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Chen W, Zhang JW, Qin BX, Xie HT, Zhang Z, Qiao XZ, Li SK, Asif M, Guo S, Cui LX, Wang PP, Dong LH, Guo QG, Jiang WJ, Ma P, Xia ZY, Lu CH, Zhang LQ. Quantitative detection of the Ralstonia solanacearum species complex in soil by qPCR combined with a recombinant internal control strain. Microbiol Spectr 2023; 11:e0021023. [PMID: 37966217 PMCID: PMC10715031 DOI: 10.1128/spectrum.00210-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE DNA-based detection and quantification of soil-borne pathogens, such as the Ralstonia solanacearum species complex (RSSC), plays a vital role in risk assessment, but meanwhile, precise quantification is difficult due to the poor purity and yield of the soil DNA retrieved. The internal sample process control (ISPC) strain RsPC we developed solved this problem and significantly improved the accuracy of quantification of RSSC in different soils. ISPC-based quantitative PCR detection is a method especially suitable for the quantitative detection of microbes in complex matrices (such as soil and sludge) containing various PCR inhibitors and for those not easy to lyse (like Gram-positive bacteria, fungi, and thick-wall cells like resting spores). In addition, the use of ISPC strains removes additional workload on the preparation of high-quality template DNA and facilitates the development of high-throughput quantitative detection techniques for soil microbes.
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Affiliation(s)
- Wei Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Jun-Wei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Bi-Xia Qin
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Hui-Ting Xie
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Zhi Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Xiu-Ze Qiao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Shan-Kui Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Muhammad Asif
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Song Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Li-Xian Cui
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Pei-Pei Wang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Li-Hong Dong
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Qing-Gang Guo
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Wen-Jun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Li-Qun Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
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2
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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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4
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Oliveira M, Mason-Buck G, Ballard D, Branicki W, Amorim A. Biowarfare, bioterrorism and biocrime: A historical overview on microbial harmful applications. Forensic Sci Int 2020; 314:110366. [PMID: 32683271 PMCID: PMC7305902 DOI: 10.1016/j.forsciint.2020.110366] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022]
Abstract
Microbial Forensics is a field that continues to grow in interest and application among the forensic community. This review, divided into two sections, covers several topics associated with this new field. The first section presents a historic overview concerning the use of microorganisms (or its product, i.e. toxins) as harmful biological agents in the context of biological warfare (biowarfare), bioterrorism, and biocrime. Each case is illustrated with the examination of case reports that span from prehistory to the present day. The second part of the manuscript is devoted to the role of MF and highlights the necessity to prepare for the pressing threat of the harmful use of biological agents as weapons. Preventative actions, developments within the field to ensure a timely and effective response and are discussed herein.
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MESH Headings
- Bacterial Infections
- Biological Warfare/history
- Bioterrorism/history
- Crime/history
- Forensic Sciences
- HIV Infections
- High-Throughput Screening Assays
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Machine Learning
- Microbiological Techniques
- Toxins, Biological/adverse effects
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
| | | | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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5
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Hennechart-Collette C, Dehan O, Fraisse A, Martin-Latil S, Perelle S. Evaluation of three different filters and two methods for recovering viruses from drinking water. J Virol Methods 2020; 284:113939. [PMID: 32673640 DOI: 10.1016/j.jviromet.2020.113939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 01/13/2023]
Abstract
Among the enteric viruses implicated in waterborne outbreaks, human norovirus and hepatitis A virus (HAV) are a serious public health issue. Most foodborne viruses are difficult or currently unlikely to cultivate. Because of the lack of a cell culture method, real-time reverse transcriptase PCR is commonly used for the detection of norovirus in foodstuffs and environmental samples. Due to low infectious doses in humans and low virus concentration in water sample, filter adsorption methods were used for concentrating viruses from water. The ISO (Anonymous, ISO 15216-1, 2017) describes standardized molecular methods for detecting HAV and norovirus in bottled water. This method includes a two-step procedure: concentrating the virus using a microporous electropositive filter (47 mm diameter, 0.45 μm pore size) then molecular detection. The Zetapor filter, which had a charged membrane with a pore size of 0.45 μm, was commonly used in the past to concentrate viruses from water or from salad leaves following virus elution. But, unfortunately, the Zetapor filter is no longer marketed and it is therefore necessary to assess an alternative filter. The aim of this study was to compare the ability of two electropositive filters with a pore size of 0.45 μm or 0.22 μm and one uncharged filter (0.45 μm) to recover norovirus and HAV from two different types of drinking water (bottled water and tap water) with the adsorption-elution method proposed by ISO (Anonymous, ISO 15216-1, 2017) (method A) and with direct viral extraction using filters (method B). The mean extraction yields for norovirus and HAV calculated with RNA extracts ranged from 0.2 % - 4.81 % with method A and from 5.05 % - 53.58 % with method B, and did not differ significantly between the two types of drinking water tested. For method B, the mean extraction yields for HAV and norovirus were evaluated according to results from the three filters used. The recovery rate of HAV and norovirus ranged between 3.47 % and 62.41 % with the 0.45 μm electropositive filter and were higher than the other filters. The 0.45 μm electropositive filter could be used to concentrate viruses for routine viral monitoring of drinking water for researchers who want to adopt the method in their lab routine.
