1
|
Capela N, Xu M, Simões S, Azevedo-Pereira HMSV, Peters J, Sousa JP. Exposure and risk assessment of acetamiprid in honey bee colonies under a real exposure scenario in Eucalyptus sp. landscapes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156485. [PMID: 35688249 PMCID: PMC9247745 DOI: 10.1016/j.scitotenv.2022.156485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Honey bee colonies have shown abnormal mortality rates over the last decades. Colonies are exposed to biotic and abiotic stressors including landscape changes caused by human pressure. Modern agriculture and even forestry, rely on pesticide inputs and these chemicals have been indicated as one of the major causes for colony losses. Neonicotinoids are a common class of pesticides used worldwide that are specific to kill insect pests, with acetamiprid being the only neonicotinoid allowed to be applied outdoors in the EU. To evaluate honeybees' exposure to acetamiprid under field conditions as well as to test the use of in-situ tools to monitor pesticide residues, two honeybee colonies were installed in five Eucalyptus sp. plantations having different area where Epik® (active substance: acetamiprid) was applied as in a common spraying event to control the eucalyptus weevil pest. Flowers, fresh nectar, honey bees and colony products samples were collected and analyzed for the presence of acetamiprid residues. Our main findings were that (1) acetamiprid residues were found in samples collected outside the spraying area, (2) the amount of residues transported into the colonies increased with the size of the sprayed area, (3) according to the calculated Exposure to Toxicity Ratio (ETR) values, spraying up to 22 % of honeybees foraging area does not harm the colonies, (4) colony products can be used as a valid tool to monitor colony accumulation of acetamiprid and (5) the use of Lateral Flow Devices (LFDs) can be a cheap, fast and easy tool to apply in the field, to evaluate the presence of acetamiprid residues in the landscape and colony products.
Collapse
Affiliation(s)
- Nuno Capela
- Centre for Functional Ecology, Department of Life Sciences, Associated Laboratory TERRA, University of Coimbra, Portugal.
| | - Mang Xu
- Wageningen Food safety Research, Wageningen, the Netherlands
| | - Sandra Simões
- Centre for Functional Ecology, Department of Life Sciences, Associated Laboratory TERRA, University of Coimbra, Portugal
| | - Henrique M S V Azevedo-Pereira
- Centre for Functional Ecology, Department of Life Sciences, Associated Laboratory TERRA, University of Coimbra, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Jeroen Peters
- Wageningen Food safety Research, Wageningen, the Netherlands
| | - José Paulo Sousa
- Centre for Functional Ecology, Department of Life Sciences, Associated Laboratory TERRA, University of Coimbra, Portugal
| |
Collapse
|
2
|
Hao X, Chen J, Xu M, Zheng H, Li X, Wang M, Liu T. Separation and purification of enveloped and non-enveloped viruses from water samples using an aqueous two-phase system. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
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]
|
4
|
Kumar M, Kuroda K, Barcelo D, Furumai H. Monsoon dilutes the concurrence but increases the correlation of viruses and Pharmaceuticals and Personal Care Products (PPCPs) in the urban waters of Guwahati, India: The context of pandemic viruses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152282. [PMID: 34902398 DOI: 10.1016/j.scitotenv.2021.152282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/18/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Concurrence of pharmaceuticals and personal care products (PPCPs), pathogenic viruses, metals and microbial pollution along with their seasonal variations in the water environment are overarching in the context of existing pandemic, especially for tropical countries. The present study focuses on the seasonal influence on the vulnerability of urban water in Guwahati, the largest city in North-eastern India, through examining the concurrence of seven PPCPs, five viruses, faecal bacteria and nine metals in surface waters during monsoon (Summer-July 2017) and pre-monsoon (Winter-March 2018). Surface water sampling was carried out at different locations of the Brahmaputra River, its tributary Bharalu River (an unlined urban drain), and Dipor Bill Lake (Ramsar-recognized wetland). Both PPCPs and viruses were at high concentrations (e.g. up to 970 ng L-1 caffeine, 2.5 × 103 copies mL-1 pepper mild mottle virus (PMMoV)) at the confluence points of urban drains and the river, while they were mostly undetectable at both upstream and downstream locations, implying strong self-purification ability of the river. All the analysed PPCPs and viruses were at much higher concentrations during pre-monsoon i.e., winter than during monsoon, implying heavy dilution and temperature effect during the monsoon. Overall, PPCPs and viruses were more correlated in monsoon but the risk quotient in the urban tributary was higher in pre-monsoon (e.g. 5061 in pre-monsoon and 1515 in monsoon for caffeine). PMMoV was found to be an excellent faecal pollution indicator due to its prevalence, detectability and specificity in all seasons. Overall, the seasonal fluctuations of the non-enveloped viruses monitored in this study is likely to be relevant for SARS-CoV-2. We contribute to address the literature scarcity pertaining to seasonal variations in the prevalence of viruses and their concurrences with contaminants of emerging concern.
