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Girón-Guzmán I, Cuevas-Ferrando E, Barranquero R, Díaz-Reolid A, Puchades-Colera P, Falcó I, Pérez-Cataluña A, Sánchez G. Urban wastewater-based epidemiology for multi-viral pathogen surveillance in the Valencian region, Spain. Water Res 2024; 255:121463. [PMID: 38537489 DOI: 10.1016/j.watres.2024.121463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/24/2024]
Abstract
Wastewater-based epidemiology (WBE) has lately arised as a promising tool for monitoring and tracking viral pathogens in communities. In this study, we analysed WBE's role as a multi-pathogen surveillance strategy to detect the presence of several viral illness causative agents. Thus, an epidemiological study was conducted from October 2021 to February 2023 to estimate the weekly levels of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Respiratory Syncytial virus (RSV), and Influenza A virus (IAV) in influent wastewater samples (n = 69). In parallel, a one-year study (October 2021 to October 2022) was performed to assess the presence of pathogenic human enteric viruses. Besides, monitoring of proposed viral fecal contamination indicators crAssphage and Pepper mild mottle virus (PMMoV) was also assessed, along with plaque counting of somatic coliphages. Genetic material of rotavirus (RV), human astrovirus (HAStV), and norovirus genogroup I (GI) and GII was found in almost all samples, while hepatitis A and E viruses (HAV and HEV) only tested positive in 3.77 % and 22.64 % of the samples, respectively. No seasonal patterns were overall found for enteric viruses, although RVs had a peak prevalence in the winter months. All samples tested positive for SARS-CoV-2 RNA, with a mean concentration of 5.43 log genome copies per liter (log GC/L). The tracking of the circulating SARS-CoV-2 variants of concern (VOCs) was performed by both duplex RT-qPCR and next generation sequencing (NGS). Both techniques reliably showed how the dominant VOC transitioned from Delta to Omicron during two weeks in Spain in December 2021. RSV and IAV viruses peaked in winter months with mean concentrations 6.40 and 4.10 log GC/L, respectively. Moreover, the three selected respiratory viruses strongly correlated with reported clinical data when normalised by wastewater physico-chemical parameters and presented weaker correlations when normalising sewage concentration levels with crAssphage or somatic coliphages titers. Finally, predictive models were generated for each respiratory virus, confirming high reliability on WBE data as an early-warning system and communities illness monitoring system. Overall, this study presents WBE as an optimal tool for multi-pathogen tracking reflecting viral circulation and diseases trends within a selected area, its value as a multi-pathogen early-warning tool stands out due to its public health interest.
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Affiliation(s)
- Inés Girón-Guzmán
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Enric Cuevas-Ferrando
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
| | - Regino Barranquero
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Azahara Díaz-Reolid
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Pablo Puchades-Colera
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Irene Falcó
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Alba Pérez-Cataluña
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Gloria Sánchez
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
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Cuevas-Ferrando E, Sánchez G, Pérez-Cataluña A. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters. Methods Mol Biol 2024; 2732:119-131. [PMID: 38060121 DOI: 10.1007/978-1-0716-3515-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Due to the excretion of SARS-CoV-2 in faeces, the use of wastewater-based epidemiology (WBE) is a useful tool for virus surveillance in large populations. The analysis of this virus includes a concentration step prior to virus detection by RT-qPCR. In addition, the use of massive sequencing allows the detection of specific mutations of clinical importance, as well as the detection of the introduction of new lineages in a specific population. In this chapter, we describe the analysis of SARS-CoV-2 in urban wastewater by the concentration of the samples by precipitation with aluminum chloride, the detection, and quantification of SARS-CoV-2 RNA by RT-qPCR and the genomic sequencing using two different sequencing platforms.
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Affiliation(s)
- Enric Cuevas-Ferrando
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain.
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Hufsky F, Abecasis AB, Babaian A, Beck S, Brierley L, Dellicour S, Eggeling C, Elena SF, Gieraths U, Ha AD, Harvey W, Jones TC, Lamkiewicz K, Lovate GL, Lücking D, Machyna M, Nishimura L, Nocke MK, Renard BY, Sakaguchi S, Sakellaridi L, Spangenberg J, Tarradas-Alemany M, Triebel S, Vakulenko Y, Wijesekara RY, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2023. Viruses 2023; 15:2031. [PMID: 37896809 PMCID: PMC10612056 DOI: 10.3390/v15102031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24-26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Ana B. Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Artem Babaian
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sebastian Beck
- Leibniz Institute of Virology, Department Viral Zoonoses—One Health, 20251 Hamburg, Germany;
| | - Liam Brierley
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Health Data Science, University of Liverpool, Liverpool L69 3GF, UK
| | - Simon Dellicour
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050 Bruxelles, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, University of Leuven, 3000 Leuven, Belgium
| | - Christian Eggeling
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Santiago F. Elena
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
| | - Udo Gieraths
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Will Harvey
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Terry C. Jones
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Gabriel L. Lovate
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Dominik Lücking
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Martin Machyna
- Paul-Ehrlich-Institut, Host-Pathogen-Interactions, 63225 Langen, Germany
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Maximilian K. Nocke
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department for Molecular & Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bernard Y. Renard
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, 14482 Potsdam, Germany
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan;
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Jannes Spangenberg
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Maria Tarradas-Alemany
- Computational Genomics Lab., Department of Genetics, Microbiology and Statistics, Institut de Biomedicina UB (IBUB), Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Sandra Triebel
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Yulia Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Rajitha Yasas Wijesekara
- Institute for Bioinformatics, University of Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Fernando González-Candelas
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO, University of Valencia, 46010 Valencia, Spain
| | - Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Walter Randazzo
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Gloria Sánchez
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, Germany
- Leibniz Institute for Age Research—Fritz Lippman Institute, 07745 Jena, Germany
