DNA synthesis.
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Affiliation(s)
- Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, China
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22
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Lee JL, Levin RE. Selective Detection of Mixed Bacterial Survivors from Fish Fillets after Freezing and Thawing by Ethidium Bromide Monoazide Real-Time PCR. FOOD BIOTECHNOL 2010. [DOI: 10.1080/08905436.2010.507154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Wang S, Levin RE. Interference of Real-Time PCR Quantification ofVibrio vulnificusby a Novel DNase from the Eastern Oyster (Crassostrea virginica). FOOD BIOTECHNOL 2010. [DOI: 10.1080/08905431003784721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Lee JL, Levin RE. Discrimination of viable and dead Vibrio vulnificus after refrigerated and frozen storage using EMA, sodium deoxycholate and real-time PCR. J Microbiol Methods 2009; 79:184-8. [DOI: 10.1016/j.mimet.2009.08.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 08/25/2009] [Indexed: 11/16/2022]
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25
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Abstract
Species of the Cronobacter genus ("Enterobacter sakazakii" s. l.) are emergent food-borne pathogens that can cause rare but severe neonatal meningitis, bacteriaemia, and necrotizing enterocolitis. Preterm, low-birth-weight, and immuno-compromised infants exposed to these bacterial species are at particular risk. Over the last 50 years, the literature has reported, mainly in newborn children, more than one hundred cases of infection due to these pathogens. The objective of this review was to synthesize the recent advances in knowledge of species of the Cronobacter genus, in particular with regards to taxonomy, physiology, pathogenicity, clinical cases, the methods for detection, isolation, and characterization, and their presence in powdered formulae for infants and young children, which were identified as the main infection vector. Researchers and international public health authorities have explored the ways contamination occur to better control the risks of pathogen development. Appropriate analysis and control measures were implemented in areas processing powdered formulae for infants and young children, and caregivers and families were informed to undertake good hygienic practices.
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Affiliation(s)
- Isabelle Proudy
- Service de microbiologie, Equipe d'accueil 2128, Centre hospitalier universitaire, Université de Caen Basse-Normandie, avenue Côte de Nacre, Caen CEDEX, France.
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26
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Lee JL, Levin RE. Detection ofVibrio vulnificusBefore and After γ-irradiation in Quahog Clam (Mercenaria mercenaria) Tissue Using Real-Time Polymerase Chain Reaction. FOOD BIOTECHNOL 2009. [DOI: 10.1080/08905430902875853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Lee JL, Levin R. Discrimination of γ-irradiated and nonirradiated Vibrio vulnificus by using real-time polymerase chain reaction. J Appl Microbiol 2008; 104:728-34. [DOI: 10.1111/j.1365-2672.2007.03589.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Gu W, Levin RE. Innovative Methods for Removal of PCR Inhibitors for Quantitative Detection ofPlesiomonas shigelloidesin Oysters by Real-Time PCR. FOOD BIOTECHNOL 2008. [DOI: 10.1080/08905430701866012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Lee JL, Levin RE. New approach for discrimination of Vibrio vulnificus by real-time PCR before and after gamma-irradiation. J Microbiol Methods 2008; 73:1-6. [PMID: 18262296 DOI: 10.1016/j.mimet.2007.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/15/2022]
Abstract
The effects of gamma-irradiation on the destruction of Vibrio vulnificus by real-time PCR were studied. gamma-irradiation was found to result in extensive reduction in the molecular size of DNA. Irradiation of viable cells (1 x 10(6) CFU/ml) at 1.08 KGy resulted in 100% destruction determined by plate counts, with most of the DNA from the irradiated cells having a bp-length of less than 1000. The use of a pair of primers to amplify a 1000-bp sequence of DNA from cells exposed to 1.08 KGy failed to yield amplification. In contrast, primers designed to amplify sequences of 700, 300, and 70-bp yielded amplification with C(t) values resulting in 13.4, 27.6, and 45.4% detection of genomic targets. When viable cells of V. vulnificus were exposed to 1.08, 3.0, and 5.0 kGy, the average molecular size of genomic DNA visualized in an agarose gel decreased with increasing dose, corresponding to an increased probability of amplification with primers targeting sequences of decreasing size.