Collapse
Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India.
| | - Keisuke Kuroda
- Department of Environmental and Civil Engineering, Toyama Prefectural University, Imizu 939-0398, Japan
| | - Damia Barcelo
- Catalan Institute for Water Research (OCRA-CERCA), Carrer Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain; Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| |
Collapse
|
5
|
Hrdy J, Vasickova P, Nesvadbova M, Novotny J, Mati T, Kralik P. MOL-PCR and xMAP Technology: A Multiplex System for Fast Detection of Food- and Waterborne Viruses. J Mol Diagn 2021; 23:765-776. [PMID: 33864939 DOI: 10.1016/j.jmoldx.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 100 (AdV, HEV, and RVA) and 5 × 101 (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.
Collapse
Affiliation(s)
- Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Petra Vasickova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic
| | - Michaela Nesvadbova
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiri Novotny
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Tomas Mati
- Military Veterinary Institute, Hlucin, Czech Republic
| | - Petr Kralik
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| |
Collapse
|
6
|
Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
Collapse
Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| |
Collapse
|
7
|
Ashby M, Rajko-Nenow P, Batten C, Flannery J. Simultaneous Detection of Bluetongue Virus Serotypes Using xMAP Technology. Microorganisms 2020; 8:microorganisms8101564. [PMID: 33050655 PMCID: PMC7650804 DOI: 10.3390/microorganisms8101564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
Bluetongue is an economically important disease of ruminants caused by the bluetongue virus (BTV). BTV is serologically diverse, which complicates vaccination strategies. Rapid identification of the causative BTV serotypes is critical, however, real-time PCR (RT-qPCR) can be costly and time consuming to perform when the circulating serotypes are unknown. The Luminex xMAP technology is a high-throughput platform that uses fluorescent beads to detect multiple targets simultaneously. We utilized existing BTV serotyping RT-qPCR assays for BTV-1 to BTV-24 and adapted them for use with the xMAP platform. The xMAP assay specifically detected all 24 BTV serotypes when testing reference strains. In all BTV-positive samples, the sensitivity of the BTV xMAP was 87.55% whereas the sensitivity of the serotype-specific RT-qPCR was 79.85%. The BTV xMAP assay allowed for the specific detection of BTV serotypes 1-24 at a lower cost than current RT-qPCR assays. Overall, the assay provides a useful novel diagnostic tool, particularly when analyzing large sample sets. The use of the BTV xMAP assay will allow for the rapid assessment of BTV epidemiology and may inform decision-making related to control and prevention measures.
Collapse
|
8
|
Kumar M, Ram B, Honda R, Poopipattana C, Canh VD, Chaminda T, Furumai H. Concurrence of antibiotic resistant bacteria (ARB), viruses, pharmaceuticals and personal care products (PPCPs) in ambient waters of Guwahati, India: Urban vulnerability and resilience perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133640. [PMID: 31377355 DOI: 10.1016/j.scitotenv.2019.133640] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/26/2019] [Indexed: 05/28/2023]
Abstract
Multi-drug resistant microbes, pathogenic viruses, metals, and pharmaceuticals and personal care products (PPCPs) in water has become the crux of urban sustainability issues. However, vulnerability due to pollutant concurrences, source apportionment, and identification of better faecal indicators needs to be better understood. The present study focuses on the vulnerability of urban Guwahati, the largest city in Northeastern India, through analyzing the concurrence of PPCPs, enteric viruses, antibiotic resistant bacteria, metal, and faecal contamination in water. The study strives to identify a relevant marker of anthropogenic pollution for the Indian scenario. Samples from the Brahmaputra River (n = 4), tributary Bharalu River (an unlined urban drain; n = 3), and Ramsar recognized Lake (Dipor Bil; n = 1) indicate caffeine > acetaminophen > theophylline > carbamazepine > crotamiton for PPCPs and pepper mild mottle virus (PMMoV) > aichi > hepatitis A > norovirus GII > norovirus GI for enteric viruses. PMMoV was the better indicator of faecal pollution due to its prevalence, specificity and ease of detection. Antibiotic resistance was neither correlated with the prevalence of PPCPs nor E. coli. As, Co and Mn appear to be inducing antibiotic resistance in E. coli. While the risk quotient of the urban drain (Bharalu River) indicates one order higher magnitude than reported for other Indian rivers, the Lake exhibited the least pollution and better resilience. The concurrence of pollutants and multi-drug resistant E. coli, owing to the complete absence of wastewater treatment, puts the city in a highly vulnerable state. Pollution is being regulated only by the dilution capability of the Brahmaputra River, which needs to be further researched for seasonal variation.
