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Sacristán-Soriano O, Jarma D, Sánchez MI, Romero N, Alonso E, Green AJ, Sànchez-Melsió A, Hortas F, Balcázar JL, Peralta-Sánchez JM, Borrego CM. Winged resistance: Storks and gulls increase carriage of antibiotic resistance by shifting from paddy fields to landfills. Sci Total Environ 2024; 914:169946. [PMID: 38199372 DOI: 10.1016/j.scitotenv.2024.169946] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Waterbirds are vectors for the dissemination of antimicrobial resistance across environments, with some species increasingly reliant on highly anthropized habitats for feeding. However, data on the impact of their feeding habits on the carriage of antibiotic resistance genes (ARGs) are still scarce. To fill this gap, we examined the microbiota (16S rRNA amplicon gene sequencing) and the prevalence of ARG (high-throughput qPCR of 47 genes) in faeces from white storks (Ciconia ciconia) and lesser black-backed gulls (Larus fuscus) feeding in highly (landfill) and less (paddy fields) polluted habitats. Faecal bacterial richness and diversity were higher in gulls feeding upon landfills and showed a greater abundance of potential pathogens, such as Staphylococcus. In contrast, faecal bacterial communities from storks were similar regardless of habitat preferences, maybe due to a less intense habitat use compared to gulls. In addition, birds feeding in the landfill carried a higher burden of ARGs compared to the surrounding soil and surface waters. Network analysis revealed strong correlations between ARGs and potential pathogens, particularly between tetM (resistance to tetracyclines), blaCMY (beta-lactam resistance), sul1 (sulfonamide resistance) and members of the genera Streptococcus, Peptostreptococcus, and Peptoclostridium. Our work demonstrates how transitioning from paddy fields to landfills fosters the carriage of ARGs and potential pathogens in the bird gut, shedding light on the ecological role of these avian vectors in antimicrobial resistance dissemination.
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Affiliation(s)
| | - Dayana Jarma
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain; Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510, Puerto Real, Cádiz, Spain.
| | - Marta I Sánchez
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Noelia Romero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Esteban Alonso
- Departamento de Química Analítica, Escuela Politécnica Superior, Universidad de Sevilla, C/Virgen de África, 7, 41011 Sevilla, Spain
| | - Andy J Green
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | | | - Francisco Hortas
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510, Puerto Real, Cádiz, Spain
| | - José Luis Balcázar
- Institut Català de Recerca de l'Aigua (ICRA), Emili Grahit 101, E-17003 Girona, Spain
| | - Juan Manuel Peralta-Sánchez
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain; Departamento de Zoología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Carles M Borrego
- Institut Català de Recerca de l'Aigua (ICRA), Emili Grahit 101, E-17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Campus de Montilivi, E-17003 Girona, Spain
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Mejías-Molina C, Pico-Tomàs A, Martínez-Puchol S, Itarte M, Torrell H, Canela N, Borrego CM, Corominas L, Rusiñol M, Bofill-Mas S. Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals. Hum Genomics 2024; 18:10. [PMID: 38303015 PMCID: PMC10832175 DOI: 10.1186/s40246-024-00580-1] [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: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome. RESULTS The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression. CONCLUSIONS This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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Zammit I, Badia S, Mejías-Molina C, Rusiñol M, Bofill-Mas S, Borrego CM, Corominas L. Zooming in to the neighborhood level: A year-long wastewater-based epidemiology monitoring campaign for COVID-19 in small intraurban catchments. Sci Total Environ 2024; 907:167811. [PMID: 37852481 DOI: 10.1016/j.scitotenv.2023.167811] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
In recent years, wastewater-based epidemiology (WBE) has emerged as a valuable and cost-effective tool for monitoring the prevalence of COVID-19. Large-scale monitoring efforts have been implemented in numerous countries, primarily focusing on sampling at the entrance of wastewater treatment plants (WWTPs) to cover a large population. However, sampling at a finer spatial scale, such as at the neighborhood level (NGBs), pose new challenges, including the absence of composite sampling infrastructure and increased uncertainty due to the dynamics of small catchments. This study aims to investigate the feasibility and accuracy of WBE when deployed at the neighborhood level (sampling in sewers) compared to the city level (sampling at the entrance of a WWTP). To achieve this, we deployed specific WBE sampling stations at the intraurban scale within three NGBs in Barcelona, Spain. The study period covers the 5th and the 6th waves of COVID-19 in Spain, spanning from March 2021 to March 2022, along with the WWTP downstream from the NGBs. The results showed a strong correlation between the dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 loads at both the NGB and city levels. Notably, during the 5th wave, which was dominated by the Delta SARS-CoV-2 variant, wastewater loads were higher than during the 6th wave (Omicron variant), despite a lower number of clinical cases recorded during the 5th wave. The correlations between wastewater loads and clinical cases at the NGB level were stronger than at the WWTP level. However, the early warning potential varied across neighborhoods and waves, with some cases showing a one-week early warning and others lacking any significant early warning signal. Interestingly, the prevalence of COVID-19 did not exhibit major differences among NGBs with different socioeconomic statuses.
