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Itarte M, Forés E, Martínez-Puchol S, Scheiber L, Vázquez-Suñé E, Bofill-Mas S, Rusiñol M. Exploring viral contamination in urban groundwater and runoff. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174238. [PMID: 38925381 DOI: 10.1016/j.scitotenv.2024.174238] [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: 02/07/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024]
Abstract
The reliance of the global population on urban aquifers is steadily increasing, and urban aquifers are susceptible to pathogenic contamination through sources such as sewer leakage or urban runoff. However, there is insufficient monitoring of groundwater quality in urban areas. In this study, quantitative polymerase chain reaction (qPCR) was employed to evaluate the presence of human fecal viral indicators and viral pathogens in urban wastewater (n = 13) and groundwater (n = 12) samples from four locations in Barcelona with different degrees of urbanization, as well as in runoff samples (n = 2). Additionally, a target enrichment sequencing (TES) approach was utilized to explore the viral diversity within groundwater and runoff samples, offering insights into viral contamination and potential virus transmission routes in urban areas. Human adenovirus (HAdV) was identified in all wastewater samples, 67 % (8/12) of groundwater samples, and one runoff sample by qPCR indicating human viral fecal contamination. The viral pathogen Norovirus genogroup GI (NoV GI) was detected in wastewater and two winter groundwater samples from highly and medium urbanized areas. NoV genogroup GII (NoV GII), Enterovirus (EV) and SARS-CoV-2 were exclusively detected in wastewater. Human and other vertebrate viruses were detected in groundwater and runoff samples using TES. This study gives insights about the virome present in urban water sources, emphasizing the need for thorough monitoring and deeper understanding to address emerging public health concerns.
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Affiliation(s)
- Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain.
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Vicerectorat de Recerca, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Laura Scheiber
- Department of Geosciences, Institute of Environmental Assessment and Water Research (IDAEA), Severo Ochoa Excellence Center of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
| | - Enric Vázquez-Suñé
- Department of Geosciences, Institute of Environmental Assessment and Water Research (IDAEA), Severo Ochoa Excellence Center of the Spanish Council for Scientific Research (CSIC), 08034 Barcelona, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), 08001 Barcelona, Spain
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2
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Peng L, Yang F, Shi J, Liu Y, Pan L, Mao D, Luo Y. Insights into the panorama of multiple DNA viruses in municipal wastewater and recycled sludge in Tianjin, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124215. [PMID: 38797349 DOI: 10.1016/j.envpol.2024.124215] [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: 02/04/2024] [Revised: 05/06/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Environmental viruses in wastewater and sludge are widely recognized for their roles in waterborne diseases. However, previous studies mainly focused on RNA viruses, and little is known about the diversity of DNA viral communities and their driving factors in municipal wastewater treatment environments. Herein, we conducted a pilot study to explore DNA virus profiles in municipal wastewater and recycled sludge by metagenomics method, and track their temporal changes in northern China. Results showed that 467 viral species were co-shared among all the samples. We identified six families of human viruses with a prevalence of 0.1%, which were rare but relatively stable in wastewater and sludge for six months. Adenoviridae, Parvoviridae, and Herpersviridae were the most dominant human viral families in municipal wastewater and recycled sludge. A time series of samples revealed that the dynamic changes of human DNA viruses were stable based on qPCR results, particularly for high-risk fecal-oral transmission viruses of adenovirus, bocavirus, polyomavirus, human gamma herpesvirus, human papillomavirus, and hepatitis B virus. Concentrations of Adenovirus (5.39-7.48 log10 copies/L) and bocavirus (4.36-7.48 log10 copies/L) were observed to be the highest in these samples compared to other viruses. Our findings demonstrated the DNA viruses' high prevalence and persistence in municipal wastewater treatment environments, highlighting the value of enhancing public health responses based on wastewater-based epidemiology.
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Affiliation(s)
- Liang Peng
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jingliang Shi
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - YiXin Liu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Liuzhu Pan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China.