Collapse
Affiliation(s)
- Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gujarat, India.
| | - Bhagwana Ram
- Discipline of Civil Engineering, Indian Institute of Technology Gandhinagar, Gujarat, India
| | - Ryo Honda
- Faculty of Environmental Design, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | | | - Vu Duc Canh
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| | - Tushara Chaminda
- Department of Civil and Environmental Engineering, University of Ruhuna, Sri Lanka
| | - Hiroaki Furumai
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
9
|
Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
Collapse
Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| |
Collapse
|
10
|
A novel multiplex xMAP assay for generic detection of avian, fish, and ruminant DNA in feed and feedstuffs. Appl Microbiol Biotechnol 2019; 103:4575-4584. [PMID: 31001745 DOI: 10.1007/s00253-019-09833-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/30/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
Abstract
The identification of animal species in feed and feedstuffs is important for detecting contamination and fraudulent replacement of animal components that might cause health and economic problems. A novel multiplex assay, based on xMAP technology and the generic detection of closely related species, was developed for the simultaneous differential detection of avian, fish, and ruminant DNA in products. Universal primers and probes specific to avian, fish, or ruminant species were designed to target a conserved mitochondrial DNA sequence in the 12S ribosomal RNA gene (rRNA). The assay specificity was validated using samples of 27 target and 10 nontarget animal species. The limits of detection of the purified DNA were determined to be 0.2 pg/μL-0.1 ng/μL by testing the meat samples of six species and four feedstuffs. The detection sensitivity of the experimental mixtures was demonstrated to be 0.01% (weight percentage). The assay's suitability for practical application was evaluated by testing feed samples; unlabeled animal ingredients were detected in 32% of the 56 samples. The assay differentially detected the three targeted categories of animal species in less than 2 h, reflecting improvements in speed and efficiency. Based on these results, this novel multiplex xMAP assay provides a reliable and highly efficient technology for the routine detection of animal species in feed and other products for which this information is needed.
Collapse
|
11
|
Tatte VS, Gopalkrishna V. Detection of different enteric viruses in children with diarrheal disease: evidence of the high frequency of mixed infections. Access Microbiol 2019; 1:e000010. [PMID: 32974508 PMCID: PMC7470349 DOI: 10.1099/acmi.0.000010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 01/19/2023] Open
Abstract
Enteric viruses play a major role in causing diarrhea in children. Early identification of the causative pathogen is still a challenge in the clinical laboratory. A multiplex PCR assay is a useful tool to screen a large number of clinical samples especially in an outbreak situation. In this study, a multiplex reverse transcription (RT)-PCR assay was developed to detect nine enteric viruses such as group A rotavirus, norovirus GGII, sapovirus, adenovirus, astrovirus, aichivirus, parechovirus, bocavirus and enterovirus in clinical samples of diarrheal cases. Stool samples (n=185) collected from infants and children with acute gastroenteritis cases in Pune, western India were analysed for nine different enteric viruses by currently developed multiplex RT- PCR. Predominance of group A rotavirus (76%) followed by enterovirus (11.5%), astrovirus (4.5%), adenovirus (2.7%) and norovirus GII (1.6%) was observed. A total of 44.8 % (82/185) samples analysed by this method showed high frequency of mixed infections. These results highlighted high prevalence and diversity of different enteric viruses in children. The multiplex PCR showed good concordance with monoplex RT-PCR for detection of these enteric viruses in clinical samples. This is the first report on the development of a multiplex RT-PCR assay for detection of multiple enteric viruses in diarrheal diseases from India.
