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Renault T, Faury N, Morga B. Propidium monoazide PCR, a method to determine OsHV-1 undamaged capsids and to estimate virus Lethal Dose 50. Virus Res 2024; 340:199307. [PMID: 38160910 PMCID: PMC10800765 DOI: 10.1016/j.virusres.2023.199307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Ostreid herpes virus 1 (OsHV-1) has been classified within the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 is the etiological agent of a contagious viral disease of Pacific oysters, C. gigas, affecting also other bivalve species. Mortality rates reported associated with the viral infection vary considerably between sites and countries and depend on the age of affected stocks. A variant called μVar has been reported since 2008 in Europe and other variants in Australia and in New Zealand last decade. These variants are considered as the main causative agents of mass mortality events affecting C. gigas. Presently there is no established cell line that allows for the detection of infectious OsHV-1. In this context, a technique of propidium monoazide (PMA) PCR was developed in order to quantify "undamaged" capsids. This methodology is of interest to explore the virus infectivity. Being able to quantify viral particles getting an undamaged capsid (not only an amount of viral DNA) in tissue homogenates prepared from infected oysters or in seawater samples can assist in the definition of a Lethal Dose (LD) 50 and gain information in the experiments conducted to reproduce the viral infection. The main objectives of the present study were (i) the development/optimization of a PMA PCR technique for OsHV-1 detection using the best quantity of PMA and verifying its effectiveness through heat treatment, (ii) the definition of the percentage of undamaged capsids in four different tissue homogenates prepared from infected Pacific oysters and (iii) the approach of a LD50 during experimental viral infection assays on the basis of a number of undamaged capsids. Although the developped PMA PCR technique was unable to determine OsHV-1 infectivity in viral supensions, it could greatly improve interpretation of virus positive results obtained by qPCR. This technique is not intended to replace the quantification of viral DNA by qPCR, but it does make it possible to give a form of biological meaning to the detection of this DNA.
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Affiliation(s)
- Tristan Renault
- Département Ressources Biologiques et Environnement, Ifremer, Nantes, France.
| | - Nicole Faury
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
| | - Benjamin Morga
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
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2
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Roy PK, Jeon EB, Kim JY, Park SY. Application of High-Pressure Processing (or High Hydrostatic Pressure) for the Inactivation of Human Norovirus in Korean Traditionally Preserved Raw Crab. Viruses 2023; 15:1599. [PMID: 37515285 PMCID: PMC10386741 DOI: 10.3390/v15071599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Human norovirus (HuNoV) is a common cause of outbreaks linked to food. In this study, the effectiveness of a non-thermal method known as high-pressure processing (HPP) on the viable reduction of an HuNoV GII.4 strain on raw crabs was evaluated at three different pressures (200, 400, and 600 MPa). HuNoV viability in raw crabs was investigated by using propidium monoazide/sarkosyl (PMA) as a nucleic acid intercalating dye prior to performing a real-time reverse transcription-polymerase chain reaction (RT-qPCR). The effect of the HPP exposure on pH, sensory, and Hunter colors were also assessed. HuNoV was reduced in raw crabs compared with control to HPP (0.15-1.91 log) in non-PMA and (0.67-2.23 log) in PMA. HuNoV genomic titer reduction was <2 log copy number/µL) when HPP was treated for 5 min without PMA pretreatment, but it was reduced to >2 log copy number/µL after PMA. The pH and Hunter colors of the untreated and HPP-treated raw crabs were significantly different (p < 0.05), but sensory attributes were not significant. The findings indicate that PMA/RT-qPCR could be used to detect HuNoV infectivity without altering the quality of raw crabs after a 5 min treatment with HPP. Therefore, HuNoV GII.4 could be reduced up to 2.23 log in food at a commercially acceptable pressure duration of 600 MPa for 5 min.
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Affiliation(s)
- Pantu Kumar Roy
- Institute of Marine Industry, Department of Seafood Science and Technology, Gyeongsang National University, Tongyeong 53064, Republic of Korea
| | - Eun Bi Jeon
- Institute of Marine Industry, Department of Seafood Science and Technology, Gyeongsang National University, Tongyeong 53064, Republic of Korea
| | - Ji Yoon Kim
- West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 22383, Republic of Korea
| | - Shin Young Park
- Institute of Marine Industry, Department of Seafood Science and Technology, Gyeongsang National University, Tongyeong 53064, Republic of Korea
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3
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Kim KH, Kang G, Woo WS, Sohn MY, Son HJ, Park CI. Development of a Propidium Monoazide-Based Viability Quantitative PCR Assay for Red Sea Bream Iridovirus Detection. Int J Mol Sci 2023; 24:ijms24043426. [PMID: 36834834 PMCID: PMC9958570 DOI: 10.3390/ijms24043426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Red sea bream iridovirus (RSIV) is an important aquatic virus that causes high mortality in marine fish. RSIV infection mainly spreads through horizontal transmission via seawater, and its early detection could help prevent disease outbreaks. Although quantitative PCR (qPCR) is a sensitive and rapid method for detecting RSIV, it cannot differentiate between infectious and inactive viruses. Here, we aimed to develop a viability qPCR assay based on propidium monoazide (PMAxx), which is a photoactive dye that penetrates damaged viral particles and binds to viral DNA to prevent qPCR amplification, to distinguish between infectious and inactive viruses effectively. Our results demonstrated that PMAxx at 75 μM effectively inhibited the amplification of heat-inactivated RSIV in viability qPCR, allowing the discrimination of inactive and infectious RSIV. Furthermore, the PMAxx-based viability qPCR assay selectively detected the infectious RSIV in seawater more efficiently than the conventional qPCR and cell culture methods. The reported viability qPCR method will help prevent the overestimation of red sea bream iridoviral disease caused by RSIV. Furthermore, this non-invasive method will aid in establishing a disease prediction system and in epidemiological analysis using seawater.
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4
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Chin NA, Salihah NT, Shivanand P, Ahmed MU. Recent trends and developments of PCR-based methods for the detection of food-borne Salmonella bacteria and Norovirus. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:4570-4582. [PMID: 36276542 PMCID: PMC9579247 DOI: 10.1007/s13197-021-05280-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
In recent years, rapid detection methods such as polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR) have been continuously developed to improve the detection of food-borne pathogens in food samples. The recent developments of PCR and qPCR in the detection and identification of these food-borne pathogens are described and elaborated throughout this review. Specifically, further developments and improvements of qPCR are discussed in detecting Salmonella and norovirus. Promising advances in these molecular detection methods have been widely used to prevent human food-borne illnesses and death caused by the food-borne pathogens. In addition, this review presents the limitations and challenges of the detection methods which include conventional culture method and conventional PCR method in detecting Salmonella and norovirus. Furthermore, several advances of qPCR such as viability PCR (vPCR) and digital PCR (dPCR) have been discussed in the detection of Salmonella and norovirus. Good practice of analysis of the food-borne pathogens and other contaminants in the food industry as well as the advancement of molecular detection methods will help improve and ensure food safety and food quality.
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Affiliation(s)
- Nur Areena Chin
- Biosensors and Nanobiotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410 Brunei Darussalam
| | - Nur Thaqifah Salihah
- Universiti Islam Sultan Sharif Ali, Jalan Pasar Baharu, Gadong, BE1310 Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410 Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Nanobiotechnology Laboratory, Integrated Science Building, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410 Brunei Darussalam
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5
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Luz IS, Miagostovich MP. Evaluation of heat treatment for inactivation of norovirus genogroup II in foods. Braz J Microbiol 2022; 53:1159-1165. [PMID: 35312990 PMCID: PMC9433490 DOI: 10.1007/s42770-022-00731-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 11/02/2022] Open
Abstract
The effective food processing technology is a key step in eliminating human noroviruses in foods mainly due to their stability in diverse environmental conditions. The aim of this study was to evaluate the effect of rising temperatures for inactivation of norovirus genogroup (G) II and murine norovirus 1 in samples of tomato sauce (72-74 °C for 1 min) and ground meat (100 °C for 30 min). Spiking experiments were carried out in triplicate using TRIzol® reagent method associated with quantitative polymerase chain reaction (qPCR) TaqMan™ system combined with previous free RNA digestion. Success rate and efficiency recoveries of both viruses as well limit of detection of a method for each matrix were also conducted. The heat treatment applied here proved to be efficient to reduce the burden of norovirus GII in a range of 1-4 log10 genomic copies per gram (percentage ranging from 0.45 to 104.54%) in both matrices. The experiments in this study showed that the results of norovirus GII and murine norovirus 1 in tomato sauce and ground meat tested during thermal treatments cannot be generalized to other food matrices, since there may be food-specific protective effects, as the presence of different components, that can interfere in virus inactivation. Studies using different food matrices reinforce the importance to investigate viruses' inactivation thermal processes in foods due to the resistance of these viruses to adverse conditions, contributing to food security in food virology.