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3
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Itarte M, Calvo M, Martínez-Frago L, Mejías-Molina C, Martínez-Puchol S, Girones R, Medema G, Bofill-Mas S, Rusiñol M. Assessing environmental exposure to viruses in wastewater treatment plant and swine farm scenarios with next-generation sequencing and occupational risk approaches. Int J Hyg Environ Health 2024; 259:114360. [PMID: 38555823 DOI: 10.1016/j.ijheh.2024.114360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Occupational exposure to pathogens can pose health risks. This study investigates the viral exposure of workers in a wastewater treatment plant (WWTP) and a swine farm by analyzing aerosol and surfaces samples. Viral contamination was evaluated using quantitative polymerase chain reaction (qPCR) assays, and target enrichment sequencing (TES) was performed to identify the vertebrate viruses to which workers might be exposed. Additionally, Quantitative Microbial Risk Assessment (QMRA) was conducted to estimate the occupational risk associated with viral exposure for WWTP workers, choosing Human Adenovirus (HAdV) as the reference pathogen. In the swine farm, QMRA was performed as an extrapolation, considering a hypothetical zoonotic virus with characteristics similar to Porcine Adenovirus (PAdV). The modelled exposure routes included aerosol inhalation and oral ingestion through contaminated surfaces and hand-to-mouth contact. HAdV and PAdV were widespread viruses in the WWTP and the swine farm, respectively, by qPCR assays. TES identified human and other vertebrate viruses WWTP samples, including viruses from families such as Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, and Parvoviridae. In the swine farm, most of the identified vertebrate viruses were porcine viruses belonging to Adenoviridae, Astroviridae, Circoviridae, Herpesviridae, Papillomaviridae, Parvoviridae, Picornaviridae, and Retroviridae. QMRA analysis revealed noteworthy risks of viral infections for WWTP workers if safety measures are not taken. The probability of illness due to HAdV inhalation was higher in summer compared to winter, while the greatest risk from oral ingestion was observed in workspaces during winter. Swine farm QMRA simulation suggested a potential occupational risk in the case of exposure to a hypothetical zoonotic virus. This study provides valuable insights into WWTP and swine farm worker's occupational exposure to human and other vertebrate viruses. QMRA and NGS analyses conducted in this study will assist managers in making evidence-based decisions, facilitating the implementation of protection measures, and risk mitigation practices for workers.
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Affiliation(s)
- Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Miquel Calvo
- Secció d'Estadística, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Lola Martínez-Frago
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | | | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Secció de Microbiologia, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
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4
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da Silva TCB, Chaúque BJM, Benitez GB, Rott MB. Global prevalence of potentially pathogenic free-living amoebae in sewage and sewage-related environments-systematic review with meta-analysis. Parasitol Res 2024; 123:148. [PMID: 38433138 DOI: 10.1007/s00436-024-08164-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
Free-living amoebae (FLA) include amphizoic microorganisms important in public health, widely isolated from air, water, and soil. However, its occurrence in sewage-related environments still needs to be systematically documented. This study summarizes the occurrence of FLA in sewage-related environments through a systematic review with meta-analysis. A total of 1983 scientific article were retrieved from different databases, of which 35 were selected and analyzed using a random effects forest plot model with a 95% confidence interval (IC). The pooled overall prevalence of FLA in sewage across 12 countries was 68.96% (95% IC = 58.5-79.42). Subgroup analysis indicates high prevalence in all environments analyzed, including sewage water from the sewage treatment plant (81.19%), treated sewage water (75.57%), sewage-contaminated water (67.70%), sediment contaminated by sewage (48.91%), and sewage water (47.84%). Prevalence values of Acanthamoeba spp., Hartmanella/Vermamoeba spp., and Naegleria spp. are 47.48%, 28.24%, and 16.69%, respectively. Analyzing the species level, the distribution is as follows: Acanthamoeba palestinensis (88%), A. castellanii (23.74%), A. astronyxis (19.18%), A. polyphaga (13.59%), A. culbertsoni (12.5%), A. stevensoni (8.33%), A. tubiashi (4.35%) and A. hatchetti (1.1%), Naegleria fowleri (28.4%), N. gruberi (25%), N. clarki (8.33%), N. australiensis (4.89%) and N. italica (4.29%), Hartmannella/Vermamoeba exundans (40%) and H.V. vermiform (32.61%). Overall, our findings indicate a high risk associated with sewage-related environments, as the prevalence of FLA, including pathogenic strains, is high, even in treated sewage water. The findings of this study may be valuable both for risk remediation actions against amoebic infections and for future research endeavors.