Collapse
Affiliation(s)
- Vaishali S Tatte
- Enteric Viruses Group, National Institute of Virology, Pune, India
| | | |
Collapse
|
12
|
Ahmed W, Zhang Q, Kozak S, Beale D, Gyawali P, Sadowsky MJ, Simpson S. Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region. WATER RESEARCH 2019; 149:511-521. [PMID: 30500686 DOI: 10.1016/j.watres.2018.10.088] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 05/26/2023]
Abstract
There is a growing move towards using the quantitative polymerase chain (qPCR)-based sewage-associated marker genes to assess surface water quality. However, a lack of understanding about the persistence of many sewage-associated markers creates uncertainty for those tasked with investigating microbial water quality. In this study, we investigated the decay of two qPCR FIB [E. coli (EC), and Enterococcus spp. (ENT) 23S rRNA genes] and four sewage-associated microbial source tracking (MST) marker genes [human Bacteroides HF183 16S rRNA, adenovirus (HAdV), and polyomavirus (HPyV), and crAssphage, a recently described bacteriophage in feces], in outdoor mesocosms containing fresh and marine waters and their corresponding sediments. Decay rates of EC 23S rRNA, ENT 23S rRNA, and HF183 16S rRNA were significantly (p < 0.05) faster than the HAdV, HPyV and crAssphage markers in water samples from all mesocosms. In general, decay rates of bacterial targets were similar in the water columns of the studied mesocosms. Similarly, decay rates of viral targets were also alike in mesocosm water columns in relation to each other. The decay rates of FIB and sewage-associated markers were significantly faster in water samples compared to sediments in all three mesocosms. In the event of resuspension, FIB and marker genes from sediments can potentially recontaminate overlying waters. Thus, care should be taken when interpreting the occurrence of FIB and sewage-associated MST markers in water, which may have originated from sediments. The differential decay of these targets may also influence health outcomes and need to be considered in risk assessment models.
Collapse
Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld, 4102, Australia.
| | - Qian Zhang
- BioTechnology Institute, Departments of Soil, Water & Climate, and Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sonya Kozak
- School of Medicine, Griffith University, Gold Coast, Australia
| | - David Beale
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld, 4102, Australia
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd., Kenepuru Science Center, Porirura, 5240, New Zealand
| | - Michael J Sadowsky
- BioTechnology Institute, Departments of Soil, Water & Climate, and Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Stuart Simpson
- CSIRO Land and Water, Lucas Heights, NSW, 2234, Australia
| |
Collapse
|
13
|
Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
Collapse
Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
| |
Collapse
|
14
|
Mackowiak M, Leifels M, Hamza IA, Jurzik L, Wingender J. Distribution of Escherichia coli, coliphages and enteric viruses in water, epilithic biofilms and sediments of an urban river in Germany. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:650-659. [PMID: 29358142 DOI: 10.1016/j.scitotenv.2018.01.114] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 05/21/2023]
Abstract
Fecal contamination of surface water is commonly evaluated by quantification of bacterial or viral indicators such as Escherichia coli and coliphages, or by direct testing for pathogens such as enteric viruses. Retention of fecally derived organisms in biofilms and sediments is less frequently considered. In this study, we assessed the distribution of E. coli, somatic coliphages, and enteric viruses including human adenovirus (HAdV), enterovirus (EV), norovirus genogroup GII (NoV GII) and group A rotavirus (RoV) in an urban river environment in Germany. 24 samples each of water, epilithic biofilms and sediments were examined. E. coli and somatic coliphages were prevalent not only in the flowing water, but also in epilithic biofilms and sediments, where they were accumulated compared to the overlying water. During enhanced rainfall, E. coli and coliphage concentrations increased by approximately 2.5 and 1 log unit, respectively, in the flowing water, whereas concentrations did not change significantly in epilithic biofilms and sediments. The occurrence of human enteric viruses detected by qPCR was higher in water than in biofilms and sediments. 87.5% of all water samples were positive for HAdV. Enteric viruses found less frequently were EV, RoV and NoV GII in 20.8%, 16.7% and 8.3% of the water samples, respectively. In epilithic biofilms and sediments, HAdV was found in 54.2% and 50.0% of the samples, respectively, and EV was found in 4.2% of both biofilm and sediment samples. RoV and NoV GII were not detected in any of the biofilms and sediments. Overall, the prevalence of enteric viruses was in the order of HAdV > EV > RoV ≥ NoV GII. In conclusion, epilithic biofilms and sediments can be reservoirs for fecal indicators and enteric viruses and thus should be taken into consideration when assessing microbial pollution of surface water environments.