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Affiliation(s)
- Isabelle S Luz
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation/FIOCRUZ, Rio de Janeiro, 21040-360, Brazil.
| | - Marize P Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation/FIOCRUZ, Rio de Janeiro, 21040-360, Brazil
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6
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Liang G, Long Y, Li Q, Yang L, Huang Y, Yu D, Song W, Zhou M, Xu G, Huang C, Tang X. Propidium Monoazide Combined With RT-qPCR Detects Infectivity of Porcine Epidemic Diarrhea Virus. Front Vet Sci 2022; 9:931392. [PMID: 35909686 PMCID: PMC9334817 DOI: 10.3389/fvets.2022.931392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) allows sensitive detection of viral particles and viruses in epidemic samples but it cannot discriminate noninfectious viruses from infectious ones. Propidium monoazide (PMA) coupled with quantitative polymerase chain reaction (qPCR) was assessed to detect infectious viruses. Currently, there is no established test method to detect the infection of the porcine epidemic diarrhea virus (PEDV). In this study, propidium monoazide coupled with qPCR detects infectivity of PEDV. We optimized the method from the selection of primers, the working concentration of PMA, and the inactivation method using heat or ultraviolet (UV). The viruses which were treated with PMA before qPCR were inactivated using heat or UV. However, the addition of PMA alone did not affect the detection of live viruses, which indicates that a viral capsid break may be essential for PMA to bind to the genome. A repetition of the method on naked PEDV RNA suggests that it can be used to detect potentially infectious PEDV. The results indicated that an optimal plan of PMA could be extremely useful for evaluating infectious and noninfectious viruses.
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7
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Canh VD, Liu M, Sangsanont J, Katayama H. Capsid integrity detection of pathogenic viruses in waters: Recent progress and potential future applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154258. [PMID: 35248642 DOI: 10.1016/j.scitotenv.2022.154258] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Waterborne diseases caused by pathogenic human viruses are a major public health concern. To control the potential risk of viral infection through contaminated waters, a rapid, reliable tool to assess the infectivity of pathogenic viruses is required. Recently, an advanced approach (i.e., capsid integrity (RT-)qPCR) was developed to discriminate intact viruses (potentially infectious) from inactivated viruses. In this approach, samples were pretreated with capsid integrity reagents (e.g., monoazide dyes or metal compounds) before (RT -)qPCR. These reagents can only penetrate inactivated viruses with compromised capsids to bind to viral genomes and prevent their amplification, but they cannot enter viruses with intact capsids. Therefore, only viral genomes of intact viruses were amplified or detected by (RT-)qPCR after capsid integrity treatment. In this study, we reviewed recent progress in the development and application of capsid integrity (RT-)qPCR to assess the potential infectivity of viruses (including non-enveloped and enveloped viruses with different genome structures [RNA and DNA]) in water. The efficiency of capsid integrity (RT-)qPCR has been shown to depend on various factors, such as conditions of integrity reagent treatment, types of viruses, environmental matrices, and the capsid structure of viruses after disinfection treatments (e.g., UV, heat, and chlorine). For the application of capsid integrity (RT-)qPCR in real-world samples, the use of suitable virus concentration methods and process controls is important to control the efficiency of capsid integrity (RT-)qPCR. In addition, potential future applications of capsid integrity (RT-)qPCR for determining the mechanism of disinfection treatment on viral structure (e.g., capsid or genome) and a combination of capsid integrity treatment and next-generation sequencing (NGS) (capsid integrity NGS) for monitoring the community of intact pathogenic viruses in water are also discussed. This review provides essential information on the application of capsid integrity (RT-)qPCR as an efficient tool for monitoring the presence of pathogenic viruses with intact capsids in water.
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Affiliation(s)
- Vu Duc Canh
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Miaomiao Liu
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hiroyuki Katayama
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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8
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Chakaroun R, Massier L, Musat N, Kovacs P. New Paradigms for Familiar Diseases: Lessons Learned on Circulatory Bacterial Signatures in Cardiometabolic Diseases. Exp Clin Endocrinol Diabetes 2022; 130:313-326. [PMID: 35320847 DOI: 10.1055/a-1756-4509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Despite the strongly accumulating evidence for microbial signatures in metabolic tissues, including the blood, suggesting a novel paradigm for metabolic disease development, the notion of a core blood bacterial signature in health and disease remains a contentious concept. Recent studies clearly demonstrate that under a strict contamination-free environment, methods such as 16 S rRNA gene sequencing, fluorescence in-situ hybridization, transmission electron microscopy, and several more, allied with advanced bioinformatics tools, allow unambiguous detection and quantification of bacteria and bacterial DNA in human tissues. Bacterial load and compositional changes in the blood have been reported for numerous disease states, suggesting that bacteria and their components may partially induce systemic inflammation in cardiometabolic disease. This concept has been so far primarily based on measurements of surrogate parameters. It is now highly desirable to translate the current knowledge into diagnostic, prognostic, and therapeutic approaches.This review addresses the potential clinical relevance of a blood bacterial signature pertinent to cardiometabolic diseases and outcomes and new avenues for translational approaches. It discusses pitfalls related to research in low bacterial biomass while proposing mitigation strategies for future research and application approaches.
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Affiliation(s)
- Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Gothenburg, Sweden
| | - Lucas Massier
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Deutsches Zentrum für Diabetesforschung eV, Neuherberg, Germany
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9
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Song MG, Jeon EB, Kim JY, Park SY. Effects of sodium hypochlorite on the potential infectivity of human norovirus
GII
.4 using propidium monoazide with
RT‐qPCR
and quality assessments in Manila clams (
Ruditapes philippinarum
). J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Gyu Song
- Institute of Marine Industry Gyeongsang National University Tongyeong Republic of Korea
- Department of Seafood Science and Technology Gyeongsang National University Tongyeong Republic of Korea
| | - Eun Bi Jeon
- Institute of Marine Industry Gyeongsang National University Tongyeong Republic of Korea
- Department of Seafood Science and Technology Gyeongsang National University Tongyeong Republic of Korea
| | - Ji Yoon Kim
- Institute of Marine Industry Gyeongsang National University Tongyeong Republic of Korea
- Department of Seafood Science and Technology Gyeongsang National University Tongyeong Republic of Korea
| | - Shin Young Park
- Institute of Marine Industry Gyeongsang National University Tongyeong Republic of Korea
- Department of Seafood Science and Technology Gyeongsang National University Tongyeong Republic of Korea
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10
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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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11
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Canh VD, Torii S, Yasui M, Kyuwa S, Katayama H. Capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148342. [PMID: 34139497 PMCID: PMC8184355 DOI: 10.1016/j.scitotenv.2021.148342] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes have been detected in wastewater worldwide. However, the assessment of SARS-CoV-2 infectivity in wastewater has been limited due to the stringent requirements of biosafety level 3. The main objective of this study is to investigate the applicability of capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. Three capsid integrity reagents, namely ethidium monoazide (EMA, 0.1-100 μM), propidium monoazide (PMA, 0.1-100 μM), and cis-dichlorodiammineplatinum (CDDP, 0.1-1000 μM), were tested for their effects on different forms (including free genomes, intact and heat-inactivated) of murine hepatitis virus (MHV), which was used as a surrogate for SARS-CoV-2. CDDP at a concentration of 100 μM was identified as the most efficient reagent for the selective detection of infectious MHV by RT-qPCR (CDDP-RT-qPCR). Next, two common virus concentration methods including ultrafiltration (UF) and polyethylene glycol (PEG) precipitation were investigated for their compatibility with capsid integrity RT-qPCR. The UF method was more suitable than the PEG method since it recovered intact MHV (mean ± SD, 38% ± 29%) in wastewater much better than the PEG method did (0.013% ± 0.015%). Finally, CDDP-RT-qPCR was compared with RT-qPCR alone for the detection of SARS-CoV-2 in 16 raw wastewater samples collected in the Greater Tokyo Area. Five samples were positive for SARS-CoV-2 when evaluated by RT-qPCR alone. However, intact SARS-CoV-2 was detected in only three positive samples when determined by CDDP-RT-qPCR. Although CDDP-RT-qPCR was unable to determine the infectivity of SARS-CoV-2 in wastewater, this method could improve the interpretation of positive results of SARS-CoV-2 obtained by RT-qPCR.