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Affiliation(s)
- Ian Zammit
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Sergi Badia
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | - Lluís Corominas
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain.
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Rožman M, Lekunberri I, Grgić I, Borrego CM, Petrović M. Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities. Sci Total Environ 2023; 877:162818. [PMID: 36914121 DOI: 10.1016/j.scitotenv.2023.162818] [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: 12/05/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 05/06/2023]
Abstract
Freshwater ecosystems are characterised by the co-occurrence of stressors that simultaneously affect the biota. Among these, flow intermittency and chemical pollution severely impair the diversity and functioning of streambed bacterial communities. Using an artificial streams mesocosm facility, this study examined how desiccation and pollution caused by emerging contaminants affect the composition of stream biofilm bacterial communities, their metabolic profiles, and interactions with their environment. Through an integrative analysis of the composition of biofilm communities, characterization of their metabolome and composition of the dissolved organic matter, we found strong genotype-to-phenotype interconnections. The strongest correlation was found between the composition and metabolism of the bacterial community, both of which were influenced by incubation time and desiccation. Unexpectedly, no effect of the emerging contaminants was observed, which was due to the low concentration of the emerging contaminants and the dominant impact of desiccation. However, biofilm bacterial communities modified the chemical composition of their environment under the effect of pollution. Considering the tentatively identified classes of metabolites, we hypothesised that the biofilm response to desiccation was mainly intracellular while the response to chemical pollution was extracellular. The present study demonstrates that metabolite and dissolved organic matter profiling may be effectively integrated with compositional analysis of stream biofilm communities to yield a more complete picture of changes in response to stressors.
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Affiliation(s)
- Marko Rožman
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain.
| | - Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain
| | - Ivana Grgić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, E-17001 Girona, Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Pico-Tomàs A, Mejías-Molina C, Zammit I, Rusiñol M, Bofill-Mas S, Borrego CM, Corominas L. Surveillance of SARS-CoV-2 in sewage from buildings housing residents with different vulnerability levels. Sci Total Environ 2023; 872:162116. [PMID: 36773920 PMCID: PMC9911146 DOI: 10.1016/j.scitotenv.2023.162116] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
During the last three years, various restrictions have been set up to limit the transmission of the Coronavirus Disease (COVID-19). While these rules apply at a large scale (e.g., country-wide level) human-to-human transmission of the virus that causes COVID-19, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), occurs at a small scale. Different preventive policies and testing protocols were implemented in buildings where COVID-19 poses a threat (e.g., elderly residences) or constitutes a disruptive force (e.g., schools). In this study, we sampled sewage from different buildings (a school, a university campus, a university residence, and an elderly residence) that host residents of different levels of vulnerability. Our main goal was to assess the agreement between the SARS-CoV-2 concentration in wastewater and the policies applied in these buildings. All buildings were sampled using passive samplers while 24 h composite samples were also collected from the elderly residence. Results showed that passive samplers performed comparably well to composite samples while being cost-effective to keep track of COVID-19 prevalence. In the elderly residence, the comparison of sampling protocols (passive vs. active) combined with the strict clinical testing allowed us to compare the sensitivities of the two methods. Active sampling was more sensitive than passive sampling, as the former was able to detect a COVID-19 prevalence of 0.4 %, compared to a prevalence of 2.2 % for passive sampling. The number of COVID-19-positive individuals was tracked clinically in all the monitored buildings. More frequent detection of SARS-CoV-2 in wastewater was observed in residential buildings than in non-residential buildings using passive samplers. In all buildings, sewage surveillance can be used to complement COVID-19 clinical testing regimes, as the detection of SARS-CoV-2 in wastewater remained positive even when no COVID-19-positive individuals were reported. Passive sampling is useful for building managers to adapt their COVID-19 mitigation policies.