Collapse
Affiliation(s)
- Martin Mackowiak
- University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Aquatic Microbiology, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
| | - Mats Leifels
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Ibrahim Ahmed Hamza
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany
| | - Lars Jurzik
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Jost Wingender
- University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Aquatic Microbiology, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
15
|
Hamza H, Hamza IA. Oncogenic papillomavirus and polyomavirus in urban sewage in Egypt. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:1413-1420. [PMID: 28854484 DOI: 10.1016/j.scitotenv.2017.08.218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 05/23/2023]
Abstract
Recently, the occurrence of oncogenic viruses in contaminated water and their potential for waterborne transmission has been reported. We addressed an environmental surveillance of both HPyVs (JCPyV and BKPyV) and HPVs in three wastewater treatment plants in Egypt. A high level of dissemination was found for both viruses. HPyVs (JCPyV and BKPyV) were found in ~73% of examined samples, while HPVs were detected in 30.5%. Sequence analysis of HPV positive samples revealed a wide variety of circulating genotypes representing both anogenital (HPV-6, HPV-16, HPV-53, HPV-44, HPV-31, HPV-43) and cutaneous (HPV-37, HPV-21, HPV-120, HPV-111, HPV-5) types. In addition, two unclassified sequences were identified, suggesting putative types. The median concentrations of HPyVs in inflow samples were 3.03×1005, 3.9×1005, and 1.44×1005GC/l in the three WWTPs, respectively. Whereas, the viral concentration in outflow reduced by one order of magnitude in WWTP-A and WWTP-C and two orders of magnitude in WWTP-B. On the other hand, the mean concentration of the quantified HPVs positive samples was 1.68×1003GC/l for inflow and a quite similar pattern in the outflow as well. These data provide an evidence about the actual circulation pattern of both viruses in the population. Also, the high abundance of HPyVs supports its potential as a possible fecal indicator. However, further investigations are required for both viruses to elucidate the potential health risk via contaminated water.
Collapse
Affiliation(s)
- Hazem Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt; Department of Hygiene, Social- and Environmental Medicine, Ruhr-University Bochum, Germany
| | - Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| |
Collapse
|
16
|
Detection of biomarkers of acute myocardial infarction by high-throughput suspension array technology in serum sample. Bioanalysis 2018; 10:47-58. [PMID: 29239660 DOI: 10.4155/bio-2017-0188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: In order to assist and support early diagnosis of acute myocardial infarction (AMI), suspension array technology was established for multiplexed, rapid and accurate measurement of AMI biomarkers in serum samples. Methodology & results: It was developed by coating AMI biomarkers on distinguishable microbeads and competing with free biomarkers for complementary antibodies. The limits of detection of three AMI biomarkers were 2.5- to 50-times lower than that of the previous methods and the working ranges were four to five orders of magnitude. Accuracy and stability also met satisfying acceptance criteria in both of the intra- and interbatch testing. The variation coefficients and relative standard deviations were all less than 10%. Conclusion: Suspension array technology is completely applicable for requirements of rapid clinical diagnosis in serum sample.
Collapse
|
17
|
Shukla S, Cho H, Kwon OJ, Chung SH, Kim M. Prevalence and evaluation strategies for viral contamination in food products: Risk to human health-a review. Crit Rev Food Sci Nutr 2017; 58:405-419. [PMID: 27245816 DOI: 10.1080/10408398.2016.1182891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nowadays, viruses of foodborne origin such as norovirus and hepatitis A are considered major causes of foodborne gastrointestinal illness with widespread distribution worldwide. A number of foodborne outbreaks associated with food products of animal and non-animal origins, which often involve multiple cases of variety of food streams, have been reported. Although several viruses, including rotavirus, adenovirus, astrovirus, parvovirus, and other enteroviruses, significantly contribute to incidence of gastrointestinal diseases, systematic information on the role of food in transmitting such viruses is limited. Most of the outbreak cases caused by infected food handlers were the source of 53% of total outbreaks. Therefore, prevention and hygiene measures to reduce the frequency of foodborne virus outbreaks should focus on food workers and production site of food products. Pivotal strategies, such as proper investigation, surveillance, and reports on foodborne viral illnesses, are needed in order to develop more accurate measures to detect the presence and pathogenesis of viral infection with detailed descriptions. Moreover, molecular epidemiology and surveillance of food samples may help analysis of public health hazards associated with exposure to foodborne viruses. In this present review, we discuss different aspects of foodborne viral contamination and its impact on human health. This review also aims to improve understanding of foodborne viral infections as major causes of human illness as well as provide descriptions of their control and prevention strategies and rapid detection by advanced molecular techniques. Further, a brief description of methods available for the detection of viruses in food and related matrices is provided.