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Affiliation(s)
| | - Océane Dehan
- Université Paris-Est, ANSES, Laboratory for Food Safety, F-94700 Maisons-Alfort, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Laboratory for Food Safety, F-94700 Maisons-Alfort, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Laboratory for Food Safety, F-94700 Maisons-Alfort, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Laboratory for Food Safety, F-94700 Maisons-Alfort, France.
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6
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Sánchez G, Sánchez G. Food and Viral Contamination: Analytical Methods. Food Saf (Tokyo) 2016. [DOI: 10.1002/9781119160588.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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7
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Mikel P, Vasickova P, Tesarik R, Malenovska H, Kulich P, Vesely T, Kralik P. Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices. Front Microbiol 2016; 7:1911. [PMID: 28133456 PMCID: PMC5234545 DOI: 10.3389/fmicb.2016.01911] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/15/2016] [Indexed: 01/26/2023] Open
Abstract
The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices.
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Affiliation(s)
- Pavel Mikel
- Veterinary Research Institute, Department of Food and Feed SafetyBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petra Vasickova
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Radek Tesarik
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Hana Malenovska
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Pavel Kulich
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Tomas Vesely
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Petr Kralik
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
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8
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Cormier J, Janes M. Concentration and detection of hepatitis A virus and its indicator from artificial seawater using zeolite. J Virol Methods 2016; 235:1-8. [PMID: 27150045 DOI: 10.1016/j.jviromet.2016.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/29/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
Abstract
Hepatitis A virus (HAV) infection is the leading worldwide cause of acute viral hepatitis, and outbreaks caused by this virus often occur in fecal polluted waters. Rapid concentration and detection of viral contamination in water environments can prevent economic loss and can identify the source of contamination within a short time. However, conventional methods for virus concentration are often laborious, time consuming, and subject to clogging. Furthermore, most methods require a secondary concentration step to reduce the final volume of samples. We developed a method to concentrate HAV from seawater using zeolite in aid of rapid detection. In this method,artificial seawater was inoculated with HAV (7-8 log TCID50) and filtered with zeolite. The viruses were then eluted from zeolite with sodium dodecyl sulfate and detected via real-time PCR (qPCR). Zeolite was able to concentrate HAV from artificial seawater with ∼99% efficiency in less than 5min and was more efficient in seawater than in fresh water. The entire concentration and detection can be done in approximately 2h. Compared to existing methods, this method eliminated the need for a secondary concentration step as well as the necessity to modify the pH or salinity of the seawater during concentration, and was simple and inexpensive.
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Affiliation(s)
- Jiemin Cormier
- Department of Food Science, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Marlene Janes
- Department of Food Science, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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9
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Diduch M, Polkowska Ż, Namieśnik J. The role of heterotrophic plate count bacteria in bottled water quality assessment. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Suzuki Y, Kobayashi T, Nishiyama M, Kono T. Concentration of MS2 phage in river water by a combined ferric colloid adsorption and foam separation-based method, with MS2 phage leaching from ferric colloid. J Biosci Bioeng 2016; 122:252-6. [PMID: 26868517 DOI: 10.1016/j.jbiosc.2016.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 01/17/2023]
Abstract
The concentration of MS2 phage as a model RNA virus in river water using a combined ferric colloid adsorption and foam separation-based method was examined. The MS2 phage concentrations were determined by the plaque-forming unit (PFU) method and reverse transcription quantitative PCR (RT-qPCR) analysis. When ferric colloid adsorption was performed prior to foam separation, MS2 phage was effectively removed from river water and concentrated in the generated foam within 7 min. The removal efficiency was >99% at the optimum iron and casein concentrations of 5 mg-Fe/L and 10 mg/L, respectively. Furthermore, based on the analysis of the collected ferric colloid dissolved using deferoxamine, the MS2 concentration in the colloid-dissolved solution was 190-fold higher than that found in raw water according to RT-qPCR analysis. This is a novel method for concentrating RNA viruses to facilitate their detection in river water using coagulation and foam separation combined with chelate dissolution of ferric flocs.