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Affiliation(s)
- Anna Pico-Tomàs
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Ian Zammit
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | - Lluís Corominas
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain.
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Perlas A, Bertran K, Abad FX, Borrego CM, Nofrarías M, Valle R, Pailler-García L, Ramis A, Cortey M, Acuña V, Majó N. Persistence of low pathogenic avian influenza virus in artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate. Sci Total Environ 2023; 863:160902. [PMID: 36526195 DOI: 10.1016/j.scitotenv.2022.160902] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Avian influenza viruses (AIVs) can affect wildlife, poultry, and humans, so a One Health perspective is needed to optimize mitigation strategies. Migratory waterfowl globally spread AIVs over long distances. Therefore, the study of AIV persistence in waterfowl staging and breeding areas is key to understanding their transmission dynamics and optimizing management strategies. Here, we used artificial streams mimicking natural conditions of waterfowl habitats in the Mediterranean climate (day/night cycles of photosynthetic active radiation and temperature, low water velocity, and similar microbiome to lowland rivers and stagnant water bodies) and then manipulated temperature and sediment presence (i.e., 10-13 °C vs. 16-18 °C, and presence vs. absence of sediments). An H1N1 low pathogenic AIV (LPAIV) strain was spiked in the streams, and water and sediment samples were collected at different time points until 14 days post-spike to quantify viral RNA and detect infectious particles. Viral RNA was detected until the end of the experiment in both water and sediment samples. In water samples, we observed a significant combined effect of temperature and sediments in viral decay, with higher viral genome loads in colder streams without sediments. In sediment samples, we didn't observe any significant effect of temperature. In contrast to prior laboratory-controlled studies that detect longer persistence times, infectious H1N1 LPAIV was isolated in water samples till 2 days post-spike, and none beyond. Infectious H1N1 LPAIV wasn't isolated from any sediment sample. Our results suggest that slow flowing freshwater surface waters may provide conditions facilitating bird-to-bird transmission for a short period when water temperature are between 10 and 18 °C, though persistence for extended periods (e.g., weeks or months) may be less likely. We hypothesize that experiments simulating real environments, like the one described here, provide a more realistic approach for assessing environmental persistence of AIVs.
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Affiliation(s)
- Albert Perlas
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Kateri Bertran
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Francesc Xavier Abad
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona (UdG), Plaça Sant Domènec 3, 17004 Girona, Spain.
| | - Miquel Nofrarías
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Rosa Valle
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Lola Pailler-García
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia. Spain.
| | - Antonio Ramis
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Martí Cortey
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona (UdG), Plaça Sant Domènec 3, 17004 Girona, Spain.
| | - Natàlia Majó
- Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra 08193, Catalonia, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
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7
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Gros M, Mas-Pla J, Sànchez-Melsió A, Čelić M, Castaño M, Rodríguez-Mozaz S, Borrego CM, Balcázar JL, Petrović M. Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment. Sci Total Environ 2023; 857:159202. [PMID: 36208750 DOI: 10.1016/j.scitotenv.2022.159202] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L-1. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L-1 to μg L-1. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 102 to 5.6 × 106 gene copies L-1 water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.