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Affiliation(s)
- Thaisla Cristiane Borella da Silva
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Beni Jequicene Mussengue Chaúque
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
- Postgraduate Program in Biological Sciences: Pharmacology and Therapeutics, UFRGS, Porto Alegre, Rio Grande Do Sul, Brazil
- Center of Studies in Science and Technology (NECET), Biology Course, Universidade Rovuma, Niassa Branch, Lichinga, Mozambique
| | - Guilherme Brittes Benitez
- Industrial and Systems Engineering Graduate Program, Polytechnic School, Pontifical Catholic University of Parana (PUCPR), Curitiba, Paraná, Brazil
| | - Marilise Brittes Rott
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil.
- Laboratory 520, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Department of Parasitology, Universidade Federal Do Rio Grande Do Sul, Ramiro Barcelos Street, Porto Alegre, Rio Grande Do Sul, N 2600, Brazil.
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5
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Maksimović O, Bačnik K, Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Gutiérrez-Aguirre I, Kutnjak D. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems. WATER RESEARCH 2024; 249:120712. [PMID: 38134622 DOI: 10.1016/j.watres.2023.120712] [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: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 12/24/2023]
Abstract
Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem.
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Affiliation(s)
- Olivera Maksimović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Jožef Stefan International Postgraduate School, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Mark Paul Selda Rivarez
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Department of Entomology and Plant Pathology, North Carolina State University, USA; College of Agriculture and Agri-Industries, Caraga State University, Philippines
| | - Ana Vučurović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; School for Viticulture and Enology, University of Nova Gorica, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | | | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
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Rozo-Montoya N, Bedoya-Urrego K, Alzate JF. Monitoring potentially pathogenic protists in sewage sludge using Metataxonomics. Food Waterborne Parasitol 2023; 33:e00210. [PMID: 37808003 PMCID: PMC10558727 DOI: 10.1016/j.fawpar.2023.e00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Intestinal parasites continue to pose a significant threat to human health worldwide, particularly among children. Contaminated water and soil serve as major transmission vehicles for these parasites and intestinal protists are among the most prevalent parasites in both developed and developing nations. Traditionally, parasites have been studied using human or animal fecal samples, while studying them in environmental samples has been challenging due to technical limitations. However, advancements in Next-Generation Sequencing (NGS) and bioinformatic approaches now enable the detection of parasite DNA in environmental samples. In this study, we applied a metataxonomic and phylogenetic strategy to detect and classify DNA of protists present in sewage sludge from two major cities in Colombia: Medellin and Cali. We successfully detected several human pathogenic parasites including Giardia intestinalis, Entamoeba histolytica, and Blastocystis sp., among other protists, in all sludge samples examined. We also investigated the entry and exit of parasite DNA from the San Fernando wastewater treatment plant (WWTP). We observed a higher number of parasite DNA sequences in the plant's influent wastewater, but we also detected the discharge of DNA from pathogenic parasites in both effluent waters and biosolids.
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Affiliation(s)
- Nicolas Rozo-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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Zhang Y, Kitazumi A, Liao YT, de Los Reyes BG, Wu VCH. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiol Spectr 2023; 11:e0022623. [PMID: 37754684 PMCID: PMC10581182 DOI: 10.1128/spectrum.00226-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/10/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.
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Affiliation(s)
- Yujie Zhang
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | - Ai Kitazumi
- Department of Plant and Soil Science, Texas Tech University , Lubbock, Texas, USA
| | - Yen-Te Liao
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
| | | | - Vivian C H Wu
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center , Albany, California, USA
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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Santos-Silva S, da Silva Dias Moraes DF, López-López P, Rivero-Juarez A, Mesquita JR, Nascimento MSJ. Hepatitis E Virus in the Iberian Peninsula: A Systematic Review. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:193-211. [PMID: 37434079 PMCID: PMC10499749 DOI: 10.1007/s12560-023-09560-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
One of the most frequent causes of acute viral hepatitis is hepatitis E virus (HEV) causing 20 million infections worldwide each year and 44,000 deaths. Studies on HEV in the Iberian Peninsula have been increasing through time with HEV infection being identified in humans and animals. The aim of the present systematic review was to compile and evaluate all the published data on HEV from studies performed in humans, animals and environmental samples in the Iberian Peninsula. The electronic databases Mendeley, PubMed, Scopus, and Web of Science were thoroughly searched, and research published up until February 01, 2023 were included. Resulting in a total of 151 eligible papers by full reading and application of PRISMA exclusion/inclusion criteria. Overall, the present review shows that several HEV genotypes, namely HEV-1, 3, 4, and 6 as well as Rocahepevirus, are circulating in humans, animals, and in the environment in the Iberian Peninsula. HEV-3 was the most common genotype circulating in humans in Portugal and Spain, as expected for developed countries, with HEV-1 only being detected in travelers and emigrants from HEV endemic regions. Spain is the biggest pork producer in Europe and given the high circulation of HEV in pigs, with HEV-3 being primarily associated to zoonotic transmission through consumption of swine meat and meat products, in our opinion, the introduction of an HEV surveillance system in swine and inclusion of HEV in diagnostic routines for acute and chronic human hepatitis would be important. Additionally, we propose that establishing a monitoring mechanism for HEV is crucial in order to gain a comprehensive understanding of the prevalence of this illness and the various strains present in the Iberian Peninsula, as well as their potential impact on public health.