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Affiliation(s)
- Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan.
| | - Takumi Kobayashi
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Masateru Nishiyama
- Department of Environment and Resource Science, Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki 889-2192, Japan
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11
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Mikel P, Vasickova P, Kralik P. Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:96-111. [PMID: 25711389 PMCID: PMC7090958 DOI: 10.1007/s12560-015-9188-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review.
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Affiliation(s)
- P Mikel
- Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic,
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Vecchia AD, Rigotto C, Soliman MC, Souza FGD, Giehl IC, Spilki FR. Recovery rate of multiple enteric viruses artificially seeded in water and concentrated by adsorption-elution with negatively charged membranes: interaction and interference between different virus species. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 72:2291-2300. [PMID: 26676018 DOI: 10.2166/wst.2015.458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Viral concentration method by adsorption-elution with negative membranes has been widely employed for concentrating viruses from environmental samples. In order to provide an adequate assessment of its recovery efficiency, this study was conducted to assess viral recovery rates for viral species commonly found in water (HAdV-5, EV, RV, BAdV and CAV-2), quantifying viral genomes at the end of the five different steps of the process. Recovery rates were analyzed for several viruses combined in a single water sample and for each virus assayed separately. Ultrapure water samples were artificially contaminated and analyzed by real-time quantitative polymerase chain reaction (qPCR). High recovery rates were found after the final stage when assessed individually (89 to 125%) and combined in the same sample (23 to > 164%). HAdV-5 exhibited >100% recovery when assayed with human viruses and other AdVs, whereas BAdV and CAV-2 were not detected. These data suggest that recovery efficiency could be related to viral structural characteristics, their electric charges and other interactions, so that they are retained with greater or lesser efficiency when coupled. This protocol could be applied to environmental samples, since high recovery rates were observed and infectious viruses were detected at the end of the concentration process.
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Affiliation(s)
- Andréia Dalla Vecchia
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Caroline Rigotto
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Mayra Cristina Soliman
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Fernanda Gil de Souza
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Isabel Cristina Giehl
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, CEP 93352-000, Novo Hamburgo, RS, Brasil E-mail:
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van Alphen LB, Dorléans F, Schultz AC, Fonager J, Ethelberg S, Dalgaard C, Adelhardt M, Engberg JH, Fischer TK, Lassen SG. The application of new molecular methods in the investigation of a waterborne outbreak of norovirus in Denmark, 2012. PLoS One 2014; 9:e105053. [PMID: 25222495 PMCID: PMC4164364 DOI: 10.1371/journal.pone.0105053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/19/2014] [Indexed: 01/15/2023] Open
Abstract
In December 2012, an outbreak of acute gastrointestinal illness occurred in a geographical distinct area in Denmark covering 368 households. A combined microbiological, epidemiological and environmental investigation was initiated to understand the outbreak magnitude, pathogen(s) and vehicle in order to control the outbreak. Norovirus GII.4 New Orleans 2009 variant was detected in 15 of 17 individual stool samples from 14 households. Norovirus genomic material from water samples was detected and quantified and sequencing of longer parts of the viral capsid region (>1000 nt) were applied to patient and water samples. All five purposely selected water samples tested positive for norovirus GII in levels up to 1.8×104 genomic units per 200 ml. Identical norovirus sequences were found in all 5 sequenced stool samples and 1 sequenced water sample, a second sequenced water sample showed 1 nt (<0.1%) difference. In a cohort study, including 256 participants, cases were defined as residents of the area experiencing diarrhoea or vomiting onset on 12–14 December 2012. We found an attack rate of 51%. Being a case was associated with drinking tap-water on 12–13 December (relative risk = 6.0, 95%CI: 1.6–22) and a dose-response relation for the mean glasses of tap-water consumed was observed. Environmental investigations suggested contamination from a sewage pipe to the drinking water due to fall in pressure during water supply system renovations. The combined microbiological, epidemiological and environmental investigations strongly indicates the outbreak was caused by norovirus contamination of the water supply system.