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Falcó I, Tudela JA, Hernández N, Pérez-Cataluña A, García MR, Truchado P, Garrido A, Allende A, Sánchez G, Gil MI. Antiviral capacity of sanitizers against infectious viruses in process water from the produce industry under batch and continuous conditions. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Pérez-Cataluña A, Randazzo W, Martínez-Blanch JF, Codoñer FM, Sánchez G. Sample and library preparation approaches for the analysis of the virome of irrigation water. J Sci Food Agric 2023; 103:4450-4457. [PMID: 36823282 DOI: 10.1002/jsfa.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters. RESULTS Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families. CONCLUSION Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
| | | | - Francisco M Codoñer
- ADM-Lifesequencing - Health and Wellness - Adm Nutrition, Valencia, Spain
- Danone Nutricia Research, Singapore, Singapore
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Valencia, Spain
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Girón-Guzmán I, Díaz-Reolid A, Cuevas-Ferrando E, Falcó I, Cano-Jiménez P, Comas I, Pérez-Cataluña A, Sánchez G. Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing. Sci Total Environ 2023; 862:160914. [PMID: 36526211 PMCID: PMC9744676 DOI: 10.1016/j.scitotenv.2022.160914] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 05/05/2023]
Abstract
During the current COVID-19 pandemic, wastewater-based epidemiology (WBE) emerged as a reliable strategy both as a surveillance method and a way to provide an overview of the SARS-CoV-2 variants circulating among the population. Our objective was to compare two different concentration methods, a well-established aluminum-based procedure (AP) and the commercially available Maxwell® RSC Enviro Wastewater TNA Kit (TNA) for human enteric virus, viral indicators and SARS-CoV-2 surveillance. Additionally, both concentration methods were analyzed for their impact on viral infectivity, and nucleic acids obtained from each method were also evaluated by massive sequencing for SARS-CoV-2. The percentage of SARS-CoV-2 positive samples using the AP method accounted to 100 %, 83.3 %, and 33.3 % depending on the target region while 100 % positivity for these same three target regions was reported using the TNA procedure. The concentrations of norovirus GI, norovirus GII and HEV using the TNA method were significantly greater than for the AP method while no differences were reported for rotavirus, astrovirus, crAssphage and PMMoV. Furthermore, TNA kit in combination with the Artic v4 primer scheme yields the best SARS-CoV-2 sequencing results. Regarding impact on infectivity, the concentration method used by the TNA kit showed near-complete lysis of viruses. Our results suggest that although the performance of the TNA kit was higher than that of the aluminum procedure, both methods are suitable for the analysis of enveloped and non-enveloped viruses in wastewater by molecular methods.
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Affiliation(s)
- Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Pablo Cano-Jiménez
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain.
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
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Girón-Guzmán I, Díaz-Reolid A, Truchado P, Carcereny A, García-Pedemonte D, Hernáez B, Bosch A, Pintó RM, Guix S, Allende A, Alcamí A, Pérez-Cataluña A, Sánchez G. Spanish wastewater reveals the current spread of Monkeypox virus. Water Res 2023; 231:119621. [PMID: 36693290 PMCID: PMC9845017 DOI: 10.1016/j.watres.2023.119621] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/01/2022] [Accepted: 01/15/2023] [Indexed: 05/09/2023]
Abstract
Besides nasopharyngeal swabs, monkeypox virus (MPXV) DNA has been detected in a variety of samples such as saliva, semen, urine and fecal samples. Using the environmental surveillance network previously developed in Spain for the routine wastewater surveillance of SARS-CoV-2 (VATar COVID-19), we have analyzed the presence of MPXV DNA in wastewater from different areas of Spain. Samples (n = 312) from 24 different wastewater treatment plants were obtained between May 9 (week 19 of 2022) and August 4 (week 31 of 2022). Following concentration of viral particles by a validated aluminum adsorption-precipitation method, a qPCR procedure allowed us to detect MPXV DNA in 56 wastewater samples collected from May 16 to August 4, 2022, with values ranging between 2.2 × 103 to 8.7 × 104 genome copies (gc)/L. This study shows that MPXV DNA can be reproducibly detected by qPCR in longitudinal samples collected from different Spanish wastewater treatment plants. According to data from the National Epidemiological Surveillance Network (RENAVE) in Spain a total of 6,119 cases have been confirmed as of August 19, 2022. However, and based on the wastewater data, the reported clinical cases seem to be underestimated and asymptomatic infections may be more frequent than expected.
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Affiliation(s)
- Inés Girón-Guzmán
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Azahara Díaz-Reolid
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Pilar Truchado
- Department of Food Science and Technology, CEBAS-CSIC, Research Group on Quality and Safety of Fruits and Vegetables, Campus Universitario de Espinardo, 25, Murcia 30100, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - David García-Pedemonte
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Bruno Hernáez
- Molecular Biology Center Severo Ochoa, CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Rosa María Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Ana Allende
- Department of Food Science and Technology, CEBAS-CSIC, Research Group on Quality and Safety of Fruits and Vegetables, Campus Universitario de Espinardo, 25, Murcia 30100, Spain
| | - Antonio Alcamí
- Molecular Biology Center Severo Ochoa, CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
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8
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de Llanos R, Cejudo-Marín R, Barneo M, Pérez-Cataluña A, Barberá-Riera M, Rebagliato M, Bellido-Blasco J, Sánchez G, Hernández F, Bijlsma L. Monitoring the evolution of SARS-CoV-2 on a Spanish university campus through wastewater analysis: A pilot project for the reopening strategy. Sci Total Environ 2022; 845:157370. [PMID: 35842154 PMCID: PMC9278994 DOI: 10.1016/j.scitotenv.2022.157370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 06/03/2023]
Abstract
Wastewater surveillance is a fast and cost-effective tool that enables tracing of both symptomatic and asymptomatic transmission of SARS-CoV-2. In this paper, a pilot program carried out at the University Jaume I for monitoring the trends of the presence of SARS-CoV-2 in wastewater. To the best of our knowledge, this is the first such project conducted on a university campus in Spain. Wastewater samples (n = 838) were collected when students returned to campus, from October 2020 until August 2021, at a confluence sewer point and at the building level including different academic departments and services, the library, administration offices and the university student residence. It has been observed that the probability of SARS-CoV-2 RNA detection in wastewater depended on COVID-19 incidence on campus and visitors/occupants of the buildings i.e., high-, or low-traffic buildings with high or low frequency of potential contacts. Moreover, the third wave in Spain (after Christmas 2020) and an outbreak that occurred at the university student's residence could be carefully followed, allowing confirmation of the end of the outbreak. In addition, viral variants (i.e., mutations and linages) from selected time points were detected by sequencing and gave an indication of the evolution of the virus over time. The results illustrate the potential of wastewater-based epidemiology to provide an early warning for SARS-CoV-2 within the university, especially in buildings with low traffic and more defined populations, like the student residence. The strategy and experience gathered in this study will allow for implementation of improvements for reliable monitoring in the future.