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Affiliation(s)
- Sérgio Santos-Silva
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | - Pedro López-López
- Grupo de Virología Clínica y Zoonosis, Unidad de Enfermedades Infecciosas, Instituto Maimónides de Investigación Biomédica de Córdoba, Hospital Reina Sofía, Universidad de Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - António Rivero-Juarez
- Grupo de Virología Clínica y Zoonosis, Unidad de Enfermedades Infecciosas, Instituto Maimónides de Investigación Biomédica de Córdoba, Hospital Reina Sofía, Universidad de Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - João R Mesquita
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal.
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
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10
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Kuo HWD, Zure D, Lin CR. Occurrences of similar viral diversity in campus wastewater and reclaimed water of a university dormitory. CHEMOSPHERE 2023; 330:138713. [PMID: 37088208 DOI: 10.1016/j.chemosphere.2023.138713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Water reuse from wastewater sources still remain some critical safety concerns associated with treacherous contaminants like pathogenic viruses. In this study, viral diversities in campus wastewater (CWW) and its reclaimed water (RCW) recycled for toilet flushing and garden irrigation of a university dormitory were assessed using metagenomic sequencing for acquisition of more background data. Results suggested majority (>80%) of gene sequences within assembled contigs predicted by open reading frame (ORF) finder were no-hit yet believed to be novel/unrevealed viral genomic information whereas hits matched bacteriophages (i.e., mainly Myoviridae, Podoviridae, and Siphoviridae families) were predominant in both CWW and RCW samples. Moreover, few pathogenic viruses (<1%) related to infections of human skin (e.g., Molluscum contagiosum virus, MCV), digestion system (e.g., hepatitis C virus, HCV), and gastrointestinal tract (e.g., human norovirus, HuNoV) were also noticed raising safety concerns about application of reclaimed waters. Low-affinity interactions of particular viral exterior proteins (e.g., envelope glycoproteins or spike proteins) for disinfectant ligand (e.g., chlorite) elucidated treatment limitations of current sewage processing systems even with membrane bioreactor and disinfectant contactor. Revolutionary disinfection approaches together with routine monitoring and new regulations are prerequisite to secure pathogen-correlated water quality for safer reuse of reclaimed waters.
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Affiliation(s)
- Hsion-Wen David Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taiwan.
| | - Diaiti Zure
- Department of Environmental Science and Engineering, Tunghai University, Taiwan
| | - Chih-Rong Lin
- Department of Environmental Science and Engineering, Tunghai University, Taiwan
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11
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Maksimovic Carvalho Ferreira O, Lengar Ž, Kogej Z, Bačnik K, Bajde I, Milavec M, Županič A, Mehle N, Kutnjak D, Ravnikar M, Gutierrez-Aguirre I. Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:384-400. [PMID: 35999429 PMCID: PMC9398038 DOI: 10.1007/s12560-022-09533-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/01/2022] [Indexed: 05/15/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
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Affiliation(s)
- Olivera Maksimovic Carvalho Ferreira
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia.
| | - Živa Lengar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Zala Kogej
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Irena Bajde
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anže Županič
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri, Glavni trg 8, 5271, Vipava, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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12
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Malayil L, Ramachandran P, Chattopadhyay S, Allard SM, Bui A, Butron J, Callahan MT, Craddock HA, Murray R, East C, Sharma M, Kniel K, Micallef S, Hashem F, Gerba CP, Ravishankar S, Parveen S, May E, Handy E, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Haymaker J, Betancourt W, Zhu L, Mongodin EF, Sapkota A, Pop M, Sapkota AR. Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15019-15033. [PMID: 36194536 PMCID: PMC9632240 DOI: 10.1021/acs.est.2c02281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.