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Affiliation(s)
- Jung-Lim Lee
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA 01003, USA
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30
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Levin RE. Campylobacter jejuni: A Review of its Characteristics, Pathogenicity, Ecology, Distribution, Subspecies Characterization and Molecular Methods of Detection. FOOD BIOTECHNOL 2007. [DOI: 10.1080/08905430701536565] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Li H, Lv X, Wang J, Li J, Yang H, Qin Y. Quantitative determination of soybean meal content in compound feeds: comparison of near-infrared spectroscopy and real-time PCR. Anal Bioanal Chem 2007; 389:2313-22. [PMID: 17901946 DOI: 10.1007/s00216-007-1624-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 09/09/2007] [Accepted: 09/11/2007] [Indexed: 10/22/2022]
Abstract
Standard methods for determining the raw material content of compound feed are little exploited, except for the identification of meat and bone meal in feeds. In this work, near-infrared (NIR) spectroscopy and real-time polymerase chain reaction (PCR) were applied in order to establish new and fast methods for quantification of soybean meal content in compound feeds. The best prediction quality was achieved by using a model based on NIR spectroscopy (R2 = 0.9857, standard error of cross-validation 1.1065). Furthermore, a sensitive qualitative detection method by using the real-time PCR was developed (R2 = 0.976, slope -3.7599). Finally, the differences between the real-time PCR result and the NIR spectroscopy result for a given sample were also treated, and we found that the NIR spectroscopy method provided quite accurate results which approach closely those of the real-time PCR method.
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Affiliation(s)
- Hui Li
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Zhongguanchun South Street 12, 100081, Beijing, China
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33
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Lee JL, Levin RE. Quantification of total viable bacteria on fish fillets by using ethidium bromide monoazide real-time polymerase chain reaction. Int J Food Microbiol 2007; 118:312-7. [PMID: 17727991 DOI: 10.1016/j.ijfoodmicro.2007.07.048] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2006] [Revised: 04/10/2007] [Indexed: 11/18/2022]
Abstract
Real-time PCR based on universal primers for amplification of a highly conserved bacterial 16S rDNA sequence was utilized in conjunction with the treatment of extracted bacterial cells with ethidium bromide monoazide (EMA) for the differential enumeration of viable and dead cells on cod fillets. Amplification of DNA from dead bacterial cells was successfully inhibited by EMA, whereas the DNA from viable cells was readily amplified. The detection range of the EMA real-time PCR assay was linear from 1 x 10(1) to 1 x 10(5) mixed bacterial genomic targets per PCR derived from broth cultures of fish tissue. The minimum detection limit of bacteria was found to be 1 x 10(1) genomic units/real-time PCR, equivalent to 1 x 10(5) CFU per gram of tissue. The EMA real-time PCR allowed construction of a standard curve obtained by plotting the log of genomic targets from strictly viable cells against resulting PCR cycles (Ct values) that facilitated quantification of total viable bacteria from fish fillets. The log of the total number of genomic DNA targets from EMA treated cells and plate counts from six randomly procured cod fillets were found not to be statistically different with the exception of one fillet. The process of freezing and thawing fillet tissue resulted in a drop in mean colony forming units (CFU) detected by plate counts from log 8.5+/-0.2 to log 8.1+/-0.1. A similar reduction in genomic targets from 8.5+/-0.1 to 8.0+/-0.16 was detected by EMA real-time PCR.
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Affiliation(s)
- Jung-Lim Lee
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA 01003, USA
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34
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Wang S, Levin RE. Thermal factors influencing detection of Vibrio vulnificus using real-time PCR. J Microbiol Methods 2007; 69:358-63. [PMID: 17383036 DOI: 10.1016/j.mimet.2007.02.003] [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: 12/07/2006] [Revised: 02/12/2007] [Accepted: 02/12/2007] [Indexed: 10/23/2022]
Abstract
Five thermal factors, including initial denaturation temperature, cycling denaturation temperature, annealing temperature, extension temperature and the temperature at which the intensity of the fluorescent signal is read, were evaluated for their effects on the detection of Vibrio vulnificus via real-time PCR. Fluorescent signal detection after extension was set between the Tm value of the primer-dimers (79 degrees C) and that of the PCR target amplicons (84 degrees C). This effectively eliminated the overestimation of the yield of PCR amplicons due to the presence of primer-dimers which otherwise led to erroneously lower Ct values (1.91+/-0.22 cycles lower). The annealing and extension steps were combined to convert a three-step PCR to a two-step PCR. This consisted of initial denaturation at 95 degrees C for 3 min, cycling denaturation at 94 degrees C for 15 s and a combined annealing and extension step at 60 degrees C for 5 s in each PCR cycle. One genomic target per real-time PCR reaction was detected with the simplified two-step PCR.