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Affiliation(s)
- Rosa de Llanos
- Faculty of Health Sciences, University Jaume I, Castellón, Spain.
| | | | - Manuela Barneo
- Faculty of Health Sciences, University Jaume I, Castellón, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - María Barberá-Riera
- Faculty of Health Sciences, University Jaume I, Castellón, Spain; Epidemiology and Public Health Center of Castellón, Spain
| | - Marisa Rebagliato
- Faculty of Health Sciences, University Jaume I, Castellón, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Bellido-Blasco
- Faculty of Health Sciences, University Jaume I, Castellón, Spain; Epidemiology and Public Health Center of Castellón, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Félix Hernández
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castellón, Spain
| | - Lubertus Bijlsma
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, Castellón, Spain.
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9
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Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:v14071522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
- Correspondence: (F.H.); (M.M.)
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
- Correspondence: (F.H.); (M.M.)
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Hufsky F, Beslic D, Boeckaerts D, Duchene S, González-Tortuero E, Gruber AJ, Guo J, Jansen D, Juma J, Kongkitimanon K, Luque A, Ritsch M, Lencioni Lovate G, Nishimura L, Pas C, Domingo E, Hodcroft E, Lemey P, Sullivan MB, Weber F, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2022. Viruses 2022; 14:973. [PMID: 35632715 PMCID: PMC9144528 DOI: 10.3390/v14050973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/22/2022] Open
Abstract
The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Denis Beslic
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (D.B.); (C.P.)
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia;
| | - Enrique González-Tortuero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- School of Science, Engineering and Environment (SEE), University of Salford, Salford M5 4WT, UK
| | - Andreas J. Gruber
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Jiarong Guo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Departments of Microbiology, and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Daan Jansen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, KU Leuven, 3000 Leuven, Belgium
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya;
- South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, Cape Town 7530, South Africa
| | - Kunaphas Kongkitimanon
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Antoni Luque
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Viral Information Institute, San Diego State University, San Diego, CA 92116, USA
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, USA
| | - Muriel Ritsch
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Gabriel Lencioni Lovate
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- JRG Analytical MicroBioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Célia Pas
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (D.B.); (C.P.)
| | - Esteban Domingo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Emma Hodcroft
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Philippe Lemey
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Matthew B. Sullivan
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Departments of Microbiology, and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Friedemann Weber
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Virology, Veterinary Medicine, Justus-Liebig University, 35390 Gießen, Germany
| | - Fernando González-Candelas
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Joint Research Unit “Infection and Public Health” FISABIO, University of Valencia, 46010 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC, University of Valencia, 46010 Valencia, Spain
| | - Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Walter Randazzo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Gloria Sánchez
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
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Cuevas-Ferrando E, Pérez-Cataluña A, Falcó I, Randazzo W, Sánchez G. Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse. Front Microbiol 2022; 13:836193. [PMID: 35464930 PMCID: PMC9026171 DOI: 10.3389/fmicb.2022.836193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 01/22/2023] Open
Abstract
Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log10 GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log10 GC/L in influent and from 4.56 to 6.96 log10 GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.
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Pérez-Cataluña A, Chiner-Oms Á, Cuevas-Ferrando E, Díaz-Reolid A, Falcó I, Randazzo W, Girón-Guzmán I, Allende A, Bracho MA, Comas I, Sánchez G. Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater. Water Res 2022; 211:118007. [PMID: 35033744 PMCID: PMC8702378 DOI: 10.1016/j.watres.2021.118007] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/15/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.
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Affiliation(s)
- Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
| | - Álvaro Chiner-Oms
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain
| | - Enric Cuevas-Ferrando
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Azahara Díaz-Reolid
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Irene Falcó
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Walter Randazzo
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Inés Girón-Guzmán
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Ana Allende
- Department of Food Science and Technology, CEBAS-CSIC, Research Group on Quality and Safety of Fruits and Vegetables, Campus Universitario de Espinardo, 25, Murcia 30100, Spain
| | - María A Bracho
- FISABIO - Public Health, Department of Genomics and Health, Av. Catalunya, 21, Valencia 46020, Spain; Joint Research Unit "Infection and Public Health" FISABIO-Universitat de Valencia I2SysBio, Av. Catalunya, 21, Valencia 46020, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
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Cuevas-Ferrando E, Girón-Guzmán I, Falcó I, Pérez-Cataluña A, Díaz-Reolid A, Aznar R, Randazzo W, Sánchez G. Discrimination of non-infectious SARS-CoV-2 particles from fomites by viability RT-qPCR. Environ Res 2022; 203:111831. [PMID: 34352235 PMCID: PMC8327643 DOI: 10.1016/j.envres.2021.111831] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/01/2021] [Accepted: 08/01/2021] [Indexed: 05/05/2023]
Abstract
The ongoing coronavirus 2019 (COVID-19) pandemic constitutes a concerning global threat to public health and economy. In the midst of this pandemic scenario, the role of environment-to-human COVID-19 spread is still a matter of debate because mixed results have been reported concerning SARS-CoV-2 stability on high-touch surfaces in real-life scenarios. Up to now, no alternative and accessible procedures for cell culture have been applied to evaluate SARS-CoV-2 infectivity on fomites. Several strategies based on viral capsid integrity have latterly been developed using viability markers to selectively remove false-positive qPCR signals resulting from free nucleic acids and damaged viruses. These have finally allowed an estimation of viral infectivity. The present study aims to provide a rapid molecular-based protocol for detection and quantification of viable SARS-CoV-2 from fomites based on the discrimination of non-infectious SARS-CoV-2 particles by platinum chloride (IV) (PtCl4) viability RT-qPCR. An initial assessment compared two different swabbing procedures to recover inactivated SARS-CoV-2 particles from fomites coupled with two RNA extraction methods. Procedures were validated with human (E229) and porcine (PEDV) coronavirus surrogates, and compared with inactivated SARS-CoV-2 suspensions on glass, steel and plastic surfaces. The viability RT-qPCR efficiently removed the PCR amplification signals from heat and gamma-irradiated inactivated SARS-CoV-2 suspensions that had been collected from specified surfaces. This study proposes a rapid viability RT-qPCR that discriminates non-infectious SARS-CoV-2 particles on surfaces thus helping researchers to better understand the risk of contracting COVID-19 through contact with fomites and to develop more efficient epidemiological measures.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Rosa Aznar
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
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14
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Cuevas-Ferrando E, Randazzo W, Pérez-Cataluña A, Falcó I, Navarro D, Martin-Latil S, Díaz-Reolid A, Girón-Guzmán I, Allende A, Sánchez G. Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples. Sci Rep 2021; 11:18120. [PMID: 34518622 PMCID: PMC8438079 DOI: 10.1038/s41598-021-97700-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Sandra Martin-Latil
- ANSES Laboratory for Food Safety, Université Paris-Est, 94700, Maisons-Alfort, France