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Affiliation(s)
- Vu Duc Canh
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shotaro Torii
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Midori Yasui
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shigeru Kyuwa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Katayama
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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12
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 DOI: 10.1101/2020.05.08.20095364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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13
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 PMCID: PMC7811166 DOI: 10.1016/j.wroa.2020.100080] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C. Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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14
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Razafimahefa RM, Ludwig-Begall LF, Le Guyader FS, Farnir F, Mauroy A, Thiry E. Optimisation of a PMAxx™-RT-qPCR Assay and the Preceding Extraction Method to Selectively Detect Infectious Murine Norovirus Particles in Mussels. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:93-106. [PMID: 33389671 DOI: 10.1007/s12560-020-09454-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Human noroviruses are a major cause for gastroenteritis outbreaks. Filter-feeding bivalve molluscs, which accumulate noroviruses in their digestive tissues, are a typical vector for human infection. RT-qPCR, the established method for human norovirus detection in food, does not allow discrimination between infectious and non-infectious viruses and can overestimate potentially infectious viral loads. To develop a more accurate method of infectious norovirus load estimation, we combined intercalating agent propidium monoazide (PMAxx™)-pre-treatment with RT-qPCR assay using in vitro-cultivable murine norovirus. Three primer sets targeting different genome regions and diverse amplicon sizes were used to compare one-step amplification of a short genome fragment to three two-step long-range RT-qPCRs (7 kbp, 3.6 kbp and 2.3 kbp amplicons). Following initial assays performed on untreated infectious, heat-, or ultraviolet-inactivated murine noroviruses in PBS suspension, PMAxx™ RT-qPCRs were implemented to detect murine noroviruses subsequent to their extraction from mussel digestive tissues; virus extraction via anionic polymer-coated magnetic beads was compared with the proteinase K-dependent ISO norm. The long-range RT-qPCR process detecting fragments of more than 2.3 kbp allowed accurate estimation of the infectivity of UV-damaged murine noroviruses. While proteinase K extraction limited later estimation of PMAxx™ pre-treatment effects and was found to be unsuited to the assay, magnetic bead-captured murine noroviruses retained their infectivity. Genome copies of heat-inactivated murine noroviruses differed by 2.3 log10 between RT-qPCR and PMAxx™-RT-qPCR analysis in bivalve molluscs, the PMAxx™ pre-treatment allowing a closer approximation of infectious titres. The combination of bead-based virus extraction and PMAxx™ RT-qPCR thus provides a more accurate model for the estimation of noroviral bivalve mollusc contamination than the conjunction of proteinase K extraction and RT-qPCR and has the potential (once validated utilising infectious human norovirus) to provide an added measure of security to food safety authorities in the hazard assessment of potential bivalve mollusc contamination.
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Affiliation(s)
- Ravo M Razafimahefa
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium
| | - Louisa F Ludwig-Begall
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium
| | | | - Frédéric Farnir
- Biostatistics and Bioinformatics Applied To Veterinary Science, FARAH Research Centre, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Axel Mauroy
- Staff Direction for Risk Assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Bld du Jardin Botanique 55, 1000, Brussels, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium.
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15
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Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. MICROBIOME 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
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Choi MS, Jeon EB, Kim JY, Choi EH, Lim JS, Choi J, Ha KS, Kwon JY, Jeong SH, Park SY. Virucidal Effects of Dielectric Barrier Discharge Plasma on Human Norovirus Infectivity in Fresh Oysters ( Crassostrea gigas). Foods 2020; 9:E1731. [PMID: 33255577 PMCID: PMC7760321 DOI: 10.3390/foods9121731] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/04/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
This study investigates the effects of dielectric barrier discharge (DBD) plasma treatment (1.1 kV, 43 kHz, N2 1.5 L/min, 10~60 min) on human norovirus (HuNoV) GII.4 infectivity in fresh oysters. HuNoV viability in oysters was assessed by using propidium monoazide (PMA) as a nucleic acid intercalating dye before performing a real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Additionally, the impact of the DBD plasma treatment on pH and Hunter colors was assessed. When DBD plasma was treated for 60 min, the HuNoV genomic titer reduction without PMA pretreatment was negligible (<1 log copy number/µL), whereas when PMA treatment was used, HuNoV titer was reduced to >1 log copy number/µL in just 30 min. D1 and D2-value of HuNoV infectivity were calculated as 36.5 and 73.0 min of the DBD plasma treatment, respectively, using the first-order kinetics model (R2 = 0.98). The pH and Hunter colors were not significantly different (p > 0.05) between the untreated and DBD-plasma-treated oysters. The results suggest that PMA/RT-qPCR could help distinguish HuNoV infectivity without negatively affecting oyster quality following >30 min treatment with DBD plasma. Moreover, the inactivation kinetics of nonthermal DBD plasma against HuNoV in fresh oysters might provide basic information for oyster processing and distribution.
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Affiliation(s)
- Man-Seok Choi
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Eun Bi Jeon
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Ji Yoon Kim
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Jun Sup Lim
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Jinsung Choi
- Department of Electrical and Biological Physics, Plasma Bioscience Research Center, Kwangwoon University, Seoul 01987, Korea; (E.H.C.); (J.S.L.); (J.C.)
| | - Kwang Soo Ha
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Ji Young Kwon
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Sang Hyeon Jeong
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science, Tongyeong 53085, Korea; (K.S.H.); (J.Y.K.); (S.H.J.)
| | - Shin Young Park
- Institute of Marine Industry, Gyeongsang National University, Tongyeong 53064, Korea; (M.-S.C.); (E.B.J.); (J.Y.K.)
- Department of Seafood and Aquaculture Science, Gyeongsang National University, Tongyeong 53064, Korea
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Shirasaki N, Matsushita T, Matsui Y, Koriki S. Suitability of pepper mild mottle virus as a human enteric virus surrogate for assessing the efficacy of thermal or free-chlorine disinfection processes by using infectivity assays and enhanced viability PCR. WATER RESEARCH 2020; 186:116409. [PMID: 32942179 DOI: 10.1016/j.watres.2020.116409] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 05/05/2023]
Abstract
Evaluating the efficacy of disinfection processes to inactivate human enteric viruses is important for the prevention and control of waterborne diseases caused by exposure to those viruses via drinking water. Here, we evaluated the inactivation of two representative human enteric viruses (adenovirus type 40 [AdV] and coxsackievirus B5 [CV]) by thermal or free-chlorine disinfection. In addition, we compared the infectivity reduction ratio of a plant virus (pepper mild mottle virus [PMMoV], a recently proposed novel surrogate for human enteric viruses for the assessment of virus removal by coagulation‒rapid sand filtration and membrane filtration) with that of the two human enteric viruses to assess the suitability of PMMoV as a human enteric virus surrogate for use in thermal and free-chlorine disinfection processes. Finally, we examined whether conventional or enhanced viability polymerase chain reaction (PCR) analysis using propidium monoazide (PMA) or improved PMA (PMAxx) with or without an enhancer could be used as alternatives to infectivity assays (i.e., plaque-forming unit method for AdV and CV; local lesion count assay for PMMoV) for evaluating virus inactivation by disinfection processes. We found that PMMoV was more resistant to heat treatment than AdV and CV, suggesting that PMMoV is a potential surrogate for these two enteric viruses with regard to thermal disinfection processes. However, PMMoV was much more resistant to chlorine treatment compared with AdV and CV (which is chlorine-resistant) (CT value for 4-log10 inactivation: PMMoV, 84.5 mg-Cl2·min/L; CV, 1.15-1.19 mg-Cl2·min/L), suggesting that PMMoV is not useful as a surrogate for these enteric viruses with regard to free-chlorine disinfection processes. For thermal disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was comparable with the magnitude of reduction in infectivity, indicating that PMAxx-Enhancer-PCR is a potential alternative to infectivity assay. However, for free-chlorine disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was smaller than the magnitude of the reduction in infectivity, indicating that PMAxx-Enhancer-PCR underestimated the efficacy of virus inactivation (i.e., overestimated the infectious virus concentration) by chlorine treatment. Nevertheless, among the PCR approaches examined in the present study (PCR alone, PMA-PCR or PMAxx-PCR either with or without enhancer), PMAxx-Enhancer-PCR provided the most accurate assessment of the efficacy of virus inactivation by thermal or free chlorine disinfection processes.
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Affiliation(s)
- N Shirasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - T Matsushita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - Y Matsui
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - S Koriki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
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18
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Navarro Y, Torija MJ, Mas A, Beltran G. Viability-PCR Allows Monitoring Yeast Population Dynamics in Mixed Fermentations Including Viable but Non-Culturable Yeasts. Foods 2020; 9:E1373. [PMID: 32992467 PMCID: PMC7600988 DOI: 10.3390/foods9101373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The use of controlled mixed inocula of Saccharomyces cerevisiae and non-Saccharomyces yeasts is a common practice in winemaking, with Torulaspora delbrueckii, Lachancea thermotolerans and Metschnikowia pulcherrima being the most commonly used non-Saccharomyces species. Although S. cerevisiae is usually the dominant yeast at the end of mixed fermentations, some non-Saccharomyces species are also able to reach the late stages; such species may not grow in culture media, which is a status known as viable but non-culturable (VBNC). Thus, an accurate methodology to properly monitor viable yeast population dynamics during alcoholic fermentation is required to understand microbial interactions and the contribution of each species to the final product. Quantitative PCR (qPCR) has been found to be a good and sensitive method for determining the identity of the cell population, but it cannot distinguish the DNA from living and dead cells, which can overestimate the final population results. To address this shortcoming, viability dyes can be used to avoid the amplification and, therefore, the quantification of DNA from non-viable cells. In this study, we validated the use of PMAxx dye (an optimized version of propidium monoazide (PMA) dye) coupled with qPCR (PMAxx-qPCR), as a tool to monitor the viable population dynamics of the most common yeast species used in wine mixed fermentations (S. cerevisiae, T. delbrueckii, L. thermotolerans and M. pulcherrima), comparing the results with non-dyed qPCR and colony counting on differential medium. Our results showed that the PMAxx-qPCR assay used in this study is a reliable, specific and fast method for quantifying these four yeast species during the alcoholic fermentation process, being able to distinguish between living and dead yeast populations. Moreover, the entry into VBNC status was observed for the first time in L. thermotolerans and S. cerevisiae during alcoholic fermentation. Further studies are needed to unravel which compounds trigger this VBNC state during alcoholic fermentation in these species, which would help to better understand yeast interactions.
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Affiliation(s)
| | - María-Jesús Torija
- Department of Biochemistry and Biotechnology, Faculty of Oenology, University Rovira i Virgili (URV), Marcel·lí Domingo 1, 43007 Tarragona, Catalonia, Spain; (Y.N.); (A.M.); (G.B.)
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19
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Fuzawa M, Bai H, Shisler JL, Nguyen TH. The Basis of Peracetic Acid Inactivation Mechanisms for Rotavirus and Tulane Virus under Conditions Relevant for Vegetable Sanitation. Appl Environ Microbiol 2020; 86:e01095-20. [PMID: 32709728 PMCID: PMC7499037 DOI: 10.1128/aem.01095-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
We determined the disinfection efficacy and inactivation mechanisms of peracetic acid (PAA)-based sanitizer using pH values relevant for vegetable sanitation against rotavirus (RV) and Tulane virus (TV; a human norovirus surrogate). TV was significantly more resistant to PAA disinfection than RV: for a 2-log10 reduction of virus titer, RV required 1 mg/liter PAA for 3.5 min of exposure, while TV required 10 mg/liter PAA for 30 min. The higher resistance of TV can be explained, in part, by significantly more aggregation of TV in PAA solutions. The PAA mechanisms of virus inactivation were explored by quantifying (i) viral genome integrity and replication using reverse transcription-quantitative PCR (RT-qPCR) and (ii) virus-host receptor interactions using a cell-free binding assay with porcine gastric mucin conjugated with magnetic beads (PGM-MBs). We observed that PAA induced damage to both RV and TV genomes and also decreased virus-receptor interactions, with the latter suggesting that PAA damages viral proteins important for binding its host cell receptors. Importantly, the levels of genome-versus-protein damage induced by PAA were different for each virus. PAA inactivation correlated with higher levels of RV genome damage than of RV-receptor interactions. For PAA-treated TV, the opposite trends were observed. Thus, PAA inactivates each of these viruses via different molecular mechanisms. The findings presented here potentially contribute to the design of a robust sanitation strategy for RV and TV using PAA to prevent foodborne disease.IMPORTANCE In this study, we examined the inactivation mechanisms of peracetic acid (PAA), a sanitizer commonly used for postharvest vegetable washing, for two enteric viruses: Tulane virus (TV) as a human norovirus surrogate and rotavirus (RV). PAA disinfection mechanisms for RV were mainly due to genome damage. In contrast, PAA disinfection in TV was due to damage of the proteins important for binding to its host receptor. We also observed that PAA triggered aggregation of TV to a much greater extent than RV. These studies demonstrate that different viruses are inactivated via different PAA mechanisms. This information is important for designing an optimal sanitation practice for postharvest vegetable washing to minimize foodborne viral diseases.
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Affiliation(s)
- Miyu Fuzawa
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hezi Bai
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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20
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Boles C, Brown G, Park JH, Nonnenmann M. The Optimization of Methods for the Collection of Aerosolized Murine Norovirus. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:199-208. [PMID: 32524378 DOI: 10.1007/s12560-020-09430-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/30/2020] [Indexed: 05/25/2023]
Abstract
Globally, norovirus is the most common gastroenteritis causing pathogen. Annually, norovirus causes 685 million cases of acute gastroenteritis and 200,000 deaths, worldwide. Recent evidence has suggested that norovirus can also be spread via aerosolization; however, an indoor generation source has yet to be determined. We optimized a sampling method for the collection of aerosolized norovirus using murine norovirus (MNV) as a surrogate. Optimization of the sampling method was performed using two bioaerosol samplers (SKC BioSampler and the NIOSH Bioaerosol Cyclone Sampler 251) and two sampling media (Hanks Balanced Salt Solution [HBSS] and Phosphate Buffered Saline [PBS]). Murine norovirus was aerosolized in a bioaerosol chamber and later collected using each sampler/media combination. Collected MNV was quantified using quantitative polymerase chain reaction (qPCR). Intact capsids of MNV were assessed using propidium monoazide dye in combination with qPCR and confirmed with transmission electron microscopy. Ten trials were conducted, with each trial lasting for 30 min. The SKC BioSampler collected a significantly higher concentration of MNV than the NIOSH-251 sampler did (p-value < 0.0001). However, there were no significant differences in the relative percent of MNV that remained viable between both samplers (p-value = 0.2215). The use of HBSS sampling media yielded a higher concentration of MNV than PBS media (p-value = 0.0125). However, PBS media maintained viability at a significantly higher percentage than HBSS media (p-value < 0.0001). The results support the optimization of a sampling method for the collection of aerosolized MNV and possibly norovirus in different sampling environments.
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Affiliation(s)
| | - Grant Brown
- College of Public Health, University of Iowa, Iowa City, USA
| | - Jae Hong Park
- School of Health Sciences, Purdue University, West Lafayette, USA
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21
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Sarmento SK, Guerra CR, Malta FC, Coutinho R, Miagostovich MP, Fumian TM. Human norovirus detection in bivalve shellfish in Brazil and evaluation of viral infectivity using PMA treatment. MARINE POLLUTION BULLETIN 2020; 157:111315. [PMID: 32658680 DOI: 10.1016/j.marpolbul.2020.111315] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Noroviruses are the most common cause of gastroenteritis outbreaks in humans and bivalve shellfish consumption is a recognized route of infection. Our aim was to detect and characterize norovirus in bivalves from a coastal city of Brazil. Nucleic acid was extracted from the bivalve's digestive tissue concentrates using magnetic beads. From March 2018 to June 2019, 77 samples were screened using quantitative RT-PCR. Noroviruses were detected in 41.5%, with the GII being the most prevalent (37.7%). The highest viral load was 3.5 × 106 and 2.5 × 105 GC/g in oysters and mussels, respectively. PMA-treatment demonstrated that a large fraction of the detected norovirus corresponded to non-infectious particles. Genetic characterization showed the circulation of the GII.2[P16] and GII.4[P4] genotypes. Norovirus detection in bivalves reflects the anthropogenic impact on marine environment and serves as an early warning for the food-borne disease outbreaks resulting from the consumption of contaminated molluscs.
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Affiliation(s)
- Sylvia Kahwage Sarmento
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Caroline Rezende Guerra
- Laboratório de Genética Marinha, Departamento de Biotecnologia Marinha, Instituto de Estudos do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo , RJ CEP 28930-000, Brazil
| | - Fábio Correia Malta
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Ricardo Coutinho
- Laboratório de Genética Marinha, Departamento de Biotecnologia Marinha, Instituto de Estudos do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo , RJ CEP 28930-000, Brazil
| | - Marize Pereira Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil.
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Sangsanont J, Kurisu F, Furumai H, Katayama H. Ozone disinfection kinetics of poliovirus 1 determined by cell culture assay, RT-qPCR and ethidium monoazide qPCR reduction in a continuous quench-flow reactor. J Appl Microbiol 2020; 129:1530-1540. [PMID: 32681543 DOI: 10.1111/jam.14787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
AIMS A continuous quench-flow (CQF) reactor was developed to collect samples at the reaction times of less than one second. The reactor is applied to determine ozone disinfection kinetics of poliovirus and to study whether EMA-qPCR can assess the viral infectivity after ozone disinfection. METHODS Ozone disinfection of poliovirus was conducted in the developed CQF, and the disinfection kinetics were tested in the range of 0·7-5·0 s at ozone concentration of 0·08 and 0·25 mg l-1 . Inactivation, damage on viral genome and damage on capsid integrity were determined by plaque assay, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and ethidium monoazide treatment coupled with RT-qPCR (EMA-qPCR), respectively. RESULTS By using CQF, 2·18 and 2·76 log10 reductions were observed at the reaction time of 0·7 s and ozone concentration of 0·08 and 0·25 mg l-1 , respectively, followed by tailing. Ozone disinfection kinetics of poliovirus 1 were better fit by the efficiency factor Hom model than by the Chick-Watson model, or the modified Chick-Watson model. Kinetics observed were similar between RT-qPCR and EMA-qPCR assays at the reaction times of <2·0 s and ozone concentrations of 0·08 and 0·25 mg l-1 . At reaction times > 5 s, viral concentration evaluated by EMA-qPCR was reduced in comparison to stable RT-qPCR results. Both assays still underestimated the virus inactivation. CONCLUSION The simple developed reactor can be used to investigate viral ozone disinfection kinetics and to elucidate inactivation characteristics or mechanisms at very short exposure times. SIGNIFICANCE AND IMPACT OF THE STUDY The developed CQF reactor is beneficial for better understanding of virus inactivation by ozone, and the reactor can be used to better elucidate disinfection kinetics and mechanisms for future research. This work constitutes an important contribution to the existing knowledge of the application and limitation of the EMA/PMA-qPCR to assess virus infectivity after ozone disinfection.
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Affiliation(s)
- J Sangsanont
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan.,Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - F Kurisu
- Research Center for Water Environment Technology, The University of Tokyo, Tokyo, Japan
| | - H Furumai
- Research Center for Water Environment Technology, The University of Tokyo, Tokyo, Japan
| | - H Katayama
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
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A Survey of Analytical Techniques for Noroviruses. Foods 2020; 9:foods9030318. [PMID: 32164213 PMCID: PMC7142446 DOI: 10.3390/foods9030318] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 12/17/2022] Open
Abstract
As the leading cause of acute gastroenteritis worldwide, human noroviruses (HuNoVs) have caused around 685 million cases of infection and nearly $60 billion in losses every year. Despite their highly contagious nature, an effective vaccine for HuNoVs has yet to become commercially available. Therefore, rapid detection and subtyping of noroviruses is crucial for preventing viral spread. Over the past half century, there has been monumental progress in the development of techniques for the detection and analysis of noroviruses. However, currently no rapid, portable assays are available to detect and subtype infectious HuNoVs. The purpose of this review is to survey and present different analytical techniques for the detection and characterization of noroviruses.
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Jeon EB, Choi MS, Kim JY, Ha KS, Kwon JY, Jeong SH, Lee HJ, Jung YJ, Ha JH, Park SY. Characterizing the effects of thermal treatment on human norovirus GII.4 viability using propidium monoazide combined with RT-qPCR and quality assessments in mussels. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Jeong SG, Lee JY, Yoon SR, Moon EW, Ha JH. A quantitative PCR based method using propidium monoazide for specific and sensitive detection of Pectobacterium carotovorum ssp. carotovorum in kimchi cabbage (Brassica rapa L. subsp. pekinensis). Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Host Range of Bacteriophages Against a World-Wide Collection of Erwinia amylovora Determined Using a Quantitative PCR Assay. Viruses 2019; 11:v11100910. [PMID: 31581574 PMCID: PMC6832558 DOI: 10.3390/v11100910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/21/2019] [Accepted: 09/27/2019] [Indexed: 01/01/2023] Open
Abstract
Erwinia amylovora is a globally devastating pathogen of apple, pear, and other Rosaceous plants. The use of lytic bacteriophages for disease management continues to garner attention as a possible supplement or alternative to antibiotics. A quantitative productive host range was established for 10 Erwinia phages using 106 wild type global isolates of E. amylovora, and the closely related Erwinia pyrifoliae, to investigate the potential regional efficacy of these phages within a biopesticide. Each host was individually infected with each of the 10 Erwinia phages and phage production after 8 h incubation was measured using quantitative real time PCR (qPCR) in conjunction with a standardized plasmid. PCR amplicons for all phages used in the study were incorporated into a single plasmid, allowing standardized quantification of the phage genome copy number after the infection process. Nine of the tested phages exhibited a broad host range, replicating their genomes by at least one log in over 88% of tested hosts. Also, every Amygdaloideae infecting E. amylovora host was able to increase at least one phage by three logs. Bacterial hosts isolated in western North America were less susceptible to most phages, as the mean genomic titre produced dropped by nearly two logs, and this phenomenon was strongly correlated to the amount of exopolysaccharide produced by the host. This method of host range analysis is faster and requires less effort than traditional plaque assay techniques, and the resulting quantitative data highlight subtle differences in phage host preference not observable with typical plaque-based host range assays. These quantitative host range data will be useful to determine which phages should be incorporated into a phage-mediated biocontrol formulation to be tested for regional and universal control of E. amylovora.
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Worley‐Morse T, Mann M, Khunjar W, Olabode L, Gonzalez R. Evaluating the fate of bacterial indicators, viral indicators, and viruses in water resource recovery facilities. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:830-842. [PMID: 30848516 PMCID: PMC6849880 DOI: 10.1002/wer.1096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 05/03/2023]
Abstract
A year-long sampling campaign at nine water resource recovery facilities (WRRFs) was conducted to assess the treatability and fate of bacterial indicators, viral indicators, and viruses. Influent concentrations of viral indicators (male-specific and somatic coliphages) and bacterial indicators (Escherichia coli and enterococci) remained relatively constant, typically varying by one order of magnitude over the course of the year. Annual average bacterial indicator reduction ranged from 4.0 to 6.7 logs, and annual average viral indicator reduction ranged from 1.6 to 5.4 logs. Bacterial and viral indicator reduction depended on the WRRF's treatment processes, and bacterial indicator reduction was greater than viral indicator reduction for many processes. Viral reduction (adenovirus 41, norovirus GI, and norovirus GII) was more similar to viral indicator reduction than bacterial indicator reduction. Overall, this work suggests that viral indicator reduction in WRRFs is variable and depends on specific unit processes. Moreover, for the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary. PRACTITIONER POINTS: A year-long sampling campaign was conducted at nine water resource recovery facilities (WRRFs). The treatability and fate of bacterial indicators, viral indicators, and viruses were assessed. Viral indicator reduction in WRRFs is variable and depends on specific unit processes. For the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary.
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Affiliation(s)
| | | | | | | | - Raul Gonzalez
- Hampton Roads Sanitation DistrictVirginia BeachVirginia
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Understanding and Exploiting Phage-Host Interactions. Viruses 2019; 11:v11060567. [PMID: 31216787 PMCID: PMC6630733 DOI: 10.3390/v11060567] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/05/2023] Open
Abstract
Initially described a century ago by William Twort and Felix d’Herelle, bacteriophages are bacterial viruses found ubiquitously in nature, located wherever their host cells are present. Translated literally, bacteriophage (phage) means ‘bacteria eater’. Phages interact and infect specific bacteria while not affecting other bacteria or cell lines of other organisms. Due to the specificity of these phage–host interactions, the relationship between phages and their host cells has been the topic of much research. The advances in phage biology research have led to the exploitation of these phage–host interactions and the application of phages in the agricultural and food industry. Phages may provide an alternative to the use of antibiotics, as it is well known that the emergence of antibiotic-resistant bacterial infections has become an epidemic in clinical settings. In agriculture, pre-harvest and/or post-harvest application of phages to crops may prevent the colonisation of bacteria that are detrimental to plant or human health. In addition, the abundance of data generated from genome sequencing has allowed the development of phage-derived bacterial detection systems of foodborne pathogens. This review aims to outline the specific interactions between phages and their host and how these interactions may be exploited and applied in the food industry.
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Capsid Integrity qPCR—An Azo-Dye Based and Culture-Independent Approach to Estimate Adenovirus Infectivity after Disinfection and in the Aquatic Environment. WATER 2019. [DOI: 10.3390/w11061196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recreational, reclaimed and drinking source waters worldwide are under increasing anthropogenic pressure, and often contain waterborne enteric bacterial, protozoan, and viral pathogens originating from non-point source fecal contamination. Recently, the capsid integrity (ci)-qPCR, utilizing the azo-dyes propidium monoazide (PMA) or ethidium monoazide (EMA), has been shown to reduce false-positive signals under laboratory conditions as well as in food safety applications, thus improving the qPCR estimation of virions of public health significance. The compatibility of two widely used human adenovirus (HAdV) qPCR protocols was evaluated with the addition of a PMA/EMA pretreatment using a range of spiked and environmental samples. Stock suspensions of HAdV were inactivated using heat, UV, and chlorine before being quantified by cell culture, qPCR, and ci-qPCR. Apparent inactivation of virions was detected for heat and chlorine treated HAdV while there was no significant difference between ci-qPCR and qPCR protocols after disinfection by UV. In a follow-up comparative analysis under more complex matrix conditions, 51 surface and 24 wastewater samples pre/post UV treatment were assessed for enteric waterborne HAdV to evaluate the ability of ci-qPCR to reduce the number of false-positive results when compared to conventional qPCR and cell culture. Azo-dye pretreatment of non-UV inactivated samples was shown to improve the ability of molecular HAdV quantification by reducing signals from virions with an accessible genome, thereby increasing the relevance of qPCR results for public health purposes, particularly suited to resource-limited low and middle-income settings.
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Yoon JH, Moon SK, Choi C, Ryu BY, Lee SY. Detection of viable but nonculturable Vibrio parahaemolyticus induced by prolonged cold-starvation using propidium monoazide real-time polymerase chain reaction. Lett Appl Microbiol 2019; 68:537-545. [PMID: 30933376 DOI: 10.1111/lam.13157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 11/26/2022]
Abstract
Viable but nonculturable (VBNC) Vibrio parahaemolyticus cannot be detected by the standard cultivation-based methods. In this study, commonly used viability assessment methods were evaluated for the detection of V. parahaemolyticus in a VBNC state. Vibrio parahaemolyticus cells exposed to nutrient deficiency at cold temperature were used for epifluorescence microscopy with SYTO9 and propidium iodide (PI) staining and real-time polymerase chain reaction (qPCR) with propidium monoazide (PMA), and its resuscitative ability was determined by a temperature upshift in freshly prepared artificial sea water (ASW; pH 7) fluids. Viable cells with intact membranes always exceeded 5·0 log CFU per ml in ASW microcosms at 4°C. After 80 days, cycle thresholds for V. parahaemolyticus ATCC 27969 were 16·15-16·69. During cold-starvation, PMA qPCR selectively excluded DNAs from heat-killed cells. However, there may be some penetration of PMA into undamaged cells that persisted in ASW for 150 days, as evidenced by their ability to resuscitate from a VBNC state after a temperature upshift (25°C); V. parahaemolyticus ATCC 33844 and V. parahaemolyticus ATCC 27969 were successfully reactivated from a VBNC state in ASW microcosms containing <5% NaCl, following enrichment in ASW medium (pH 7). SIGNIFICANCE AND IMPACT OF THE STUDY: Few studies have evaluated the characteristics of and detection methods for viable but nonculturable (VBNC) Vibrio parahaemolyticus induced by cold-starvation. Currently, VBNC cells are routinely detected by SYTO9 and propidium iodide double staining. However, viable cell counts might be overestimated by this approach, suggesting that the fluorescence dyes may be ineffective for accurately determining the viability of bacterial cells. We demonstrated that quantitative real-time polymerase chain reaction with propidium monoazide, which selectively permeates damaged cell membranes, can be used to obtain viable cell counts of V. parahaemolyticus after its evolution to a VBNC state under cold-starvation conditions.
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Affiliation(s)
- J-H Yoon
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Gyeonggi-do, Korea
| | - S-K Moon
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Gyeonggi-do, Korea
| | - C Choi
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Gyeonggi-do, Korea
| | - B-Y Ryu
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Korea
| | - S-Y Lee
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Gyeonggi-do, Korea
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31
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Manuel CS, Moore MD, Jaykus LA. Predicting human norovirus infectivity - Recent advances and continued challenges. Food Microbiol 2018; 76:337-345. [DOI: 10.1016/j.fm.2018.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/17/2018] [Accepted: 06/24/2018] [Indexed: 01/06/2023]
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32
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Byappanahalli MN, Nevers MB, Shively DA, Spoljaric A, Otto C. Real-Time Water Quality Monitoring at a Great Lakes National Park. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1086-1093. [PMID: 30272770 DOI: 10.2134/jeq2017.11.0462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) was used by the USEPA to establish new recreational water quality criteria in 2012 using the indicator bacteria enterococci. The application of this method has been limited, but resource managers are interested in more timely monitoring results. In this study, we evaluated the efficacy of qPCR as a rapid, alternative method to the time-consuming membrane filtration (MF) method for monitoring water at select beaches and rivers of Sleeping Bear Dunes National Lakeshore in Empire, MI. Water samples were collected from four locations (Esch Road Beach, Otter Creek, Platte Point Bay, and Platte River outlet) in 2014 and analyzed for culture-based (MF) and non-culture-based (i.e., qPCR) endpoints using and enterococci bacteria. The MF and qPCR enterococci results were significantly, positively correlated overall ( = 0.686, < 0.0001, = 98) and at individual locations as well, except at the Platte River outlet location: Esch Road Beach ( = 0.441, = 0.031, = 24), Otter Creek ( = 0.592, = 0.002, = 24), and Platte Point Bay ( = 0.571, = 0.004, = 24). Similarly, MF and qPCR results were significantly, positively correlated ( = 0.469, < 0.0001, = 95), overall but not at individual locations. Water quality standard exceedances based on enterococci levels by qPCR were lower than by MF method: 3 and 16, respectively. Based on our findings, we conclude that qPCR may be a viable alternative to the culture-based method for monitoring water quality on public lands. Rapid, same-day results are achievable by the qPCR method, which greatly improves protection of the public from water-related illnesses.
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Antiviral activity of Schizonepeta tenuifolia Briquet against noroviruses via induction of antiviral interferons. J Microbiol 2018; 56:683-689. [DOI: 10.1007/s12275-018-8228-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/02/2023]
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34
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Dos Santos CS, de Souza CHB, Padilha M, Gioielli LA, Ract JNR, Saad SMI. Milk fat protects Bifidobacterium animalis subsp. lactis Bb-12 from in vitro gastrointestinal stress in potentially synbiotic table spreads. Food Funct 2018; 9:4274-4281. [PMID: 30027199 DOI: 10.1039/c8fo00506k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The viability and the in vitro gastrointestinal survival of Bifidobacterium animalis subsp. lactis Bb-12 (Bifidobacterium Bb-12) in table spreads with different proportions of milk fat (MF) and palm olein (PO) (MF : PO 40 : 60 and MF : PO 20 : 80) were investigated for up to 28 days of storage at 5 °C. Moreover, qPCR alone and combined with propidium monoazide (PMA) were compared with the traditional plate count method for determining the in vitro gastrointestinal survival of Bifidobacterium Bb-12 in table spreads after 35 days of storage. Formulations showed probiotic viabilities ranging from 8 to 9 log CFU g-1 across the whole storage period, and the milk fat and palm olein in different concentrations did not affect this viability. Bifidobacterium Bb-12 showed good survival after six hours under in vitro simulated gastrointestinal conditions during the studied storage period, with average reductions of 1.70 (MF : PO 40 : 60) and 2.16 log CFU g-1 (MF : PO 20 : 80). The results of the qPCR with PMA treatment and the plate count method were similar and the qPCR without PMA treatment was shown to overestimate the Bifidobacterium Bb-12 populations. However, the MF : PO 40 : 60 spread showed a Bb-12 population between 0.76 and 1.43 log CFU g-1 higher than that of MF : PO 20 : 80. Thus, the results showed that table spreads, especially food matrices with a higher proportion of milk fat, are suitable for the incorporation of Bifidobacterium Bb-12.
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Affiliation(s)
- Clara Simone Dos Santos
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil.
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35
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Noda M. Current Status of Norovirus Food Poisoning Related to Bivalve Mollusk and Its Control Measures. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2018; 58:12-25. [PMID: 28260728 DOI: 10.3358/shokueishi.58.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Kingsley D, Kuis R, Perez R, Basaldua I, Burkins P, Marcano A, Johnson A. Oxygen-dependent laser inactivation of murine norovirus using visible light lasers. Virol J 2018; 15:117. [PMID: 30064439 PMCID: PMC6069788 DOI: 10.1186/s12985-018-1019-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/10/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Previous work indicated that an ultrashort pulse (USP) 425 nm laser is capable of inactivating murine norovirus (MNV: Virol. J. 11:20), perhaps via an impulsive stimulated Raman scattering (ISRS) mechanism, and does not substantially damage human plasma proteins (PLOS One 9:11). Here, further investigation of virus inactivation by laser light is performed. METHODS In this study, we evaluate whether inactivation of MNV is specific to the USP wavelength of 425 nm, or if it occurs at other visible wavelengths, using a tunable mode-locked Ti-Sapphire laser that has been frequency doubled to generate femtosecond pulses at wavelengths of 400, 408, 425, 450, 465, and 510 nm. Continuous Wave (CW) lasers are also applied. Singlet oxygen enhancers are used to evaluate the sensitivity of MNV to singlet oxygen and oxygen quenchers are used to evaluate effects on virus inactivation as compared to untreated controls. RESULTS > 3 log10 inactivation of MNV pfu occurs after irradiation with an average power of 150 mW at wavelengths of 408, 425 or 450 nm femtosecond-pulsed light for 3 h. Thus results suggest that the mechanism by which a laser inactivates the virus is not wavelength-specific. Furthermore, we also show that irradiation using a continuous wave (CW) laser of similar power at 408 nm also yields substantial MNV inactivation indicating that inactivation does not require a USP. Use of photosensitizers, riboflavin, rose bengal and methylene blue that generate singlet oxygen substantially improves the efficiency of the inactivation. The results indicate a photochemical mechanism of the laser-induced inactivation where the action of relatively low power blue laser light generates singlet oxygen. CONCLUSION Results suggest formation of short-lived reactive oxygen species such as singlet oxygen by visible laser light as the cause of virus inactivation rather than via an ISRS mechanism which induces resonant vibrations.
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Affiliation(s)
- David Kingsley
- USDA ARS ERRC Food Safety Intervention Technologies Research Unit, Dover, Delaware USA
| | - Robinson Kuis
- Center for Advanced Studies in Photonics Research, University of Maryland Baltimore County, Baltimore, USA
| | - Rafael Perez
- USDA ARS ERRC Food Safety Intervention Technologies Research Unit, Dover, Delaware USA
| | - Isaac Basaldua
- Center for Advanced Studies in Photonics Research, University of Maryland Baltimore County, Baltimore, USA
| | - Paul Burkins
- Center for Advanced Studies in Photonics Research, University of Maryland Baltimore County, Baltimore, USA
| | - Aristides Marcano
- Department of Physics and Engineering, Delaware State University, Dover, Delaware USA
| | - Anthony Johnson
- Center for Advanced Studies in Photonics Research, University of Maryland Baltimore County, Baltimore, USA
- Department of Physics, University of Maryland Baltimore County, Baltimore, USA
- Department of Computer Science and Electrical Engineering, University of Maryland Baltimore County, Baltimore, USA
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37
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Detection of Infectious Noroviruses from Wastewater and Seawater Using PEMAXTM Treatment Combined with RT-qPCR. WATER 2018. [DOI: 10.3390/w10070841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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38
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Oristo S, Lee HJ, Maunula L. Performance of pre-RT-qPCR treatments to discriminate infectious human rotaviruses and noroviruses from heat-inactivated viruses: applications of PMA/PMAxx, benzonase and RNase. J Appl Microbiol 2018; 124:1008-1016. [DOI: 10.1111/jam.13737] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 01/19/2023]
Affiliation(s)
- S. Oristo
- Department of Food Hygiene and Environmental Health; Faculty of Veterinary Medicine; University of Helsinki; Helsinki Finland
| | - H.-J. Lee
- Department of Food Hygiene and Environmental Health; Faculty of Veterinary Medicine; University of Helsinki; Helsinki Finland
| | - L. Maunula
- Department of Food Hygiene and Environmental Health; Faculty of Veterinary Medicine; University of Helsinki; Helsinki Finland
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Fraisse A, Niveau F, Hennechart-Collette C, Coudray-Meunier C, Martin-Latil S, Perelle S. Discrimination of infectious and heat-treated norovirus by combining platinum compounds and real-time RT-PCR. Int J Food Microbiol 2018; 269:64-74. [DOI: 10.1016/j.ijfoodmicro.2018.01.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 01/16/2023]
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40
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Lee HW, Lee HM, Yoon SR, Kim SH, Ha JH. Pretreatment with propidium monoazide/sodium lauroyl sarcosinate improves discrimination of infectious waterborne virus by RT-qPCR combined with magnetic separation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 233:306-314. [PMID: 29096303 DOI: 10.1016/j.envpol.2017.10.081] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/17/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
RT-qPCR allows sensitive detection of viral particles of both infectious and noninfectious viruses in water environments, but cannot discriminate non-infectious from infectious viruses. In this study, we aimed to optimize RT-qPCR-based detection of chlorine-inactivated human norovirus (NoV) and pepper mild mottle virus (PMMoV) in suspension by pretreatment with an optimal combination of a monoazide and a detergent that can efficiently penetrate damaged viral capsids. Four methods were compared to determine the efficacy of chlorine disinfection (at 1, 3, and 5 min mg/L): (A) RT-qPCR alone, (B) RT-qPCR assay preceded by magnetic bead separation for enrichment of viral particles (MBS-RT-qPCR), (C) MBS-RT-qPCR assay with pretreatment with propidium monoazide (PMA-MBS-RT-qPCR), and (D) PMA-MBS-RT-qPCR assay with pretreatment with sodium lauroyl sarcosinate (INCI-PMA-MBS-RT-qPCR). On the basis of a PMA optimization assay, 200 and 300 μM PMA were used in subsequent experiments for NoV GII.4 and PMMoV, respectively. Optimal INCI concentrations, having minimal influence on NoV GII.4 and PMMoV, were found to be 0.5% and 0.2% INCI, respectively. For NoV GII.4, there were significant differences (P < 0.05) in log10 genome copies between the PMA-treated and the INCI + PMA-treated samples (log10 genome copies differed by 1.11 and 0.59 log10 for 3 and 5 min mg/L of chlorine, respectively). For PMMoV, INCI induced differences in log10 genome copies of 0.92, 1.18, and 1.86, for 1, 3, and 5 min mg/L of chlorine, respectively. Overall, the results of this study indicate that an optimal combination of PMA and INCI could be very useful for evaluating disinfection methods in water treatment strategies.
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Affiliation(s)
- Hae-Won Lee
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, South Korea
| | - Hee-Min Lee
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, South Korea
| | - So-Ra Yoon
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, South Korea
| | - Sung Hyun Kim
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, South Korea
| | - Ji-Hyoung Ha
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju 61755, South Korea.
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41
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Marti E, Ferrary-Américo M, Barardi CRM. Detection of Potential Infectious Enteric Viruses in Fresh Produce by (RT)-qPCR Preceded by Nuclease Treatment. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:444-452. [PMID: 28452009 DOI: 10.1007/s12560-017-9300-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Foodborne illnesses associated with contaminated fresh produce are a common public health problem and there is an upward trend of outbreaks caused by enteric viruses, especially human noroviruses (HNoVs) and hepatitis A virus (HAV). This study aimed to assess the use of DNase and RNase coupled to qPCR and RT-qPCR, respectively, to detect intact particles of human adenoviruses (HAdVs), HNoV GI and GII and HAV in fresh produce. Different concentrations of DNase and RNase were tested to optimize the degradation of free DNA and RNA from inactivated HAdV and murine norovirus (MNV), respectively. Results indicated that 10 µg/ml of RNase was able to degrade more than 4 log10 (99.99%) of free RNA, and 1 U of DNase degraded the range of 0.84-2.5 log10 of free DNA depending on the fresh produce analysed. The treatment with nucleases coupled to (RT)-qPCR was applied to detect potential infectious virus in organic lettuce, green onions and strawberries collected in different seasons. As a result, no intact particles of HNoV GI and GII were detected in the 36 samples analysed, HAdV was found in one sample and HAV was present in 33.3% of the samples, without any reasonable distribution pattern among seasons. In conclusion, RT-qPCR preceded by RNase treatment of eluted samples from fresh produce is a good alternative to detect undamaged RNA viruses and therefore, potential infectious viruses. Moreover, this study provides data about the prevalence of enteric viruses in organic fresh produce from Brazil.
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Affiliation(s)
- Elisabet Marti
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil.
| | - Monique Ferrary-Américo
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil
| | - Célia Regina Monte Barardi
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC, CEP: 88040-970, Brazil
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Monteiro S, Santos R. Enzymatic and viability RT-qPCR assays for evaluation of enterovirus, hepatitis A virus and norovirus inactivation: Implications for public health risk assessment. J Appl Microbiol 2017; 124:965-976. [PMID: 28833965 DOI: 10.1111/jam.13568] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/08/2017] [Accepted: 08/12/2017] [Indexed: 02/03/2023]
Abstract
AIM To assess the potential of a viability dye and an enzymatic reverse transcription quantitative PCR (RT-qPCR) pretreatment to discriminate between infectious and noninfectious enteric viruses. METHODS AND RESULTS Enterovirus (EntV), norovirus (NoV) GII.4 and hepatitis A virus (HAV) were inactivated at 95°C for 10 min, and four methods were used to compare the efficiency of inactivation: (i) cell culture plaque assay for HAV and EntV, (ii) RT-qPCR alone, (iii) RT-qPCR assay preceded by RNase treatment, and (iv) pretreatment with a viability dye (reagent D (RD)) followed by RT-qPCR. In addition, heat-inactivated NoV was treated with RD coupled with surfactants to increase the efficiency of the viability dye. No treatment was able to completely discriminate infectious from noninfectious viruses. RD-RT-qPCR reduced more efficiently the detection of noninfectious viruses with little to no removal observed with RNase. RD-RT-qPCR method was the closest to cell culture assay. The combination of surfactants and RD did not show relevant improvements on the removal of inactivated viruses signal compared with viability RT-qPCR, with the exception of Triton X-100. CONCLUSION The use of surfactant/RD-RT-qPCR, although not being able to completely remove the signal from noninfectious viral particles, yielded a better estimation of viral infectivity. SIGNIFICANCE AND IMPACT OF THE STUDY Surfactant/RD-RT-qPCR may be an advantageous tool for a better detection of infectious viruses with potential significant impact in the risk assessment of the presence of enteric viruses.
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Affiliation(s)
- S Monteiro
- Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal
| | - R Santos
- Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal
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Ahmed FA, Arif M, Alvarez AM. Antibacterial Effect of Potassium Tetraborate Tetrahydrate against Soft Rot Disease Agent Pectobacterium carotovorum in Tomato. Front Microbiol 2017; 8:1728. [PMID: 28955313 PMCID: PMC5601058 DOI: 10.3389/fmicb.2017.01728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/24/2017] [Indexed: 11/13/2022] Open
Abstract
Soft rot caused by Pectobacterium carotovorum is one of most common bacterial diseases occurring in fruits and vegetables worldwide, yet consumer-acceptable options for post-harvest disease management are still insufficient. We evaluated the effect of potassium tetraborate tetrahydrate (B4K2O7.4H2O) (PTB) on the growth of P. carotovorum using strain BA17 as a representative of high virulence. Complete inhibition of bacterial growth was achieved by treatment with PTB at 100 mM both at pH 9.2 and after adjustment to pH 7.0. Bactericidal activity was quantified and validated by counting fluorescently labeled live and dead bacterial cells using flow cytometry, and reconfirmed using qPCR with high-affinity photoreactive DNA binding dye propidium monoazide (PMA). The results of flow cytometry, qPCR, and culturing confirmed that bacterial cells were killed following exposure to PTB at 100 mM. Bacterial cell membranes were damaged following a 5-min treatment and extrusion of cytoplasmic material from bacterial cells was observed using electronic transmission microscopy. Soft rot incidence on inoculated tomato fruit was significantly reduced by dipping infected fruits in PTB at 100 mM for 5 min and no lesions developed following a 10-min treatment. PTB does not pose a hazard to human health and is an effective alternative to other bactericides and antibiotics for controlling soft rot disease of tomato caused by P. carotovorum.
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Affiliation(s)
| | | | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, HonoluluHI, United States
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Li X, Huang R, Chen H. Evaluation of Assays to Quantify Infectious Human Norovirus for Heat and High-Pressure Inactivation Studies Using Tulane Virus. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:314-325. [PMID: 28238030 DOI: 10.1007/s12560-017-9288-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/19/2017] [Indexed: 06/06/2023]
Abstract
We compared the heat and high hydrostatic pressure (HHP) inactivation results of Tulane virus (TV), a human norovirus (HuNoV) surrogate, obtained by plaque assay, direct quantitative reverse transcription PCR (RT-qPCR), porcine gastric mucin magnetic beads (PGM-MBs) binding assay followed by RT-qPCR (PGM/PCR), and propidium monoazide (PMA) assay followed by RT-qPCR (PMA/PCR). Heat and HHP inactivation of a HuNoV genotype I.1 (GI.1) strain and a genotype II.4 (GII.4) strain was also evaluated using those molecular assays. Viruses were heat treated at 50-90 °C for 2 min and HHP treated at 100-550 MPa at initial temperatures of 4 or 21 °C for 2 min. For heat treatment, the three molecular methods significantly underestimated the inactivation of TV. It could be logically concluded that the PGM/PCR assay was better than the PMA/PCR and direct RT-qPCR assays in estimating the inactivation of HuNoV GI.1. The three molecular methods were comparable in estimating the heat inactivation of GII.4. For HHP treatment, both PGM/PCR and PMA/PCR assays were able to estimate inactivation of TV at ≤~2-log reduction levels, but significantly underestimated its inactivation at >~2-log reduction levels. The direct RT-qPCR assay was the worst method for estimating HHP inactivation of TV. It could be logically concluded that the PGM/PCR and PMA/PCR assays were comparable in estimating the HHP inactivation of GI.1 and both were significantly better than the direct RT-qPCR assay. Among the three molecular methods, the PGM/PCR assay was the best in estimating the HHP inactivation of GII.4. These results demonstrated that the PGM/PCR assay was probably the method of choice in estimating the inactivation of HuNoV GI.1 and GII.4 for heat and HHP treatments, but this method would likely result in underestimation of HuNoV inactivation.
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Affiliation(s)
- Xinhui Li
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI, 54601, USA
| | - Runze Huang
- Department of Animal & Food Sciences, University of Delaware, Newark, DE, 19716-2150, USA
| | - Haiqiang Chen
- Department of Animal & Food Sciences, University of Delaware, Newark, DE, 19716-2150, USA.
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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Jeong MI, Park SY, Ha SD. Thermal inactivation of human norovirus on spinach using propidium or ethidium monoazide combined with real-time quantitative reverse transcription-polymerase chain reaction. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.02.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Huang X, Zhou X, He X, Wang P, Yue S, Wu L, Zhang Y, Xie Q, Zhang B, Zhao W. Detection of infectious dengue virus by selective real-time quantitative polymerase chain reaction. Virol Sin 2017; 31:342-5. [PMID: 27245449 DOI: 10.1007/s12250-016-3757-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Xin Huang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.,Second clinical medical college, Southern Medical University, Guangzhou, 510280, China
| | - Xuan Zhou
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyan He
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Pei Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Shuai Yue
- Second clinical medical college, Southern Medical University, Guangzhou, 510280, China
| | - Lixin Wu
- Second clinical medical college, Southern Medical University, Guangzhou, 510280, China
| | - Yu Zhang
- Second clinical medical college, Southern Medical University, Guangzhou, 510280, China
| | - Qian Xie
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Bao Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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50
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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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