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Affiliation(s)
- Shishan Wang
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA 01003, USA
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35
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Helm CV, de Francisco A, Gaziola SA, Francisco Fornazier R, Bertoni Pompeu G, Antunes Azevedo R. Hull-less Barley Varieties: Storage Proteins and Amino Acid Distribution in Relation to Nutritional Quality. FOOD BIOTECHNOL 2007. [DOI: 10.1081/fbt-200040531] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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36
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37
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Abolmaaty A, Gu W, Witkowsky R, Levin RE. The use of activated charcoal for the removal of PCR inhibitors from oyster samples. J Microbiol Methods 2007; 68:349-52. [PMID: 17069910 DOI: 10.1016/j.mimet.2006.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 09/13/2006] [Accepted: 09/13/2006] [Indexed: 10/24/2022]
Abstract
Activated charcoal is a carbonaceous adsorbent with a high internal porosity, and hence a large internal surface area. Cells of a strain of Escherichia coli O157:H7 seeded into oyster tissue homogenates were completely bound to untreated charcoal after an incubation period of 15 min at room temperature. In contrast, activated charcoal particles coated with cells of Pseudomonas fluorescens resulted in 92.6%+/-3.7 recovery of E. coli O157:H7. This allowed the successful use of the coated activated charcoal for the absorption of PCR inhibitors from seeded tissue samples. With coated charcoal, real-time PCR was able to detect 1x10(3) CFU of E. coli 0157:H7/g of tissue which was equivalent to 50 genomic targets per real-time PCR. In contrast, without the use of treated charcoal, the real-time PCR failed to detect 10(7) CFU/g. This is a promising, and convenient technology that can be applied to increase the sensitivity of the PCR assay without selective enrichment, for the detection of low numbers of pathogenic microorganisms in complex matrices such as foods, clinical, and environmental samples, which frequently exhibit high levels of PCR inhibition.
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Affiliation(s)
- A Abolmaaty
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA 01003, USA
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38
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Wang S, Levin RE. Rapid quantification of Vibrio vulnificus in clams (Protochaca staminea) using real-time PCR. Food Microbiol 2006; 23:757-61. [PMID: 16943079 DOI: 10.1016/j.fm.2006.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 11/23/2005] [Accepted: 01/25/2006] [Indexed: 11/24/2022]
Abstract
We used a rapid DNA extraction and purification method to obtain the DNA from Vibrio vulnificus seeded into clam tissue homogenates for real-time PCR quantification of the organism. Without enrichment, the limit of detection was 1 x 10(2) cfu/g of tissue with a linear detection range of 1 x 10(2) to 1 x 10(8) cfu/g. With a 5 h non-selective enrichment, the limit of detection was 1 cfu/g of tissue with a linear detection range of 1 to 1 x 10(6) cfu/g of tissue. We found a 10-fold higher detection limit with seeded clam tissue homogenates compared to pure culture in TSB(+). The detection limits with pure broth culture and seeded tissue homogenates were identical, 1 cfu/ml and 1 cfu/ml, respectively, following 5 h non-selective enrichment. However, the Ct value with tissue homogenates was about 3 threshold cycles higher than with pure culture.
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Affiliation(s)
- Shishan Wang
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, 01003, USA
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39
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Gu W, Levin RE. Quantitative detection of Plesiomonas shigelloides in clam and oyster tissue by PCR. Int J Food Microbiol 2006; 111:81-6. [PMID: 16860899 DOI: 10.1016/j.ijfoodmicro.2006.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 02/22/2006] [Accepted: 05/14/2006] [Indexed: 11/25/2022]
Abstract
A quantitative assay for Plesiomonas shigelloides in clams and oysters based on the conventional polymerase chain reaction was developed. The assay involved the treatment of homogenized tissue samples with 4.0% formaldehyde that presumably denatured DNases and proteases present in the tissue which would otherwise inactivate the PCR reaction. The level of detection of P. shigelloides in clam tissue without enrichment was 200 CFU/g. The addition of 0.1% bovine serum albumin (BSA) to PCR reactions or the DNA purification system reduced the level of detection to 60 CFU/g. Formaldehyde had no effect on the level of detection with clam tissue. The level of detection of P. shigelloides in oyster tissue without enrichment was 6x10(5) CFU/g. The addition of 4.0% formaldehyde to oyster tissue homogenates reduced the level of detection to 6x10(2) CFU/g in contrast to the addition of 0.1% BSA to PCR reactions or the DNA purification system which reduced the level of detection to only 2x10(5) CFU/g. The combination of formaldehyde plus BSA, formaldehyde plus DNA purification, or formaldehyde plus BSA plus DNA purification all gave a detection level of 2x10(2) CFU/g of oyster tissue. With clam tissue, the linear range for detection of P. shigelloides was 60 to 2x10(4) CFU/g. With oyster tissue, the linear range for detection of P. shigelloides was 2x10(2) to 6x10(4 )CFU/g.