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
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15
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Cuevas-Ferrando E, Randazzo W, Pérez-Cataluña A, Falcó I, Navarro D, Martin-Latil S, Díaz-Reolid A, Girón-Guzmán I, Allende A, Sánchez G. Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples. Sci Rep 2021; 11:18120. [PMID: 34518622 DOI: 10.1101/2021.03.22.21253818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 05/21/2023] Open
Abstract
Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Sandra Martin-Latil
- ANSES Laboratory for Food Safety, Université Paris-Est, 94700, Maisons-Alfort, France
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
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16
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Carcereny A, Martínez-Velázquez A, Bosch A, Allende A, Truchado P, Cascales J, Romalde JL, Lois M, Polo D, Sánchez G, Pérez-Cataluña A, Díaz-Reolid A, Antón A, Gregori J, Garcia-Cehic D, Quer J, Palau M, Ruano CG, Pintó RM, Guix S. Monitoring Emergence of the SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). Environ Sci Technol 2021; 55:11756-11766. [PMID: 34397216 PMCID: PMC8404293 DOI: 10.1021/acs.est.1c03589] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 05/03/2023]
Abstract
Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2 has become dominant in several countries raising great concern. We developed a duplex real-time RT-qPCR assay to detect, discriminate, and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the ΔHV69/70 deletion, and used it to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). The B.1.1.7 variant was detected earlier than clinical epidemiological reporting by the local authorities, first in the southern city of Málaga (Andalucía) in week 20_52 (year_week), and multiple introductions during Christmas holidays were inferred in different parts of the country. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from wastewater treatment plants, which reached B.1.1.7 prevalences higher than 90% for ≥2 consecutive weeks showed that 8.1 ± 2.0 weeks were required for B.1.1.7 to become dominant. The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern as soon as they are identified by clinical sequencing and their integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.
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Affiliation(s)
- Albert Carcereny
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Adán Martínez-Velázquez
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Albert Bosch
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Ana Allende
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Pilar Truchado
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jenifer Cascales
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jesús L Romalde
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Marta Lois
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - David Polo
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Gloria Sánchez
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Alba Pérez-Cataluña
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Azahara Díaz-Reolid
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Andrés Antón
- Microbiology
Department, Vall d’Hebron Institut
de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital
Campus, Barcelona 08035, Spain
| | - Josep Gregori
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Damir Garcia-Cehic
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Josep Quer
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Margarita Palau
- General
Directorate of Public Health, Ministry of Health, Madrid 28014, Spain
| | - Cristina González Ruano
- Subdirección
General de Protección de las Aguas y Gestión de Riesgos,
Ministerio para la Transición Ecológica y el Reto Demográfico, Madrid 28071, Spain
| | - Rosa M Pintó
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Susana Guix
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
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17
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Cuevas-Ferrando E, Allende A, Pérez-Cataluña A, Truchado P, Hernández N, Gil MI, Sánchez G. Occurrence and Accumulation of Human Enteric Viruses and Phages in Process Water from the Fresh Produce Industry. Foods 2021; 10:foods10081853. [PMID: 34441630 PMCID: PMC8391481 DOI: 10.3390/foods10081853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022] Open
Abstract
The virological quality of process water (PW) used by the produce industry has received limited attention. As a first step to overcoming technical limitations in monitoring viruses in PW, the analytical performance of ultrafiltration was assessed to concentrate viral particles from 20 L of spiked PW. The selected method used for sample concentration of PW was carefully validated, thus enabling the accurate quantification and estimation of viral titers of human enteric viruses and phages. PW from the produce industry was collected periodically from the washing tanks of commercial facilities. The analysis of coliphages was performed by plaque assay, while the occurrence of enteric viruses and crAssphage was determined by molecular techniques. Significant differences in the physicochemical composition of PW, mostly due to the different nature of fresh produce types and differences in the sanitizer used in commercial operation, were observed. Accumulation of crAssphage and coliphages was observed in PW, but correlation with human enteric viruses was not possible due to the low prevalence of these pathogens in the PW analyzed. The obtained results showed that depending on the type of product washed, the product/water ratio and the residual concentrations of the sanitizers, the prevalence and concentration of bacteriophages changed significantly.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980 Valencia, Spain; (E.C.-F.); (A.P.-C.)
| | - Ana Allende
- Research Group on Microbiology and Quality of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (A.A.); (P.T.); (N.H.); (M.I.G.)
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980 Valencia, Spain; (E.C.-F.); (A.P.-C.)
| | - Pilar Truchado
- Research Group on Microbiology and Quality of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (A.A.); (P.T.); (N.H.); (M.I.G.)
| | - Natalia Hernández
- Research Group on Microbiology and Quality of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (A.A.); (P.T.); (N.H.); (M.I.G.)
| | - Maria Isabel Gil
- Research Group on Microbiology and Quality of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain; (A.A.); (P.T.); (N.H.); (M.I.G.)
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980 Valencia, Spain; (E.C.-F.); (A.P.-C.)
- Correspondence:
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18
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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. Sci Total Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Cuevas-Ferrando E, Pérez-Cataluña A, Allende A, Guix S, Randazzo W, Sánchez G. Recovering coronavirus from large volumes of water. Sci Total Environ 2021; 762:143101. [PMID: 33268258 DOI: 10.1016/jscitontenv.2020.143101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 05/28/2023]
Abstract
The need for monitoring tools to better control the ongoing coronavirus disease (COVID-19) pandemic is extremely urgent and the contamination of water resources by excreted viral particles poses alarming questions to be answered. As a first step to overcome technical limitations in monitoring SARS-CoV-2 along the water cycle, we assessed the analytical performance of a dead end hollow fiber ultrafiltration coupled to different options for secondary concentrations to concentrate viral particles from large volume of spiked tap water, seawater and surface water together with two quantitative RT-qPCR detection kits. Spiking the porcine epidemic diarrhea virus (PEDV), an enveloped virus surrogate for SARS-CoV-2, together with the mengovirus, we demonstrated that PEG-precipitation and SENS-kit better recovered PEDV (13.10 ± 0.66%) from tap water, while centrifugal filtration resulted the best option to recover mengovirus regardless of the detection kit used. No statistical significant differences were found when comparing high (10,000 ×g) and low (3500 ×g) centrifugation speeds for the secondary PEG- based concentration of spiked seawater, while considerable inhibition was observed for both viruses detected by NoInh-kit assay. Similarly, the co-concentration of PCR inhibitors and viral particles was observed in surface waters detected with either SENS-kit or NoInh-kit and RNA dilution was needed to achieve acceptable recoveries at the expenses of the overall sensitivity of the method. These methodologies represent suitable options to investigate SARS-CoV-2 occurrence in different water resources and allow to conduct on site sampling of large volume of water.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Ana Allende
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain
| | - Susana Guix
- Enteric Virus laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Av. Dr. Moliner, 50, Burjassot, 46100, Valencia, Spain.