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Affiliation(s)
- Leena Malayil
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Padmini Ramachandran
- Office
of Regulatory Science, Division of Microbiology, United States Food and Drug Administration, HFS-712, 5001 Campus Drive, College Park, Maryland 20740, United States
| | - Suhana Chattopadhyay
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Sarah M. Allard
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Anthony Bui
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Jicell Butron
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mary Theresa Callahan
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Hillary A. Craddock
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Rianna Murray
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Cheryl East
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Manan Sharma
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Kalmia Kniel
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shirley Micallef
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Fawzy Hashem
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Charles P. Gerba
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Sadhana Ravishankar
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Salina Parveen
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric May
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric Handy
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Prachi Kulkarni
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Brienna Anderson-Coughlin
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shani Craighead
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Samantha Gartley
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Adam Vanore
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Rico Duncan
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Derek Foust
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Joseph Haymaker
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Walter Betancourt
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Libin Zhu
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Emmanuel F. Mongodin
- Institute
for Genome Sciences, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Amir Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mihai Pop
- Department
of Computer Science and Center for Bioinformatics and Computational
Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Amy R. Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
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13
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Elbehery AHA, Deng L. Insights into the global freshwater virome. Front Microbiol 2022; 13:953500. [PMID: 36246212 PMCID: PMC9554406 DOI: 10.3389/fmicb.2022.953500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
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Affiliation(s)
- Ali H. A. Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
- *Correspondence: Ali H. A. Elbehery,
| | - Li Deng
- Helmholtz Centre Munich – German Research Centre for Environmental Health, Institute of Virology, Neuherberg, Germany
- Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, Freising, Germany
- Li Deng,
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14
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Leal dos Santos D, Chaúque BJM, Virginio VG, Cossa VC, Pettan-Brewer C, Schrekker HS, Rott MB. Occurrence of Naegleria fowleri and their implication for health - a look under the One Health approaches. Int J Hyg Environ Health 2022; 246:114053. [DOI: 10.1016/j.ijheh.2022.114053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
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15
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Ngashangva L, Hemdan BA, El-Liethy MA, Bachu V, Minteer SD, Goswami P. Emerging Bioanalytical Devices and Platforms for Rapid Detection of Pathogens in Environmental Samples. MICROMACHINES 2022; 13:mi13071083. [PMID: 35888900 PMCID: PMC9321031 DOI: 10.3390/mi13071083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023]
Abstract
The development of robust bioanalytical devices and biosensors for infectious pathogens is progressing well with the advent of new materials, concepts, and technology. The progress is also stepping towards developing high throughput screening technologies that can quickly identify, differentiate, and determine the concentration of harmful pathogens, facilitating the decision-making process for their elimination and therapeutic interventions in large-scale operations. Recently, much effort has been focused on upgrading these analytical devices to an intelligent technological platform by integrating them with modern communication systems, such as the internet of things (IoT) and machine learning (ML), to expand their application horizon. This review outlines the recent development and applications of bioanalytical devices and biosensors to detect pathogenic microbes in environmental samples. First, the nature of the recent outbreaks of pathogenic microbes such as foodborne, waterborne, and airborne pathogens and microbial toxins are discussed to understand the severity of the problems. Next, the discussion focuses on the detection systems chronologically, starting with the conventional methods, advanced techniques, and emerging technologies, such as biosensors and other portable devices and detection platforms for pathogens. Finally, the progress on multiplex assays, wearable devices, and integration of smartphone technologies to facilitate pathogen detection systems for wider applications are highlighted.
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Affiliation(s)
- Lightson Ngashangva
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvanthapuram, Kerala 695014, India;
| | - Bahaa A. Hemdan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India; (B.A.H.); (V.B.)
- Water Pollution Research Department, Environmental and Climate Change Research Institute, National Research Centre, 33 El Buhouth Street, Cairo P.O. Box 12622, Egypt;
| | - Mohamed Azab El-Liethy
- Water Pollution Research Department, Environmental and Climate Change Research Institute, National Research Centre, 33 El Buhouth Street, Cairo P.O. Box 12622, Egypt;
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India; (B.A.H.); (V.B.)