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Affiliation(s)
- Lieke B. van Alphen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- European Programme of Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- * E-mail:
| | - Frédérique Dorléans
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anna Charlotte Schultz
- National Food Institute, Division of Food Microbiology, Danish Technical University (DTU), Lyngby, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - Camilla Dalgaard
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Marianne Adelhardt
- Danish Health and Medicines Authority, Public Health Medical Officers East, Denmark
| | | | - Thea Kølsen Fischer
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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14
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Rapid Methods for Quality Assurance of Foods: the Next Decade with Polymerase Chain Reaction (PCR)-Based Food Monitoring. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9915-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Pérez-Méndez A, Chandler JC, Bisha B, Goodridge LD. Concentration of enteric viruses from tap water using an anion exchange resin-based method. J Virol Methods 2014; 206:95-8. [PMID: 24911889 DOI: 10.1016/j.jviromet.2014.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/27/2014] [Accepted: 05/29/2014] [Indexed: 11/29/2022]
Abstract
Detecting low concentrations of enteric viruses in water is needed for public health-related monitoring and control purposes. Thus, there is a need for sensitive, rapid and cost effective enteric viral concentration methods compatible with downstream molecular detection. Here, a virus concentration method based on adsorption of the virus to an anion exchange resin and direct isolation of nucleic acids is presented. Ten liter samples of tap water spiked with different concentrations (10-10,000 TCID50/10 L) of human adenovirus 40 (HAdV-40), hepatitis A virus (HAV) or rotavirus (RV) were concentrated and detected by real time PCR or real time RT-PCR. This method improved viral detection compared to direct testing of spiked water samples where the ΔCt was 12.1 for AdV-40 and 4.3 for HAV. Direct detection of RV in water was only possible for one of the three replicates tested (Ct of 37), but RV detection was improved using the resin method (all replicates tested positive with an average Ct of 30, n=3). The limit of detection of the method was 10 TCID50/10 L for HAdV-40 and HAV, and 100 TCID50/10 L of water for RV. These results compare favorably with detection limits reported for more expensive and laborious methods.
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Affiliation(s)
- A Pérez-Méndez
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
| | - J C Chandler
- Department of Animal Science, University of Wyoming, Laramie, WY, USA.
| | - B Bisha
- Department of Animal Science, University of Wyoming, Laramie, WY, USA.
| | - L D Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Ste. Anne de Bellevue, Quebec, Canada.
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16
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Butot S, Zuber S, Baert L. Sample preparation prior to molecular amplification: complexities and opportunities. Curr Opin Virol 2014; 4:66-70. [PMID: 24441295 DOI: 10.1016/j.coviro.2013.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/02/2013] [Accepted: 12/12/2013] [Indexed: 02/01/2023]
Abstract
Molecular amplification using Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) is currently considered as the gold standard to detect enteric human pathogenic viruses such as norovirus and hepatitis A virus in food and water. However, the molecular-based detection requires an adequate sampling strategy and a sample preparation specific for viruses. Sampling for enteric human viruses in water and food should not necessarily follow bacterial sampling plans. The development of a reference detection method including sample preparation as proposed in ISO/TS 15216 represents a milestone to facilitate the evaluation of the performance and eventually validation of future virus detection methods. The potential viral infectivity linked to a positive PCR result is a remaining issue and pretreatments allowing the differentiation of infectious viruses would be useful for future risk assessments.
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Affiliation(s)
- Sophie Butot
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland.