Collapse
Affiliation(s)
- Shruti Shukla
- a Department of Food Science and Technology , Yeungnam University , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea.,b Department of Energy and Materials Engineering , Dongguk University , Seoul , Republic of Korea
| | - Hyunjeong Cho
- c Experiment and Research Institute, National Agricultural Products Quality Management Service , Gimcheon-si , Gyeongsangbuk-do , Republic of Korea
| | - O Jun Kwon
- d Evaluation Team, Gyeongbuk Institute for Regional Program Evaluation , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea
| | - Soo Hyun Chung
- e Department of Integrated Biomedical and Life Science , Korea University , Seoul , Republic of Korea
| | - Myunghee Kim
- a Department of Food Science and Technology , Yeungnam University , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea
| |
Collapse
|
18
|
Yan Y, Luo JY, Chen Y, Wang HH, Zhu GY, He PY, Guo JL, Lei YL, Chen ZW. A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses. Oncotarget 2017; 8:96913-96923. [PMID: 29228581 PMCID: PMC5722533 DOI: 10.18632/oncotarget.18533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/02/2017] [Indexed: 12/27/2022] Open
Abstract
We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). Performance of rMLA was evaluated by comparing with real-time RT-PCR. Detection data from clinical specimens showed that the rMLA had diagnostic sensitivities of 97.10% for FluA, 94.59% for FluB, 98.68% for PIV-3, 94.87% for RSV and 95.92% for MPV (No Data for MERS-CoV due to the lack of positive specimens). Data of analytical sensitivities showed that the detection limits of the rMLA assay were 5–25 viral RNA copies per μl for FluA, FluB, PIV-3 and MERS-CoV, approximate to the real-time RT-PCR assay; while the values were 8 and 22copies/μl for MPV and RSV, lower than the real-time RT-PCR(78 and 114 copies/μl respectively). The results indicated that the rMLA is a sensitive, specific detection tool and comparable to real-time RT-PCR, especially suitable for high-throughput detection of respiratory specimens.
Collapse
Affiliation(s)
- Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jian-Yong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yin Chen
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Heng-Hui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Guo-Ying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Pei-Yan He
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jin-Lei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yong-Liang Lei
- Lishui Municipal Center for Disease Control and Prevention, Lishui 323000, China
| | - Zhong-Wen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| |
Collapse
|
19
|
Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
Collapse
Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
| |
Collapse
|
20
|
Leifels M, Hamza IA, Krieger M, Wilhelm M, Mackowiak M, Jurzik L. From Lab to Lake - Evaluation of Current Molecular Methods for the Detection of Infectious Enteric Viruses in Complex Water Matrices in an Urban Area. PLoS One 2016; 11:e0167105. [PMID: 27880820 PMCID: PMC5120873 DOI: 10.1371/journal.pone.0167105] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/07/2016] [Indexed: 11/22/2022] Open
Abstract
Quantitative PCR methods are commonly used to monitor enteric viruses in the aquatic environment because of their high sensitivity, short reaction times and relatively low operational cost. However, conclusions for public health drawn from results of such molecular techniques are limited due to their inability to determine viral infectivity. Ethidium monoazide (EMA) and propidium monoazide (PMA) are capable to penetrate the damaged or compromised capsid of the inactivated viruses and bind to the viral nucleic acids. We assessed whether dye treatment is a suitable approach to improve the ability of qPCR to distinguish between infectious and non-infectious human adenovirus, enterovirus and rotavirus A in surface water of an urban river and sewage before and after UV disinfection. Like the gold standard of cell culture assays, pretreatment EMA-/PMA-qPCR succeeded in removing false positive results which would lead to an overestimation of the viral load if only qPCR of the environmental samples was considered. A dye pretreatment could therefore provide a rapid and relatively inexpensive tool to improve the efficacy of molecular quantification methods in regards to viral infectivity.
Collapse
Affiliation(s)
- Mats Leifels
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany
| | - Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt
| | - Marion Krieger
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany
| | - Michael Wilhelm
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany
| | - Martin Mackowiak
- University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre – Aquatic Microbiology, Essen, Germany
| | - Lars Jurzik
- Ruhr-University Bochum, Department of Hygiene, Social- and Environmental Medicine, Bochum, Germany
| |
Collapse
|
21
|
Rachmadi AT, Torrey JR, Kitajima M. Human polyomavirus: Advantages and limitations as a human-specific viral marker in aquatic environments. WATER RESEARCH 2016; 105:456-469. [PMID: 27665433 DOI: 10.1016/j.watres.2016.09.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/27/2023]
Abstract
Human polyomaviruses (HPyVs) cause persistent infections in organs such as kidney, brain, skin, liver, respiratory tract, etc., and some types of HPyV are constantly excreted in the urine and/or feces of infected and healthy individuals. The use of an enteric virus as an indicator for human sewage/waste contamination in aquatic environments has been proposed; HPyVs are a good candidate since they are routinely found in environmental water samples from different geographical areas with relatively high abundance. HPyVs are highly human specific, having been detected in human waste from all age ranges and undetected in animal waste samples. In addition, HPyVs show a certain degree of resistance to high temperature, chlorine, UV, and low pH, with molecular signals (i.e., DNA) persisting in water for several months. Recently, various concentration methods (electronegative/positive filtration, ultrafiltration, skim-milk flocculation) and detection methods (immunofluorescence assay, cell culture, polymerase chain reaction (PCR), integrated cell culture PCR (ICC-PCR), and quantitative PCR) have been developed and demonstrated for HPyV, which has enabled the identification and quantification of HPyV in various environmental samples, such as sewage, surface water, seawater, drinking water, and shellfish. In this paper, we summarize these recent advancements in detection methods and the accumulation of environmental surveillance and laboratory-scale experiment data, and discuss the potential advantages as well as limitations of HPyV as a human-specific viral marker in aquatic environments.
Collapse
Affiliation(s)
- Andri T Rachmadi
- Division of Environmental Engineering, Graduate School of Engineering, Hokkaido University, Japan
| | - Jason R Torrey
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Graduate School of Engineering, Hokkaido University, Japan.
| |
Collapse
|
22
|
Reducing pathogens in combined sewer overflows using performic acid. Int J Hyg Environ Health 2016; 219:700-708. [DOI: 10.1016/j.ijheh.2016.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 04/14/2016] [Accepted: 04/17/2016] [Indexed: 11/22/2022]
|
23
|
Novel bead-based platform for direct detection of unlabelled nucleic acids through Single Nucleobase Labelling. Talanta 2016; 161:489-496. [PMID: 27769437 DOI: 10.1016/j.talanta.2016.08.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/19/2016] [Accepted: 08/28/2016] [Indexed: 01/02/2023]
Abstract
Over the last decade, circulating microRNAs have received attention as diagnostic and prognostic biomarkers. In particular, microRNA122 has been demonstrated to be an early and more sensitive indicator of drug-induced liver injury than the widely used biomarkers such as alanine aminotransferase and aspartate aminotransferase. Recently, microRNA122 has been used in vitro to assess the cellular toxicity of new drugs and as a biomarker for the development of a rapid test for drug overdose/liver damage. In this proof-of-concept study, we report a PCR-free and label-free detection method that has a limit of detection (3 standard deviations) of 15 fmoles of microRNA122, by integrating a dynamic chemical approach for "Single Nucleobase Labelling" with a bead-based platform (Luminex®) thereby, in principle, demonstrating the exciting prospect of rapid and accurate profiling of any microRNAs related to diseases and toxicology.
Collapse
|
24
|
Chen H, Hu Y. Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses. Open Microbiol J 2016; 10:78-89. [PMID: 27335620 PMCID: PMC4899541 DOI: 10.2174/1874285801610010078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 02/04/2023] Open
Abstract
Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.