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, 315 South 1400 East, RM 2020, Salt Lake City, UT 84112, USA
- Correspondence: (S.D.M.); (P.G.)
| | - Pranab Goswami
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India; (B.A.H.); (V.B.)
- Correspondence: (S.D.M.); (P.G.)
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16
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Partyka ML, Bond RF. Wastewater reuse for irrigation of produce: A review of research, regulations, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154385. [PMID: 35271919 DOI: 10.1016/j.scitotenv.2022.154385] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/26/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The burden of disease caused by the contamination of ready-to-eat produce with common waterborne microbial pathogens suggests that irrigation supplies should be closely monitored and regulated. Simultaneously freshwater resources have become increasingly scarce worldwide while global demand continues to grow. Since the turn of the 20th century with the advent of modern wastewater treatment plants, the reuse of treated wastewater is considered a safe and viable water source for irrigation of ready-to-eat vegetables. However strict, and often costly, treatment regimens mean that only a fraction of the world's wastewater supplies are being put to reuse. The purpose of this review is to explore the available literature on the risks associated with reuse water for ready-to-eat produce production including different approaches to reducing those risks as the demand for reuse water increases. It is not the intent of the authors to determine which methods of treatment should be applied, which pathogens should be considered of greatest concern, or which regulations should be applied. Rather, it is meant to be a discussion of the evolving guidelines governing irrigation with reuse water, potential risks from known pathogens common to produce production and recommendations for improving the adoption of water reuse moving forward. To date, there is little evidence to suggest that adequately treated reuse water poses more risk for produce-related illness or outbreaks than other sources of irrigation water. However, multiple epidemiological and quantitative risk assessment models suggest that guidelines for the use of reuse water should be regionally specific and based on local growing practices, available technologies for wastewater treatment, and overall population health. Though research suggests water reuse is generally safe, the assumptions of risk are both personal and of public interest, they should be considered carefully before water reuse is either allowed or disallowed in produce production environments.
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Affiliation(s)
- Melissa L Partyka
- Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Ronald F Bond
- Western Center for Food Safety, Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, United States of America
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17
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Fradette MS, Culley AI, Charette SJ. Detection of Cryptosporidium spp. and Giardia spp. in Environmental Water Samples: A Journey into the Past and New Perspectives. Microorganisms 2022; 10:microorganisms10061175. [PMID: 35744692 PMCID: PMC9228427 DOI: 10.3390/microorganisms10061175] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 01/27/2023] Open
Abstract
Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was made in the early 1900s and even before, it was only in 1999 that the U.S. Environmental Protection Agency (EPA) published a standardized protocol for the detection of these parasites, modified and named today the U.S. EPA 1623.1 Method. It involves the flow-through filtration of a large volume of the water of interest, the elution of the biological material retained on the filter, the purification of the (oo)cysts, and the detection by immunofluorescence of the target parasites. Since the 1990s, several molecular-biology-based techniques were also developed to detect Cryptosporidium and Giardia cells from environmental or clinical samples. The application of U.S. EPA 1623.1 as well as numerous biomolecular methods are reviewed in this article, and their advantages and disadvantages are discussed guiding the readers, such as graduate students, researchers, drinking water managers, epidemiologists, and public health specialists, through the ever-expanding number of techniques available in the literature for the detection of Cryptosporidium spp. and Giardia spp. in water.