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
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20
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Cuevas-Ferrando E, Pérez-Cataluña A, Allende A, Guix S, Randazzo W, Sánchez G. Recovering coronavirus from large volumes of water. Sci Total Environ 2021; 762:143101. [PMID: 33268258 PMCID: PMC7563921 DOI: 10.1016/j.scitotenv.2020.143101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 05/18/2023]
Abstract
The need for monitoring tools to better control the ongoing coronavirus disease (COVID-19) pandemic is extremely urgent and the contamination of water resources by excreted viral particles poses alarming questions to be answered. As a first step to overcome technical limitations in monitoring SARS-CoV-2 along the water cycle, we assessed the analytical performance of a dead end hollow fiber ultrafiltration coupled to different options for secondary concentrations to concentrate viral particles from large volume of spiked tap water, seawater and surface water together with two quantitative RT-qPCR detection kits. Spiking the porcine epidemic diarrhea virus (PEDV), an enveloped virus surrogate for SARS-CoV-2, together with the mengovirus, we demonstrated that PEG-precipitation and SENS-kit better recovered PEDV (13.10 ± 0.66%) from tap water, while centrifugal filtration resulted the best option to recover mengovirus regardless of the detection kit used. No statistical significant differences were found when comparing high (10,000 ×g) and low (3500 ×g) centrifugation speeds for the secondary PEG- based concentration of spiked seawater, while considerable inhibition was observed for both viruses detected by NoInh-kit assay. Similarly, the co-concentration of PCR inhibitors and viral particles was observed in surface waters detected with either SENS-kit or NoInh-kit and RNA dilution was needed to achieve acceptable recoveries at the expenses of the overall sensitivity of the method. These methodologies represent suitable options to investigate SARS-CoV-2 occurrence in different water resources and allow to conduct on site sampling of large volume of water.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Ana Allende
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain
| | - Susana Guix
- Enteric Virus laboratory, Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, School of Biology, Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Av. Dr. Moliner, 50, Burjassot, 46100, Valencia, Spain.
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
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21
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Pérez-Cataluña A, Cuevas-Ferrando E, Randazzo W, Falcó I, Allende A, Sánchez G. Comparing analytical methods to detect SARS-CoV-2 in wastewater. Sci Total Environ 2021; 758:143870. [PMID: 33338788 PMCID: PMC7722604 DOI: 10.1016/j.scitotenv.2020.143870] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 05/09/2023]
Abstract
Wastewater based epidemiology (WBE) has emerged as a reliable strategy to assess the coronavirus disease 2019 (COVID-19) pandemic. Recent publications suggest that SARS-CoV-2 detection in wastewater is technically feasible; however, many different protocols are available and most of the methods applied have not been properly validated. To this end, different procedures to concentrate and extract inactivated SARS-CoV-2 and surrogates were initially evaluated. Urban wastewater seeded with gamma-irradiated SARS-CoV-2, porcine epidemic diarrhea virus (PEDV), and mengovirus (MgV) was used to test the concentration efficiency of an aluminum-based adsorption-precipitation method and a polyethylene glycol (PEG) precipitation protocol. Moreover, two different RNA extraction methods were compared in this study: a commercial manual spin column centrifugation kit and an automated protocol based on magnetic silica beads. Overall, the evaluated concentration methods did not impact the recovery of gamma-irradiated SARS-CoV-2 nor MgV, while extraction methods showed significant differences for PEDV. Mean recovery rates of 42.9 ± 9.5%, 27.5 ± 14.3% and 9.0 ± 2.2% were obtained for gamma-irradiated SARS-CoV-2, PEDV and MgV, respectively. Limits of detection (LoD95%) for five genomic SARS-CoV-2 targets (N1, N2, gene E, IP2 and IP4) ranged from 1.56 log genome equivalents (ge)/mL (N1) to 2.22 log ge/mL (IP4) when automated system was used; while values ranging between 2.08 (N1) and 2.34 (E) log ge/mL were observed when using column-based extraction method. Different targets were also evaluated in naturally contaminated wastewater samples with 91.2%, 85.3%, 70.6%, 79.4% and 73.5% positivity, for N1, N2, E, IP2 and IP4, respectively. Our benchmarked comparison study suggests that the aluminum precipitation method coupled with the automated nucleic extraction represents a method of acceptable sensitivity to provide readily results of interest for SARS-CoV-2 WBE surveillance.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Av. Dr. Moliner, 50, Burjassot, 46100, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
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22
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Göksen G, Fabra MJ, Pérez-Cataluña A, Ekiz HI, Sanchez G, López-Rubio A. Biodegradable active food packaging structures based on hybrid cross-linked electrospun polyvinyl alcohol fibers containing essential oils and their application in the preservation of chicken breast fillets. Food Packag Shelf Life 2021. [DOI: 10.1016/j.fpsl.2020.100613] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Alonso R, Girbau C, Martinez-Malaxetxebarria I, Pérez-Cataluña A, Salas-Massó N, Romalde JL, Figueras MJ, Fernandez-Astorga A. Aliarcobacter vitoriensis sp. nov., isolated from carrot and urban wastewater. Syst Appl Microbiol 2020; 43:126091. [PMID: 32690190 DOI: 10.1016/j.syapm.2020.126091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Two isolates, one recovered from a carrot and another one from urban wastewater, were characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates clustered together, and were most closely related to Aliarcobacter lanthieri. Multilocus phylogenetic analysis (MLPA) using the concatenated sequences of five housekeeping genes (atpA, gyrA, gyrB, hsp60 and rpoB) suggested that these isolates formed a distinct phylogenetic lineage among the genera derived from the former genus Arcobacter. Whole-genome sequence, in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) value between the genome of strain F199T and those of related species confirmed that these isolates represent a novel species. These strains can be differentiated from its phylogenetically closest species A. lanthieri by its inability to growth on 1% glycine and by their enzyme activity of esterase lipase (C8) and acid phosphatase. Our results, by the application of a polyphasic analysis, confirmed that these two isolates represent a novel species of the genus Aliarcobacter, for which the name Aliarcobacter vitoriensis sp. nov. is proposed. The type strain is F199T (=CECT 9230T=LMG 30050T).
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Affiliation(s)
- Rodrigo Alonso
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Cecilia Girbau
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Irati Martinez-Malaxetxebarria
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
| | - Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología & Instituto CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782 Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Aurora Fernandez-Astorga
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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24
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Cuevas-Ferrando E, Martínez-Murcia A, Pérez-Cataluña A, Sánchez G, Randazzo W. Assessment of ISO Method 15216 to Quantify Hepatitis E Virus in Bottled Water. Microorganisms 2020; 8:E730. [PMID: 32414206 PMCID: PMC7284727 DOI: 10.3390/microorganisms8050730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Hepatitis E virus (HEV) is one of the causative agents of water-borne human viral hepatitis and considered in Europe an emerging zoonotic pathogen. Analysis of bottled water through a standard method validated for HEV can contribute towards the risk management of this hazard. Putting some recent reports by the European Food Safety Authority in place, this study aimed to assess the performance of the concentration and extraction procedures described in ISO 15216-1:2017 for norovirus and hepatitis A virus on HEV detection. Following the ISO recommendation, the bottled water samples were spiked using serially diluted HEV fecal suspensions together with mengovirus as process control and concentrated by filtration via positively charged nylon membranes. In order to extract viral RNA from the resulting concentrates, two different methods were compared in this study: The one recommended in the ISO norm, NucliSens® MiniMag® system (NS), and an alternative commercially available kit NucleoSpin®RNA virus kit (MN). Finally, three reverse transcription quantitative PCR (RT-qPCR) assays were used to quantify HEV titers. The evaluated procedures resulted in average HEV recoveries of 14.08 ± 4.90% and 3.58 ± 0.30% for the MN and NS methods, respectively. The limit of detection (LoD95%) was 1.25 × 104 IU/L for both extraction methods combined with the three RT-qPCR assays tested, with the exception of NS extraction coupled with RT-qPCR1 that showed a LoD95% of 4.26 × 103 IU/L. The method characteristics generated in this study support the limited suitability of the ISO 15216-1:2017 concentration procedure coupled with the evaluated RT-qPCR assays for detecting HEV in bottled water.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Av. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (E.C.-F.); (A.P.-C.); (G.S.)
| | - Antonio Martínez-Murcia
- Area de Microbiología, EPSO, Universidad Miguel Hernández, Carretera de Beniel Km 3.2, 03312 Orihuela, Alicante, Spain;
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Av. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (E.C.-F.); (A.P.-C.); (G.S.)
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Av. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (E.C.-F.); (A.P.-C.); (G.S.)
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Av. Agustín Escardino 7, 46980 Paterna, Valencia, Spain; (E.C.-F.); (A.P.-C.); (G.S.)
- Department of Microbiology and Ecology, University of Valencia. Av. Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
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25
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Rusiñol M, Hundesa A, Cárdenas-Youngs Y, Fernández-Bravo A, Pérez-Cataluña A, Moreno-Mesonero L, Moreno Y, Calvo M, Alonso JL, Figueras MJ, Araujo R, Bofill-Mas S, Girones R. Microbiological contamination of conventional and reclaimed irrigation water: Evaluation and management measures. Sci Total Environ 2020; 710:136298. [PMID: 31923670 DOI: 10.1016/j.scitotenv.2019.136298] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/21/2019] [Accepted: 12/21/2019] [Indexed: 05/22/2023]
Abstract
The wide diversity of irrigation water sources (i.e., drinking water, groundwater, reservoir water, river water) includes reclaimed water as a requested measure for increasing water availability, but it is also a challenge as pathogen exposure may increase. This study evaluates the level of microbial contamination in different irrigation waters to improve the knowledge and analyses management measures for safety irrigation. Over a one-year period, the occurrence of a set of viruses, bacteria and protozoa, was quantified and the performance of a wetland system, producing reclaimed water intended for irrigation, was characterized. Human fecal pollution (HAdV) was found in most of the irrigation water types analysed. Hepatitis E virus (HEV), an emerging zoonotic pathogen, was present in groundwater where porcine contamination was identified (PAdV). The skin-carcinoma associated Merkel cell polyomavirus (MCPyV), was found occasionally in river water. Noroviruses were detected, as expected, in winter, in river water and reclaimed water. Groundwater, river water and reservoir water also harboured potential bacterial pathogens, like Helicobacter pylori, Legionella spp. and Aeromonas spp. that could be internalized and viable inside amoebas like Acanthamoeba castellanii, which was also detected. Neither Giardia cysts, nor any Cryptosporidium oocysts were detected. The wetland system removed 3 Log10 of viruses and 5 Log10 of bacteria, which resembled the river water quality. Irrigation waters were prone to variable contamination levels and according to the European guidance documents, the E. coli (EC) levels were not always acceptable. Sporadic detection of viral pathogens as NoV GII and HAdV was identified in water samples presenting lower EC than the established limit (100MNP/100 mL). When dealing with reclaimed water as a source of irrigation the analysis of some viral parameters, like HAdV during the peak irrigation period (summer and spring) or NoV during the coldest months, could complement existing water management tools based on bacterial indicators.
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Affiliation(s)
- Marta Rusiñol
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain.
| | - Ayalkibet Hundesa
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
| | - Yexenia Cárdenas-Youngs
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
| | - Ana Fernández-Bravo
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - Alba Pérez-Cataluña
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - Laura Moreno-Mesonero
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Valencia, Spain
| | - Yolanda Moreno
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Valencia, Spain
| | - Miquel Calvo
- Section of Statistics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Alonso
- Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, Valencia, Spain
| | - Maria José Figueras
- Microbiology Unit, Faculty of Medicine and Health Sciences, IISPV, University Rovira and Virgili, Reus, Catalonia, Spain
| | - Rosa Araujo
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
| | - Rosina Girones
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
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26
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Cuevas-Ferrando E, Randazzo W, Pérez-Cataluña A, Sánchez G. HEV Occurrence in Waste and Drinking Water Treatment Plants. Front Microbiol 2020; 10:2937. [PMID: 31993027 PMCID: PMC6971180 DOI: 10.3389/fmicb.2019.02937] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/06/2019] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV), particularly zoonotic genotype 3, is present in environmental waters worldwide, especially in industrialized countries. Thus, monitoring the presence of HEV in wastewater treatment plants (WWTPs) is an emerging topic due to the importance of reusing water on a global level. Given the limited data, this study aimed to monitor the occurrence of HEV in influent and effluent water in waste- and drinking-water treatment plants (WWTPs and DWTPs). To this end, different procedures to concentrate HEV in influent and effluent water from WWTPs and DWTPs were initially evaluated. The evaluated procedures resulted in average HEV recoveries of 15.2, 19.9, and 16.9% in influent, effluent, and drinking water samples, respectively, with detection limits ranging from 103 to 104 international units (IU)/L. Then, a one-year pilot study was performed to evaluate the performance of the selected concentration method coupled with three RT-qPCR assays in influent and effluent water samples from four different WWTPs. HEV prevalence in influent water varied based on both the RT-qPCR assay and WWTP, while HEV was not detected in effluent water samples. In addition, HEV prevalence using only RT-qPCR3 was evaluated in influent (n = 62) and effluent samples (n = 52) from four WWTPs as well as influent (n = 28) and effluent (n = 28) waters from two DWTPs. The present study demonstrated that HEV circulated in the Valencian region at around 30.65% with average concentrations of 6.3 × 103 IU/L. HEV was only detected in influent wastewater samples, effluent samples from WWTPs and influent and effluent samples from DWTPs were negative. However, given that the infective dose in waterborne epidemics settings is not yet known and the low sensibility of the assay, unfortunately, no direct conclusion could be achieved on the risk assessment of environmental contamination.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos – Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos – Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
- Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos – Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos – Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
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27
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Pérez-Cataluña A, Salas-Massó N, Figueras MJ. Arcobacter lacus sp. nov. and Arcobacter caeni sp. nov., two novel species isolated from reclaimed water. Int J Syst Evol Microbiol 2019; 69:3326-3331. [DOI: 10.1099/ijsem.0.003101] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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28
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Corrigendum (2): Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos. Front Microbiol 2019; 10:2253. [PMID: 31611866 PMCID: PMC6779803 DOI: 10.3389/fmicb.2019.02253] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alba Pérez-Cataluña
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María J Figueras
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
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29
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Corrigendum: Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Caos. Front Microbiol 2018; 9:3123. [PMID: 30622519 PMCID: PMC6308300 DOI: 10.3389/fmicb.2018.03123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 12/05/2022] Open
Affiliation(s)
- Alba Pérez-Cataluña
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria José Figueras
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
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30
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos. Front Microbiol 2018; 9:2077. [PMID: 30233547 PMCID: PMC6131481 DOI: 10.3389/fmicb.2018.02077] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/14/2018] [Indexed: 11/16/2022] Open
Abstract
Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.
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Affiliation(s)
- Alba Pérez-Cataluña
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria J Figueras
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
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Diéguez AL, Pérez-Cataluña A, Figueras MJ, Romalde JL. Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrous Diéguez et al. 2017. Int J Syst Evol Microbiol 2018; 68:2851-2854. [DOI: 10.1099/ijsem.0.002909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana L. Diéguez
- 1Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alba Pérez-Cataluña
- 2Departament de Ciéncies Médiques Bàsiques, Facultat de Medicina, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Maria José Figueras
- 2Departament de Ciéncies Médiques Bàsiques, Facultat de Medicina, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Jesús L. Romalde
- 1Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Pérez-Cataluña A, Collado L, Salgado O, Lefiñanco V, Figueras MJ. A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars. Front Microbiol 2018; 9:805. [PMID: 29755434 PMCID: PMC5934430 DOI: 10.3389/fmicb.2018.00805] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/10/2018] [Indexed: 12/01/2022] Open
Abstract
The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976T).
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Affiliation(s)
- Alba Pérez-Cataluña
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Luis Collado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - Oscar Salgado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile.,Laboratory of Microbial Ecology of Extreme Systems, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Violeta Lefiñanco
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - María J Figueras
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
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Pérez-Cataluña A, Salas-Massó N, Figueras MJ. Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage. Int J Syst Evol Microbiol 2018; 68:1258-1264. [PMID: 29488868 DOI: 10.1099/ijsem.0.002662] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Four bacterial strains recovered from shellfish (n=3) and from the water (n=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus Arcobacter (represented by strain F138-33T) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being Arcobacter marinus and Arcobactermolluscorum. However, phylogenetic analyses using the concatenated sequences of housekeeping genes (atpA, gyrB, hsp60, gyrA and rpoB) showed that all the novel strains formed a distinct lineage within the genus Arcobacter. Results of in silico DNA-DNA hybridization and the average nucleotide identity between the genome of strain F138-33T and those of the closely related species A. marinus and other relatively closely related species such as A. molluscorum and Arcobacterhalophilus were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name Arcobacter canalis sp. nov. is proposed, with the type strain F138-33T (=CECT 8984T=LMG 29148T).
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Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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Pérez-Cataluña A, Tapiol J, Benavent C, Sarvisé C, Gómez F, Martínez B, Terron-Puig M, Recio G, Vilanova A, Pujol I, Ballester F, Rezusta A, Figueras MJ. Antimicrobial susceptibility, virulence potential and sequence types associated with Arcobacter strains recovered from human faeces. J Med Microbiol 2017; 66:1736-1743. [PMID: 29120301 DOI: 10.1099/jmm.0.000638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The genus Arcobacter includes bacteria that are considered emergent pathogens because they can produce infections in humans and animals. The most common symptoms are bloody and non-bloody persistent diarrhea but cases with abdominal cramps without diarrhea or asymptomatic cases have also been described as well as cases with bacteremia. The objective was to characterize Arcobacter clinical strains isolated from the faeces of patients from three Spanish hospitals. METHODOLOGY We have characterized 28 clinical strains (27 of A. butzleri and one of A. cryaerophilus) isolated from faeces, analysing their epidemiological relationship using the multilocus sequence typing (MLST) approach and screening them for their antibiotic susceptibility and for the presence of virulence genes.Results/Key findings. Typing results showed that only one of the 28 identified sequence types (i.e. ST 2) was already present in the MLST database. The other 27 STs constituted new records because they included new alleles for five of the seven genes or new combinations of known alleles of the seven genes. All strains were positive for the ciaB virulence gene and sensitive to tetracycline. However, 7.4 % of the A. butzleri and A. cryaerophilus strains showed resistance to ciprofloxacin. CONCLUSION The fact that epidemiological unrelated strains show the same ST indicates that other techniques with higher resolution should be developed to effectively recognize the infection source. Resistance to ciprofloxacin, one of the antibiotics recommended for the treatment of Arcobacter intestinal infections, demonstrated in 10.7 % of the strains, indicates the importance of selecting the most appropriate effective treatment.
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Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
| | | | | | | | | | | | | | - Gemma Recio
- Hospital Universitari Joan XXIII, Tarragona, Spain
| | | | | | | | | | - María Jose Figueras
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
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Pérez-Cataluña A, Elizaquível P, Carrasco P, Espinosa J, Reyes D, Wacher C, Aznar R. Diversity and dynamics of lactic acid bacteria in Atole agrio, a traditional maize-based fermented beverage from South-Eastern Mexico, analysed by high throughput sequencing and culturing. Antonie van Leeuwenhoek 2017; 111:385-399. [DOI: 10.1007/s10482-017-0960-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/10/2017] [Indexed: 12/13/2022]
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Figueras MJ, Pérez-Cataluña A, Salas-Massó N, Levican A, Collado L. ' Arcobacter porcinus' sp. nov., a novel Arcobacter species uncovered by Arcobacter thereius. New Microbes New Infect 2016; 15:104-106. [PMID: 28070334 PMCID: PMC5219630 DOI: 10.1016/j.nmni.2016.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 10/26/2016] [Accepted: 11/04/2016] [Indexed: 11/11/2022] Open
Abstract
Arcobacter thereius is a species associated with human disease. A group of A. thereius pork strains (represented by strain LMG 24487) clustered separately from the type strain (LMG 24486T) in the 16S rRNA and multilocus phylogenetic trees. In silico DNA-DNA hybridization and average nucleotide identity results between their genomes (93.3 and 51.1%) confirmed ‘Arcobacter porcinus’ (LMG 24487T) as a new species.
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Affiliation(s)
- M J Figueras
- Unidad de Microbiología, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - A Pérez-Cataluña
- Unidad de Microbiología, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - N Salas-Massó
- Unidad de Microbiología, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain
| | - A Levican
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - L Collado
- Unidad de Microbiología, Facultad de Medicina y Ciencias de la Salud, IISPV, Universidad Rovira i Virgili, Reus, Spain; Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Pérez-Cataluña A, Lucena T, Tarazona E, Arahal DR, Macián MC, Pujalte MJ. An MLSA approach for the taxonomic update of the Splendidus clade, a lineage containing several fish and shellfish pathogenic Vibrio spp. Syst Appl Microbiol 2016; 39:361-9. [DOI: 10.1016/j.syapm.2016.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/22/2016] [Accepted: 03/30/2016] [Indexed: 11/29/2022]
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Mottola A, Bonerba E, Figueras MJ, Pérez-Cataluña A, Marchetti P, Serraino A, Bozzo G, Terio V, Tantillo G, Di Pinto A. Occurrence of potentially pathogenic arcobacters in shellfish. Food Microbiol 2016; 57:23-7. [PMID: 27052698 DOI: 10.1016/j.fm.2015.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/18/2015] [Accepted: 12/27/2015] [Indexed: 10/22/2022]
Abstract
Considering that several recent cases of human gastroenteritis have been associated with species from the Arcobacter genus, and that few data are currently available about the occurrence of this genus in Italian shellfish, the aim of the present study was to evaluate the occurrence of Arcobacter spp. and the presence of virulence-associated genes. The approach consisted of cultural and biomolecular (multiplex-PCR and 16S-RFLP) methods identifying isolates, followed by PCR assays aimed at the cadF, ciaB, cjl349, irgA, hecA putative virulence genes. Arcobacter spp. was detected in 16/70 (22.8%) shellfish samples. Specifically, Arcobacter spp. was highlighted in 10/42 (23.8%) mussel and in 6/28 (21.4%) clam samples. Subsequently, biomolecular assays revealed Arcobacter butzleri in 12/16 (75%) and Arcobacter cryaerophilus 1B in 4/16 (25%) isolates. PCRs aimed at the five putative virulence genes demonstrated widespread distribution of these genes among Arcobacter isolates and some differences from the results published by other authors. Our research provides more information regarding the health risks associated with the consumption of raw bivalve molluscs and underlines the need to implement an adequate control plan by performing intensive and continuous monitoring in order to guarantee human health.
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Affiliation(s)
- Anna Mottola
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy.
| | - Elisabetta Bonerba
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - Maria José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Patrizia Marchetti
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, Via Tolara di Sopra 50, 40064 Ozzano Emilia (BO), Italy
| | - Giancarlo Bozzo
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - Valentina Terio
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - Giuseppina Tantillo
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima, km 3, 70010 Valenzano, Bari, Italy
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Elizaquível P, Pérez-Cataluña A, Yépez A, Aristimuño C, Jiménez E, Cocconcelli PS, Vignolo G, Aznar R. Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina. Int J Food Microbiol 2015; 198:9-18. [DOI: 10.1016/j.ijfoodmicro.2014.12.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/09/2014] [Accepted: 12/21/2014] [Indexed: 11/16/2022]
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Tarazona E, Pérez-Cataluña A, Lucena T, Arahal DR, Macián MC, Pujalte MJ. Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio. Syst Appl Microbiol 2015; 38:169-75. [PMID: 25861826 DOI: 10.1016/j.syapm.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 01/25/2023]
Abstract
A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoenteri, both the other individual gene trees and the trees obtained from the five-genes concatenated sequences were able to consistently differentiate four subclades within the main clade, corresponding to the bona fide V. scophthalmi, V. ichthyoenteri, and two small ones that may represent a new species each. The best genes to differentiate V. scophthalmi from V. ichthyoenteri were rpoD, recA, and mreB. Vibrio ponticus failed to associate to the clade in the MLSA and in most single gene trees for which it should not be considered part of it. In this study we also confirm using genomic indexes that V. ichthyoenteri and V. scophthalmi are two separate species.
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Affiliation(s)
- Eva Tarazona
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - Alba Pérez-Cataluña
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - Teresa Lucena
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - David R Arahal
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - M Carmen Macián
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - María J Pujalte
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain.
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