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Affiliation(s)
- Weimin Gu
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Peccia J, Hernandez M. Incorporating polymerase chain reaction-based identification, population characterization, and quantification of microorganisms into aerosol science: A review. ATMOSPHERIC ENVIRONMENT (OXFORD, ENGLAND : 1994) 2006; 40:3941-3961. [PMID: 32288550 PMCID: PMC7108281 DOI: 10.1016/j.atmosenv.2006.02.029] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 02/18/2006] [Accepted: 02/18/2006] [Indexed: 05/19/2023]
Abstract
The quantity, identity, and distribution of biomass in indoor and outdoor aerosols are poorly described. This is not consistent with the current understanding of atmospheric chemistry or the microbiological characterization of aquatic and terrestrial environments. This knowledge gap is due to both difficulties in applying contemporary microbiological techniques to the low biomass concentrations present in aerosols, and the traditional reliance of aerosol researchers on culture-based techniques-the quantitative limitations and ecological biases of which have been well-documented and are now avoided in other environmental matrices. This article reviews the emergence of the polymerase chain reaction (PCR) as a nonculture-based method to determine the identity, distribution, and abundance of airborne microorganisms. To encourage the use of PCR-based techniques by a broad spectrum of aerosol researchers, emphasis is given to the critical, aerosol specific method issues of sample processing, DNA extraction, and PCR inhibition removal. These methods are synthesized into a generalized procedure for the PCR-based study of microbial aerosols-equally applicable to both indoor and outdoor aerosol environments.
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Affiliation(s)
- Jordan Peccia
- Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, CT 06520, USA
- Corresponding author. Tel.: +1 203 432 4385; fax: +1 203 432 4387.
| | - Mark Hernandez
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado-Boulder, Boulder, CO 80309, USA
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Wang S, Levin RE. Discrimination of viable Vibrio vulnificus cells from dead cells in real-time PCR. J Microbiol Methods 2006; 64:1-8. [PMID: 15932774 DOI: 10.1016/j.mimet.2005.04.023] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 04/04/2005] [Accepted: 04/05/2005] [Indexed: 11/21/2022]
Abstract
Ethidium bromide monoazide (EMA) was utilized to selectively allow the real-time PCR (RT-PCR) amplification of a targeted DNA sequence in viable but not dead cells of Vibrio vulnificus. The optimized light exposure time to achieve cross-linking of DNA by the EMA in dead cells and to photolyse the free EMA in solution was at least 15 min. The use of 3.0 microg/ml or less of EMA did not inhibit the PCR amplification of DNA derived from viable cells of V. vulnificus. The minimum amount of EMA to completely inhibit the RT-PCR amplification of DNA derived from heat-killed cells was 2.5 microg/ml. Amplification of DNA from dead cells in a mixture with viable cells was successfully inhibited by 2.5 microg/ml of EMA, whereas the DNA from viable cells present was successfully amplified by RT-PCR.
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Affiliation(s)
- Shishan Wang
- Department of Food Science, Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA 01003, USA
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42
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Harwood VJ, Gandhi JP, Wright AC. Methods for isolation and confirmation of Vibrio vulnificus from oysters and environmental sources: a review. J Microbiol Methods 2004; 59:301-16. [PMID: 15488274 DOI: 10.1016/j.mimet.2004.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 06/29/2004] [Accepted: 08/06/2004] [Indexed: 12/17/2022]
Abstract
The gram-negative bacterium Vibrio vulnificus is a natural inhabitant of estuarine waters and poses a significant health threat to humans who suffer from immune disorders, liver disease, or hemochromatosis (iron overload). V. vulnificus enters human hosts via wound infections or consumption of raw shellfish (primarily oysters), and infections frequently progress to septicemia and death in susceptible individuals. Prevalence in waters and shellfish is not correlated with fecal indicator organisms; therefore, species-specific detection and enumeration of V. vulnificus in the environment has become a priority for agencies that are responsible for shellfish safety. The many selective-differential media developed for isolation of Vibrio spp., and specifically for V. vulnificus detection, are reviewed here; however, none of the media developed to date combines the sensitivity to low numbers with the specificity necessary to inhibit growth of other organisms. Therefore, immunological and molecular protocols are needed for confirmation of the identity of the organism and are discussed in detail. Methods under development that hold promise for rapid, accurate, and sensitive detection and enumeration of the organism include multiplex and real-time PCR. Developing technologies that have proven useful for detection and investigation of other pathogens such as biosensors, spectroscopy and microarrays may provide the next generation of tools for investigation of the prevalence and ecology of V. vulnificus.
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Affiliation(s)
- Valerie J Harwood
- Department of Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA.
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Current awareness in phytochemical analysis. PHYTOCHEMICAL ANALYSIS : PCA 2004; 15:331-338. [PMID: 15508839 DOI: 10.1002/pca.750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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