Collapse
Affiliation(s)
- Haifeng Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Yuan Hu
- Northeast Region Laboratory, Office of Regulatory Affairs, U.S. Food and Drug Administration, Jamaica, NY, USA
| |
Collapse
|
25
|
Suzuki Y, Kobayashi T, Nishiyama M, Kono T. Concentration of MS2 phage in river water by a combined ferric colloid adsorption and foam separation-based method, with MS2 phage leaching from ferric colloid. J Biosci Bioeng 2016; 122:252-6. [PMID: 26868517 DOI: 10.1016/j.jbiosc.2016.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 01/17/2023]
Abstract
The concentration of MS2 phage as a model RNA virus in river water using a combined ferric colloid adsorption and foam separation-based method was examined. The MS2 phage concentrations were determined by the plaque-forming unit (PFU) method and reverse transcription quantitative PCR (RT-qPCR) analysis. When ferric colloid adsorption was performed prior to foam separation, MS2 phage was effectively removed from river water and concentrated in the generated foam within 7 min. The removal efficiency was >99% at the optimum iron and casein concentrations of 5 mg-Fe/L and 10 mg/L, respectively. Furthermore, based on the analysis of the collected ferric colloid dissolved using deferoxamine, the MS2 concentration in the colloid-dissolved solution was 190-fold higher than that found in raw water according to RT-qPCR analysis. This is a novel method for concentrating RNA viruses to facilitate their detection in river water using coagulation and foam separation combined with chelate dissolution of ferric flocs.
Collapse
Affiliation(s)
- Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan.
| | - Takumi Kobayashi
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Masateru Nishiyama
- Department of Environment and Resource Science, Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki 889-2192, Japan
| |
Collapse
|
26
|
Leifels M, Jurzik L, Wilhelm M, Hamza IA. Use of ethidium monoazide and propidium monoazide to determine viral infectivity upon inactivation by heat, UV- exposure and chlorine. Int J Hyg Environ Health 2015; 218:686-93. [DOI: 10.1016/j.ijheh.2015.02.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 01/06/2023]
|
27
|
Liu Y, Liu N, Ma X, Li X, Ma J, Li Y, Zhou Z, Gao Z. Highly specific detection of thrombin using an aptamer-based suspension array and the interaction analysis via microscale thermophoresis. Analyst 2015; 140:2762-70. [PMID: 25710359 DOI: 10.1039/c5an00081e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel aptamer-based suspension array detection platform was designed for the sensitive, specific and rapid detection of human α-thrombin as a model. Thrombin was first recognized by a 29-mer biotinylated thrombin-binding aptamer (TBA) in solution. Then 15-mer TBA modified magnetic beads (MBs) captured the former TBA-thrombin to form an aptamer-thrombin-aptamer sandwich complex. The median fluorescence intensity obtained via suspension array technology was positively correlated with the thrombin concentration. The interactions between TBAs and thrombin were analyzed using microscale thermophoresis (MST). The dissociation constants could be respectively achieved to be 44.2 ± 1.36 nM (TBA1-thrombin) and 15.5 ± 0.637 nM (TBA2-thrombin), which demonstrated the high affinities of TBA-thrombin and greatly coincided with previous reports. Interaction conditions such as temperature, reaction time, and coupling protocol were optimized. The dynamic quantitative working range of the aptamer-based suspension array was 18.37-554.31 nM, and the coefficients of determination R(2) were greater than 0.9975. The lowest detection limit of thrombin was 5.4 nM. This method was highly specific for thrombin without being affected by other analogs and interfering proteins. The recoveries of thrombin spiked in diluted human serum were in the range 82.6-114.2%. This innovative aptamer-based suspension array detection platform not only exhibits good sensitivity based on MBs facilitating highly efficient separation and amplification, but also suggests high specificity by the selective aptamer binding, thereby suggesting the expansive application prospects in research and clinical fields.
Collapse
Affiliation(s)
- Yanan Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Jang JP, Baek IC, Choi EJ, Kim TG. Multiplex genotyping of cytokine gene SNPs using fluorescence bead array. PLoS One 2015; 10:e0118008. [PMID: 25689696 PMCID: PMC4331502 DOI: 10.1371/journal.pone.0118008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 01/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.
Collapse
Affiliation(s)
- Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
- * E-mail:
| |
Collapse
|
29
|
Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|