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Affiliation(s)
- Meritxell Gros
- Catalan Institute for Water Research (ICRA), Spain; University of Girona (UdG), Spain.
| | - Josep Mas-Pla
- Catalan Institute for Water Research (ICRA), Spain; Grup de Recerca GAiA-Geocamb, Department of Environmental Sciences, University of Girona, Spain
| | | | - Mira Čelić
- Catalan Institute for Water Research (ICRA), Spain; University of Girona (UdG), Spain
| | - Marc Castaño
- Catalan Institute for Water Research (ICRA), Spain; University of Girona (UdG), Spain
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA), Spain; University of Girona (UdG), Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Spain; University of Girona (UdG), Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Spain; Catalan Institution for Research and Advanced Studies (ICREA), Spain
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8
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Guerrero-Latorre L, Collado N, Abasolo N, Anzaldi G, Bofill-Mas S, Bosch A, Bosch L, Busquets S, Caimari A, Canela N, Carcereny A, Chacón C, Ciruela P, Corbella I, Domingo X, Escoté X, Espiñeira Y, Forés E, Gandullo-Sarró I, Garcia-Pedemonte D, Girones R, Guix S, Hundesa A, Itarte M, Mariné-Casadó R, Martínez A, Martínez-Puchol S, Mas-Capdevila A, Mejías-Molina C, Rafa MMI, Munné A, Pintó RM, Pueyo-Ros J, Robusté-Cartró J, Rusiñol M, Sanfeliu R, Teichenné J, Torrell H, Corominas L, Borrego CM. The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance. Sci Rep 2022; 12:16704. [PMID: 36202959 PMCID: PMC9537440 DOI: 10.1038/s41598-022-20957-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard (https://sarsaigua.icra.cat). After 20 months of monitoring (July 20–March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.
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Affiliation(s)
- Laura Guerrero-Latorre
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Neus Collado
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Nerea Abasolo
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Gabriel Anzaldi
- Applied Artificial Intelligence Technological Unit, Eurecat, Centre Tecnològic de Catalunya, Science and Technology Park, H3, 25003, Lleida, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.,Research Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921, Santa Coloma de Gramenet, Catalonia, Spain
| | - Lluís Bosch
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Sílvia Busquets
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Antoni Caimari
- Biotechnology Area, Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.,Research Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921, Santa Coloma de Gramenet, Catalonia, Spain
| | - Carme Chacón
- Public Health Agency of Catalonia (ASPCAT), Roc Boronat 81-95, 08005, Barcelona, Catalonia, Spain
| | - Pilar Ciruela
- Public Health Agency of Catalonia (ASPCAT), Roc Boronat 81-95, 08005, Barcelona, Catalonia, Spain
| | - Irene Corbella
- Public Health Agency of Catalonia (ASPCAT), Roc Boronat 81-95, 08005, Barcelona, Catalonia, Spain
| | - Xavier Domingo
- Applied Artificial Intelligence Technological Unit, Eurecat, Centre Tecnològic de Catalunya, Science and Technology Park, H3, 25003, Lleida, Catalonia, Spain
| | - Xavier Escoté
- Technological Unit of Nutrition and Health, Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Yaimara Espiñeira
- Applied Artificial Intelligence Technological Unit, Eurecat, Centre Tecnològic de Catalunya, Science and Technology Park, H3, 25003, Lleida, Catalonia, Spain
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | | | - David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.,Research Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921, Santa Coloma de Gramenet, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.,Research Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921, Santa Coloma de Gramenet, Catalonia, Spain
| | - Ayalkibet Hundesa
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Roger Mariné-Casadó
- Technological Unit of Nutrition and Health, Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Anna Martínez
- Public Health Agency of Catalonia (ASPCAT), Roc Boronat 81-95, 08005, Barcelona, Catalonia, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Anna Mas-Capdevila
- Technological Unit of Nutrition and Health, Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Marc Moliner I Rafa
- Catalan Water Agency (ACA), Provença, 260, 08008, Barcelona, Catalonia, Spain
| | - Antoni Munné
- Catalan Water Agency (ACA), Provença, 260, 08008, