51
|
Quantitative reverse transcription PCR to determine the inactivation of Human Rotavirus by chlorine. Int J Hyg Environ Health 2017; 220:719-725. [PMID: 28292642 DOI: 10.1016/j.ijheh.2017.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 02/25/2017] [Accepted: 02/25/2017] [Indexed: 11/22/2022]
Abstract
Human rotaviruses (HRVs) are the major cause of acute diarrhea in infants and young children. Here, a real-time reverse transcription polymerase chain reaction assay targeting the rotaviral VP4 gene (VP4-RT-qPCR) was established to evaluate the inactivation of HRV upon chlorine disinfection, based on a previous report that damage to the 1227-2354bp region of the VP4 gene was associated with eliminated HRV infectivity by chlorine. In this study, inactivation of HRV by 0.6mg/L free chlorine was assessed in phosphate buffered saline (PBS; pH 7.2), and tap and river water samples, using both TCID50 and RT-qPCR (VP2- and VP4-RT-qPCR) assays, respectively. Among the samples tested, the VP2-RT-qPCR method did not show significant inactivation after chlorine disinfection; however, the reduction in VP4-RT-qPCR signal was correlated with decreased HRV infectivity. Moreover, the higher sensitivity of the VP4-RT-qPCR assay allowed for assessment of chlorine HRV inactivation at longer exposure times compared with the conventional TCID50 assay. Collectively, these results indicated that the VP4-RT-qPCR assay is a rapid, sensitive, and reliable tool to detect infectious HRV following chlorine inactivation, and highlights the potential for further development of qPCR/RT-qPCR assays to provide information regarding viral infectivity from drinking water plants.
Collapse
|
52
|
Kobayashi N, Oshiki M, Ito T, Segawa T, Hatamoto M, Kato T, Yamaguchi T, Kubota K, Takahashi M, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Motoyama T, Araki N, Sano D. Removal of human pathogenic viruses in a down-flow hanging sponge (DHS) reactor treating municipal wastewater and health risks associated with utilization of the effluent for agricultural irrigation. WATER RESEARCH 2017; 110:389-398. [PMID: 28038763 DOI: 10.1016/j.watres.2016.10.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Abstract
A down-flow hanging sponge (DHS) reactor has been developed as a cost-effective wastewater treatment system that is adaptable to local conditions in low-income countries. A pilot-scale DHS reactor previously demonstrated stable reduction efficiencies for chemical oxygen demand (COD) and ammonium nitrogen over a year at ambient temperature, but the pathogen reduction efficiency of the DHS reactor has yet to be investigated. In the present study, the reduction efficiency of a pilot-scale DHS reactor fed with municipal wastewater was investigated for 10 types of human pathogenic viruses (norovirus GI, GII and GIV, aichivirus, astrovirus, enterovirus, hepatitis A and E viruses, rotavirus, and sapovirus). DHS influent and effluent were collected weekly or biweekly for 337 days, and concentrations of viral genomes were determined by microfluidic quantitative PCR. Aichivirus, norovirus GI and GII, enterovirus, and sapovirus were frequently detected in DHS influent, and the log10 reduction (LR) of these viruses ranged from 1.5 to 3.7. The LR values for aichivirus and norovirus GII were also calculated using a Bayesian estimation model, and the average LR (±standard deviation) values for aichivirus and norovirus GII were estimated to be 1.4 (±1.5) and 1.8 (±2.5), respectively. Quantitative microbial risk assessment was conducted to calculate a threshold reduction level for norovirus GII that would be required for the use of DHS effluent for agricultural irrigation, and it was found that LRs of 2.6 and 3.7 for norovirus GII in the DHS effluent were required in order to not exceed the tolerable burden of disease at 10-4 and 10-6 disability-adjusted life years loss per person per year, respectively, for 95% of the exposed population during wastewater reuse for irrigation.
Collapse
Affiliation(s)
- Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan.
| | - Toshihiro Ito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| | - Takahiro Segawa
- Transdisciplinary Research Integration Center, 4-3-13 Toranomon, Minato-ku, Tokyo, Japan; Transdisciplinary Research Integration Center, National Institute of Polar Research, Japan
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Tsuyoshi Kato
- Department of Computer Science, Gunma University, 3-39-22 Syowamachi, Maebashi, Gunma, 371-8511, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Masanobu Takahashi
- New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 265-1 Higashiyama, Akiba-ku, Niigata, 956-0841, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Kagawa College, 355 Chokushicho, Takamatsu, Kagawa, 761-8058, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Kisarazu College, 2-11-1 Kiyomidaihigashi, Kisarazu, Chiba, 292-0041, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Kisarazu College, 2-11-1 Kiyomidaihigashi, Kisarazu, Chiba, 292-0041, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Toshiki Motoyama
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Daisuke Sano
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West-8, Sapporo, Hokkaido, 060-8628, Japan
| |
Collapse
|
53
|
Abstract
Noroviruses are the leading cause of acute gastroenteritis around the world. An individual living in the United States is estimated to develop norovirus infection five times in his or her lifetime. Despite this, there is currently no antiviral or vaccine to combat the infection, in large part because of the historical lack of cell culture and small animal models. However, the last few years of norovirus research were marked by a number of ground-breaking advances that have overcome technical barriers and uncovered novel aspects of norovirus biology. Foremost among them was the development of two different
in vitro culture systems for human noroviruses. Underappreciated was the notion that noroviruses infect cells of the immune system as well as epithelial cells within the gastrointestinal tract and that human norovirus infection of enterocytes requires or is promoted by the presence of bile acids. Furthermore, two proteinaceous receptors are now recognized for murine norovirus, marking the first discovery of a functional receptor for any norovirus. Recent work further points to a role for certain bacteria, including those found in the gut microbiome, as potential modulators of norovirus infection in the host, emphasizing the importance of interactions with organisms from other kingdoms of life for viral pathogenesis. Lastly, we will highlight the adaptation of drop-based microfluidics to norovirus research, as this technology has the potential to reveal novel insights into virus evolution. This review aims to summarize these new findings while also including possible future directions.
Collapse
Affiliation(s)
- Eric Bartnicki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Juliana Bragazzi Cunha
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| |
Collapse
|
54
|
Farkas K, Hassard F, McDonald JE, Malham SK, Jones DL. Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment. Front Microbiol 2017; 8:53. [PMID: 28174565 PMCID: PMC5258707 DOI: 10.3389/fmicb.2017.00053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/09/2017] [Indexed: 11/24/2022] Open
Abstract
The accurate detection of pathogens in environmental matrices, such as sediment, is critical in understanding pathogen fate and behavior in the environment. In this study, we assessed the usefulness of methods for the detection and quantification of Vibrio spp. and norovirus (NoV) nucleic acids in sediment. For bacteria, a commonly used direct method using hexadecyltrimethylammonium bromide (CTAB) and phenol-chloroform-isoamyl alcohol (PCI) extraction was optimized, whereas for NoV, direct and indirect (virus elution-concentration) methods were evaluated. For quantification, commercially available quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR) kits were tested alongside a digital PCR (dPCR) approach. CTAB-based extraction combined with 16 h polyethylene glycol 6000 (PEG6000) precipitation was found to be suitable for the direct extraction of high abundance bacterial and viral nucleic acids. For the indirect extraction of viral RNA, beef extract-based elution followed by PEG6000 precipitation and extraction using the NucliSENS® MiniMag® Nucleic Acid Purification System and the PowerViral® Environmental RNA/DNA Isolation Kit and qRT-PCR resulted in 83-112 and 63-69% recoveries of NoV, respectively. dPCR resulted in lower viral recoveries (47 and 9%) and ~4 orders of magnitude lower Vibrio concentrations (3.6-4.6 log10 gc/100 g sediment) than was observed using qPCR. The use of internal controls during viral quantification revealed that the RT step was more affected by inhibitors than the amplification. The methods described here are suitable for the enumeration of viral and/or bacterial pathogens in sediment, however the use of internal controls to assess efficiency is recommended.
Collapse
Affiliation(s)
- Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, Wales
| | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, Wales
| |
Collapse
|
55
|
Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
Collapse
Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
| |
Collapse
|
56
|
Chun CL, Peller JR, Shively D, Byappanahalli MN, Whitman RL, Staley C, Zhang Q, Ishii S, Sadowsky MJ. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 574:872-880. [PMID: 27665447 DOI: 10.1016/j.scitotenv.2016.09.107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.
Collapse
Affiliation(s)
- Chan Lan Chun
- Department of Civil Engineering, University of Minnesota Duluth, Duluth, MN 55812, United States; Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, United States
| | - Julie R Peller
- Department of Chemistry, Valparaiso University, Valparaiso, IN 46383, United States
| | - Dawn Shively
- Lake Michigan Ecological Research Station, U.S. Geological Survey, Chesterton, IN 46304, United States
| | | | - Richard L Whitman
- Lake Michigan Ecological Research Station, U.S. Geological Survey, Chesterton, IN 46304, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN 55108, United States
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN 55108, United States.
| |
Collapse
|
57
|
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
|
58
|
Zhang Q, Eichmiller JJ, Staley C, Sadowsky MJ, Ishii S. Correlations between pathogen concentration and fecal indicator marker genes in beach environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 573:826-830. [PMID: 27595940 DOI: 10.1016/j.scitotenv.2016.08.122] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
The concentrations of several potential pathogens were measured using a microfluidic quantitative PCR (MFQPCR) platform in beach water, sand, and sediment samples collected in Duluth, MN. Among the 19 pathogen marker genes examined, eaeA from Escherichia coli and plc from Clostridium perfringens were most frequently detected in all samples. In beach water and wastewater samples, positive correlations were observed between quantities of potential pathogens and most of the fecal indicator genetic markers. Such correlations, however, were not frequently observed in sand and sediment samples. Our results suggest that the behavior of potential pathogens and FIB may vary by sample type and source of contamination. Consequently, appropriate FIB marker genes need to be chosen for reliable water/sand quality monitoring.
Collapse
Affiliation(s)
- Qian Zhang
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, United States
| | - Jessica J Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, 135 Skok Hall, 2003 Upper Buford Cir, Saint Paul, MN 55108, United States
| | - Christopher Staley
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, United States
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, United States; Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, United States
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, United States; Department of Soil, Water, and Climate, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, United States.
| |
Collapse
|
59
|
Wang HB, Mo QH, Wang Q, Wu BM, Feng ZL, Lin JC, Yang Z. Probe-free and sensitive detection of diarrhea-causing pathogens using RT-PCR combined high resolution melting analysis. Biologicals 2016; 44:360-6. [DOI: 10.1016/j.biologicals.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 11/29/2022] Open
|
60
|
Miura T, Lhomme S, Le Saux JC, Le Mehaute P, Guillois Y, Couturier E, Izopet J, Abranavel F, Le Guyader FS. Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:194-9. [PMID: 27165600 DOI: 10.1007/s12560-016-9241-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/28/2016] [Indexed: 05/18/2023]
Abstract
A hepatitis E outbreak, which occurred on a small isolated island, provided an opportunity to evaluate the association between the number of hepatitis E cases in the community and the concentration of virus detected in sewage. Samples were collected from the different sewage treatment plants from the island and analyzed for the presence of hepatitis E (HEV) virus using real-time RT-PCR. We demonstrated that if 1-4 % of inhabitants connected to a WWTP were infected with HEV, raw sewage contained HEV at detectable levels. The finding that such a small number of infected people can contaminate municipal sewage works raises the potential of the further distribution of the virus. Indeed, investigating the routes of transmission of HEV, including the potential for sewage effluent to contain infectious HEV, may help us to better understand the epidemiology of this pathogen, which is considered to be an emerging concern in Europe.
Collapse
Affiliation(s)
- Takayuki Miura
- Laboratoire de Microbiologie, LSEM-SG2M, IFREMER, BP 21105, 44311, Nantes Cedex 03, France
- New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-04 Aoba, Aramaki, Aoba-Ku, Sendai, 980-8579, Japan
| | - Sébastien Lhomme
- National Reference Center for HEV, Centre Hospitalier Universitaire, Toulouse, France
| | - Jean-Claude Le Saux
- Laboratoire de Microbiologie, LSEM-SG2M, IFREMER, BP 21105, 44311, Nantes Cedex 03, France
| | | | - Yvonnick Guillois
- Regional Epidemiology Unit for the Brittany region, Institut de veille sanitaire, Rennes, France
| | - Elizabeth Couturier
- Department of Infectious Diseases, Institut de Veille Sanitaire, Saint-Maurice, France
| | - Jacques Izopet
- National Reference Center for HEV, Centre Hospitalier Universitaire, Toulouse, France
| | - Florence Abranavel
- National Reference Center for HEV, Centre Hospitalier Universitaire, Toulouse, France
| | - Françoise S Le Guyader
- Laboratoire de Microbiologie, LSEM-SG2M, IFREMER, BP 21105, 44311, Nantes Cedex 03, France.
| |
Collapse
|
61
|
Sano D, Amarasiri M, Hata A, Watanabe T, Katayama H. Risk management of viral infectious diseases in wastewater reclamation and reuse: Review. ENVIRONMENT INTERNATIONAL 2016; 91:220-9. [PMID: 26985655 PMCID: PMC7111293 DOI: 10.1016/j.envint.2016.03.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/04/2016] [Accepted: 03/05/2016] [Indexed: 05/18/2023]
Abstract
Inappropriate usage of reclaimed wastewater has caused outbreaks of viral infectious diseases worldwide. International and domestic guidelines for wastewater reuse stipulate that virus infection risks are to be regulated by the multiple-barrier system, in which a wastewater treatment process composed of sequential treatment units is designed based on the pre-determined virus removal efficiency of each unit. The objectives of this review were to calculate representative values of virus removal efficiency in wastewater treatment units based on published datasets, and to identify research topics that should be further addressed for improving implementation of the multiple-barrier system. The removal efficiencies of human noroviruses, rotaviruses and enteroviruses in membrane bioreactor (MBR) and conventional activated sludge (CAS) processes were obtained by a systematic review protocol and a meta-analysis approach. The log10 reduction (LR) of norovirus GII and enterovirus in MBR were 3.35 (95% confidence interval: 2.39, 4.30) and 2.71 (1.52, 3.89), respectively. The LR values of rotavirus, norovirus GI and GII in CAS processes were 0.87 (0.20, 1.53), 1.48 (0.96, 2.00) and 1.35 (0.52, 2.18), respectively. The systematic review process eliminated a substantial number of articles about virus removal in wastewater treatment because of the lack of information required for the meta-analysis. It is recommended that future publications should explicitly describe their treatment of left-censored datasets. Indicators, surrogates and methodologies appropriate for validating virus removal performance during daily operation of wastewater reclamation systems also need to be identified.
Collapse
Affiliation(s)
- Daisuke Sano
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Mohan Amarasiri
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Toru Watanabe
- Department of Food, Life and Environmental Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka, Yamagata 997-8555, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan
| |
Collapse
|
62
|
Abstract
Among the wide variety of viral agents liable to be found as food contaminants, noroviruses and hepatitis A virus are responsible for most well characterized foodborne virus outbreaks. Additionally, hepatitis E virus has emerged as a potential zoonotic threat. Molecular methods, including an ISO standard, are available for norovirus and hepatitis A virus detection in foodstuffs, although the significance of genome copy detection with regard to the associated health risk is yet to be determined through viability assays. More precise and rapid methods for early foodborne outbreak investigation are being developed and they will need to be validated versus the ISO standard. In addition, protocols for next-generation sequencing characterization of outbreak-related samples must be developed, harmonized and validated as well.
Collapse
Affiliation(s)
- Albert Bosch
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
| | - Rosa M Pintó
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
| | - Susana Guix
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
| |
Collapse
|
63
|
Kato T, Kobayashi A, Ito T, Miura T, Ishii S, Okabe S, Sano D. Estimation of concentration ratio of indicator to pathogen-related gene in environmental water based on left-censored data. JOURNAL OF WATER AND HEALTH 2016; 14:14-25. [PMID: 26837826 DOI: 10.2166/wh.2015.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A stochastic model for estimating the ratio between a fecal indicator and a pathogen based on left-censored data, which includes a substantially high number of non-detects, was constructed. River water samples were taken for 16 months at six points in a river watershed, and conventional fecal indicators (total coliforms and general Escherichia coli), genetic markers (Bacteroides spp.), and virulence genes (eaeA of enteropathogenic E. coli and ciaB of Campylobacter jejuni) were quantified. The quantification of general E. coli failed to predict the presence of the virulence gene from enteropathogenic E. coli, different from what happened with genetic markers (Total Bac and Human Bac). A Bayesian model that was adapted to left-censored data with a varying analytical quantification limit was applied to the quantitative data, and the posterior predictive distributions of the concentration ratio were predicted. When the sample size was 144, simulations conducted in this study suggested that 39 detects were enough to accurately estimate the distribution of the concentration ratio, when combined with a dataset with a positive rate higher than 99%. To evaluate the level of accuracy in the estimation, it is desirable to perform a simulation using an artificially generated left-censored dataset that has the identical number of non-detects as the actual data.
Collapse
Affiliation(s)
- Tsuyoshi Kato
- Department of Computer Science, Graduate School of Engineering, Gunma University, Tenjinmachi 1-5-1, Kiryu, Gunma 376-8515, Japan
| | - Ayano Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| | - Toshihiro Ito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| | - Takayuki Miura
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| | - Satoshi Ishii
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| | - Daisuke Sano
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan E-mail:
| |
Collapse
|
64
|
Coudray-Meunier C, Fraisse A, Martin-Latil S, Delannoy S, Fach P, Perelle S. A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System. PLoS One 2016; 11:e0147832. [PMID: 26824897 PMCID: PMC4732599 DOI: 10.1371/journal.pone.0147832] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/08/2016] [Indexed: 12/23/2022] Open
Abstract
Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health.
Collapse
Affiliation(s)
- Coralie Coudray-Meunier
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
- * E-mail:
| |
Collapse
|
65
|
Ramírez-Castillo FY, Loera-Muro A, Jacques M, Garneau P, Avelar-González FJ, Harel J, Guerrero-Barrera AL. Waterborne pathogens: detection methods and challenges. Pathogens 2015; 4:307-34. [PMID: 26011827 PMCID: PMC4493476 DOI: 10.3390/pathogens4020307] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 12/13/2022] Open
Abstract
Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.
Collapse
Affiliation(s)
- Flor Yazmín Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Abraham Loera-Muro
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Mario Jacques
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Philippe Garneau
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Francisco Javier Avelar-González
- Laboratorio de Ciencias Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| | - Josée Harel
- Centre de Recherche en Infectiologie Porcine et Avicole, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC J2S 7C6, Canada.
| | - Alma Lilián Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes 20131, Mexico.
| |
Collapse
|