| | - Sophie Zuber
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland
| | - Leen Baert
- Food Safety and Quality Competence Pillar, Nestlé Research Centre, Vers-chez-les-Blanc, Box 44, 1000 Lausanne 26, Switzerland
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17
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Coudray-Meunier C, Fraisse A, Martin-Latil S, Guillier L, Perelle S. Discrimination of infectious hepatitis A virus and rotavirus by combining dyes and surfactants with RT-qPCR. BMC Microbiol 2013; 13:216. [PMID: 24083486 PMCID: PMC3853579 DOI: 10.1186/1471-2180-13-216] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human enteric viruses are major agents of foodborne diseases. Because of the absence of a reliable cell culture method for most of the enteric viruses involved in outbreaks, real-time reverse transcriptase PCR is now widely used for the detection of RNA viruses in food samples. However this approach detects viral nucleic acids of both infectious and non infectious viruses, which limits the impact of conclusions with regard to public health concern. The aim of the study was to develop a method to discriminate between infectious and non-infectious particles of hepatitis A virus (HAV) and two strains of rotavirus (RV) following thermal inactivation by using intercalating dyes combined with RT-qPCR. RESULTS Once the binding of propidium monoazide (PMA) or ethidium monoazide (EMA) was shown to be effective on the viral ssRNA of HAV and dsRNA of two strains of RV (SA11 and Wa), their use in conjunction with three surfactants (IGEPAL CA-630, Tween 20, Triton X-100) prior to RT-qPCR assays was evaluated to quantify the infectious particles remaining following heat treatment. The most promising conditions were EMA (20 μM) and IGEPAL CA-630 (0.5%) for HAV, EMA (20 μM) for RV (WA) and PMA (50 μM) for RV (SA11). The effectiveness of the pre-treatment RT-qPCR developed for each virus was evaluated with three RT-qPCR assays (A, B, C) during thermal inactivation kinetics (at 37°C, 68 C, 72°C, 80°C) through comparison with data obtained by RT-qPCR and by infectious titration in cell culture. At 37°C, the quantity of virus (RV, HAV) remained constant regardless of the method used. The genomic titers following heat treatment at 68°C to 80°C became similar to the infectious titers only when a pre-treatment RT-qPCR was used. Moreover, the most effective decrease was obtained by RT-qPCR assay A or B for HAV and RT-qPCR assay B or C for RV. CONCLUSIONS We concluded that effectiveness of the pre-treatment RT-qPCR is influenced by the viral target and by the choice of the RT-qPCR assay. Currently, it would be appropriate to further develop this approach under specific conditions of inactivation for the identification of infectious viruses in food and environmental samples.
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Affiliation(s)
- Coralie Coudray-Meunier
- ANSES, Food Safety Laboratory, Food and Water Virology Unit, 23 Avenue du Général de Gaulle, 94706 Maisons-Alfort cedex, France
| | - Audrey Fraisse
- ANSES, Food Safety Laboratory, Food and Water Virology Unit, 23 Avenue du Général de Gaulle, 94706 Maisons-Alfort cedex, France
| | - Sandra Martin-Latil
- ANSES, Food Safety Laboratory, Food and Water Virology Unit, 23 Avenue du Général de Gaulle, 94706 Maisons-Alfort cedex, France
| | - Laurent Guillier
- ANSES, Food Safety Laboratory, Modelling of Bacterial Behaviour Unit, 23 Avenue du Général de Gaulle, 94706 Maisons-Alfort cedex, France
| | - Sylvie Perelle
- ANSES, Food Safety Laboratory, Food and Water Virology Unit, 23 Avenue du Général de Gaulle, 94706 Maisons-Alfort cedex, France
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18
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Martin-Latil S, Hennechart-Collette C, Guillier L, Perelle S. Comparison of two extraction methods for the detection of hepatitis A virus in semi-dried tomatoes and murine norovirus as a process control by duplex RT-qPCR. Food Microbiol 2012; 31:246-53. [DOI: 10.1016/j.fm.2012.03.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 02/06/2012] [Accepted: 03/12/2012] [Indexed: 11/17/2022]
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19
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Recovery comparison of two virus concentration methods from wastewater using cell culture and real-time PCR. Curr Microbiol 2012; 65:432-7. [PMID: 22767318 DOI: 10.1007/s00284-012-0174-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
Enteric viruses are shed in the feces and may be present in environmental waters. Their detection in wastewater, even at low concentration, is a major challenge. In this study, recoveries of Echovirus 7 (EV7), virions and RNA in wastewater, using virus concentration methods were determined to evaluate the detection of infectious viruses and the possibility of recovering viral genomes. Two virus concentration methods, PEG precipitation method and two-phase separation method, were applied to recovery experiments of EV7-virions from wastewater, in parallel with recovery experiments of EV7 RNA. The titration of EV7 virions was carried out by cell culture using human rhabdomyosarcoma tumor tissue and the EV7 RNA quantification was performed by real-time PCR. The mean recovery yields of EV7 virions using the PEG precipitation method and the two-phase separation method were 78.5 ± 10.99 and 83.1 ± 0.28 %, respectively. Besides, EV7 RNA recoveries obtained using the PEG precipitation method were four times higher than those using the two-phase separation method. According to our results, the two methods enable to concentrate both infectious viruses and viral genomes. Moreover, considering the protocol time and cost together with the ratio of the EV7 virion recovery to the EV7 RNA recovery, the two-phase separation method (83.1/2.71 %, or 30.6) seems to be more appropriate for selective concentration of viral virions than the PEG precipitation method (78.5/10.33 %, or 7.6).