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Affiliation(s)
- Marie-Stéphanie Fradette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Centre de Recherche en Aménagement et Développement du Territoire (CRAD), Université Laval, Québec City, QC G1V 0A6, Canada
- Correspondence:
| | - Alexander I. Culley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada; (A.I.C.); (S.J.C.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et Génie, Université Laval, Québec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec City, QC G1V 0A6, Canada
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18
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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19
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Hong T, Liu X, Zhou Q, Liu Y, Guo J, Zhou W, Tan S, Cai Z. What the Microscale Systems "See" In Biological Assemblies: Cells and Viruses? Anal Chem 2021; 94:59-74. [PMID: 34812604 DOI: 10.1021/acs.analchem.1c04244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Xing Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Qi Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Yilian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Jing Guo
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
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20
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Nagarkar M, Keely SP, Brinkman NE, Garland JL. Human- and infrastructure-associated bacteria in greywater. J Appl Microbiol 2021; 131:2178-2192. [PMID: 33905584 PMCID: PMC8682149 DOI: 10.1111/jam.15118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023]
Abstract
Greywater, the wastewater from sinks, showers and laundry, is an understudied environment for bacterial communities. Most greywater studies focus on quantifying pathogens, often via proxies used in other wastewater, like faecal indicator bacteria; there is a need to identify more greywater-appropriate surrogates, like Staphylococcus sp. Sequencing-based studies have revealed distinct communities in different types of greywater as well as in different parts of greywater infrastructure, including biofilms on pipes, holding tanks and filtration systems. The use of metagenomic sequencing provides high resolution on both the taxa and genes present, which may be of interest in cases like identifying pathogens and surrogates relevant to different matrices, monitoring antibiotic resistance genes and understanding metabolic processes occurring in the system. Here, we review what is known about bacterial communities in different types of greywater and its infrastructure. We suggest that wider adoption of environmental sequencing in greywater research is important because it can describe the entire bacterial community along with its metabolic capabilities, including pathways for removal of nutrients and organic materials. We briefly describe a metagenomic dataset comparing different types of greywater samples in a college dormitory building to highlight the type of questions these methods can address. Metagenomic sequencing can help further the understanding of greywater treatment for reuse because it allows for identification of new pathogens or genes of concern.
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Affiliation(s)
- M Nagarkar
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - S P Keely
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - N E Brinkman
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - J L Garland
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
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21
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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22
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Rajeev AC, Sahu N, Arvind K, Deori M, Grace T, Dev SA, Yadav VP, Ghosh I. Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 282:117003. [PMID: 33848911 DOI: 10.1016/j.envpol.2021.117003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/27/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered as vital members to reflect the health of a riverine system. Among them, pathogenic and fecal indicators imply health risks involved with potability of river water. The present study explores the diverse microbial communities, distribution pattern of potential pathogens, and fecal indicators between the geographically distinct Himalayan and Peninsular river systems of India. It also inquires into the environmental factors associated with community variance and distribution pattern of microbial indicators. The application of high-throughput amplicon sequencing approach unveiled significant demarcation (p < 0.004, Anosim R = 0.62) of samples suggesting unique microbial diversities in these two river sediments. Random forest analysis revealed Desulfobulbulus, PSB_M_3, and Opitutus in Himalayan, while DA101, Bacillus, and Streptomyces in the Peninsular as significant contributors to develop overall dissimilarity between the river systems. Permutational multivariate analysis of variance and co-occurrence network analysis were used to study the relationships between microbial taxa and environmental factors. Amongst the various studied environmental parameters, pH, K, Ca, Mg, Ba, and Al in the Himalayan and salinity, Na, temperature, and Th in the Peninsular significantly influenced shaping of distinct microbial communities. Furthermore, the potential pathogenic genera, including Flavobacterium, Clostridium, Arcobacter, Pseudomonas, and Bacillus were highly prevalent in both the river systems. Arcobacter, Clostridium, Acinetobacter, Bacteroides, and Caloramator were the prominent fecal indicators in these river systems. Our findings provide salient information about the crucial role and interplay between various environmental factors and anthropogenic influences in framing the microbiome of the distinct river systems in India. Moreover, assessing potential pathogenic and fecal indicators suggest the public health risk associated with untreated sewage discharge into these water sources. The detection of various F/S indicators and potentially pathogenic bacteria in Himalayan and Peninsular river systems emphasize the urgent need for future monitoring and management of major riverine systems in India.
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Affiliation(s)
| | - Nishi Sahu
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kumar Arvind
- Department of Genomic Science, Central University of Kerala, India
| | - Maushumi Deori
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tony Grace
- Department of Genomic Science, Central University of Kerala, India
| | - Suma Arun Dev
- Division of Forest Genetics and Biotechnology, Kerala Forest Research Institute, Kerala, India
| | - Vijay Pal Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ilora Ghosh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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23
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives. J Microbiol Methods 2021; 187:106269. [PMID: 34129906 DOI: 10.1016/j.mimet.2021.106269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and large eukaryotic genome, the prevalence of small parasite populations in environmental samples compared to bacteria, difficulties in extracting DNA from (oo)cysts, and limited reference databases for parasites. This calls for further research to develop optimized methods specifically looking at protozoan parasites in the environment. This study reviews the current workflow, methods and provide recommendations for the standardization of techniques. The article identifies and summarizes the key methods, advantages, and limitations associated with metagenomic analysis, like sample pre-processing, DNA extraction, sequencing approaches, and analysis methods. The study enhances the understanding and application of standardized protocols for profiling of protozoan parasite community from highly complexe samples and further creates a resourceful comparison among datasets without any biases.