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20
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Butot S, Putallaz T, Sánchez G. Improvement of Procedure for HAV Detection in Bottled Water. FOOD ANAL METHOD 2012. [DOI: 10.1007/s12161-012-9437-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Bedford NM, Pelaez M, Han C, Dionysiou DD, Steckl AJ. Photocatalytic cellulosic electrospun fibers for the degradation of potent cyanobacteria toxin microcystin-LR. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31597a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Cho MG, Jeong HM, Ahn JB, Kim KY. Detection of feline calicivirus as norovirus surrogate in food and water sources using filtration and real-time RT-PCR. Food Sci Biotechnol 2011. [DOI: 10.1007/s10068-011-0204-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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23
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Fallahi S, Mattison K. Evaluation of murine norovirus persistence in environments relevant to food production and processing. J Food Prot 2011; 74:1847-51. [PMID: 22054184 DOI: 10.4315/0362-028x.jfp-11-081] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human norovirus (NoV) causes outbreaks of acute gastroenteritis associated with many ready-to-eat foods, including fresh produce. Effective inactivation procedures must consider virus survival under conditions of produce production and processing. This study aimed to investigate the persistence of NoV in a variety of environments, using murine NoV (MNV) as a surrogate for NoV. MNV was incubated for up to 42 days at room temperature on stainless steel disks, on lettuce, on soil, and in potable water and titers determined by plaque assay. A 1-log reduction of MNV infectivity was observed after 29 days in water, 4 days on lettuce, 12 days on soil, and 15 days on stainless steel disks. MNV survived longer in water than in any of the other environments, indicating that drying may contribute to NoV inactivation. MNV genomes were not significantly reduced for up to 42 days, suggesting that genomic detection is not a reliable indicator of viability. Overall, our findings provide valuable information regarding the potential for NoV transmission in the food supply.
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Affiliation(s)
- S Fallahi
- Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Sir F. G. Banting Research Centre, Ottawa, Ontario, Canada K1A 0K9
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24
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Cloning and Characterisation of a Δ-prfA Listeria monocytogenes Strain Containing an Artificial Single Copy Genomic Internal Amplification Control (IAC) for Use as Internal Sample Process Control (ISPC). FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9212-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Schultz AC, Perelle S, Di Pasquale S, Kovac K, De Medici D, Fach P, Sommer HM, Hoorfar J. Collaborative validation of a rapid method for efficient virus concentration in bottled water. Int J Food Microbiol 2011; 145 Suppl 1:S158-66. [DOI: 10.1016/j.ijfoodmicro.2010.07.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 06/05/2010] [Accepted: 07/24/2010] [Indexed: 11/15/2022]
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26
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Knutsson R, van Rotterdam B, Fach P, De Medici D, Fricker M, Löfström C, Ågren J, Segerman B, Andersson G, Wielinga P, Fenicia L, Skiby J, Schultz AC, Ehling-Schulz M. Accidental and deliberate microbiological contamination in the feed and food chains — How biotraceability may improve the response to bioterrorism. Int J Food Microbiol 2011; 145 Suppl 1:S123-8. [DOI: 10.1016/j.ijfoodmicro.2010.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 09/27/2010] [Accepted: 10/17/2010] [Indexed: 12/01/2022]
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27
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Proof of concept for recombinant cellular controls in quantitative molecular pathogen detection. Appl Environ Microbiol 2011; 77:2531-3. [PMID: 21317266 DOI: 10.1128/aem.02601-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we present the concept of internal sample process controls (ISPCs) to monitor the efficiency of an analytical chain using sample preparation and quantitative PCR (qPCR). A recombinant Listeria monocytogenes ΔprfA (targeted deletion) strain containing a competitive artificial single-copy genomic target was applied to naturally contaminated samples to demonstrate its analytical suitability as an ISPC.
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28
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Knutsson R. A tracing tool portfolio to detect Bacillus anthracis, Clostridium botulinum and Noroviruses: bioterrorism is a food safety and security issue. Int J Food Microbiol 2010; 145 Suppl 1:S121-2. [PMID: 21324542 DOI: 10.1016/j.ijfoodmicro.2010.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Rickard Knutsson
- Department of Bacteriology, National Veterinary Institute, SVA, Sweden.
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