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Affiliation(s)
- N P Mthethwa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - P Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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24
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Pérez-Cataluña A, Cuevas-Ferrando E, Randazzo W, Sánchez G. Bias of library preparation for virome characterization in untreated and treated wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144589. [PMID: 33422963 DOI: 10.1016/j.scitotenv.2020.144589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Avda. Agustin Escardino 7, 46980 Paterna, Valencia, Spain; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany.
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Avda. Agustin Escardino 7, 46980 Paterna, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Avda. Agustin Escardino 7, 46980 Paterna, Valencia, Spain; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany; Department of Microbiology and Ecology, University of Valencia, Av. Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Avda. Agustin Escardino 7, 46980 Paterna, Valencia, Spain; European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany.
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25
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Abstract
The dairy industry produces large amounts of wastewater, including white and cleaning wastewater originating principally from rinsing and cleaning-in-place procedures. Their valorization into process water and non-fat milk solids, in the case of white wastewater, or the renewal of cleaning solutions could be achieved using pressure-driven membrane processes. However, it is crucial to determine the intrinsic characteristics of wastewaters, such as proximate composition and bacterial composition, to optimize their potential for valorization. Consequently, white and cleaning wastewaters were sampled from industrial-scale pasteurizers located in two different Canadian dairy processing plants. Bacterial profiles of dairy wastewaters were compared to those of tap waters, pasteurized skim milk and unused cleaning solutions. The results showed that the physicochemical characteristics as well as non-fat milk solids contents differed drastically between the two dairy plants due to different processing conditions. A molecular approach combining quantitative real-time polymerase chain reaction (qPCR) and metabarcoding was used to characterize the bacteria present in these solutions. The cleaning solutions did not contain sufficient genomic DNA for sequencing. In white wastewater, the bacterial contamination differed depending on the dairy plant (6.91 and 7.21 log10 16S gene copies/mL). Psychrotrophic Psychrobacter genus (50%) dominated white wastewater from plant A, whereas thermophilic Anoxybacillus genus (56%) was predominant in plant B wastewater. The use of cold or warm temperatures during the pasteurizer rinsing step in each dairy plant might explain this difference. The detailed characterization of dairy wastewaters described in this study is important for the dairy sector to clearly identify the challenges in implementing strategies for wastewater valorization.
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26
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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: 137] [Impact Index Per Article: 34.3] [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.
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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.
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27
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Labadie T, Batéjat C, Leclercq I, Manuguerra JC. Historical Discoveries on Viruses in the Environment and Their Impact on Public Health. Intervirology 2020; 63:17-32. [PMID: 33238280 DOI: 10.1159/000511575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/14/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Transmission of many viruses occurs by direct transmission during a close contact between two hosts, or by an indirect transmission through the environment. Several and often interconnected factors, both abiotic and biotic, determine the persistence of these viruses released in the environment, which can last from a few seconds to several years. Moreover, viruses in the environment are able to travel short to very long distances, especially in the air or in water. SUMMARY Although well described now, the role of these environments as intermediaries or as reservoirs in virus transmission has been extensively studied and debated in the last century. The majority of these discoveries, such as the pioneer work on bacteria transmission, the progressive discoveries of viruses, as well as the persistence of the influenza virus in the air varying along with droplet sizes, or the role of water in the transmission of poliovirus, have contributed to the improvement of public health. Recent outbreaks of human coronavirus, influenza virus, and Ebola virus have also demonstrated the contemporaneity of these research studies and the need to study virus persistence in the environment. Key Messages: In this review, we discuss historical discoveries that contributed to describe biotic and abiotic factors determining viral persistence in the environment.
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Affiliation(s)
- Thomas Labadie
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France.,Centre de Biochimie Structurale (CBS), UMR 5048, University of Montpellier, CNRS, Montpellier, France
| | - Christophe Batéjat
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France
| | - India Leclercq
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France, .,Université de Paris, Cellule Pasteur, Paris, France,
| | - Jean-Claude Manuguerra
- Unité Environnement et Risques Infectieux, Institut Pasteur, Cellule d'Intervention Biologique d'Urgence (CIBU), Paris, France
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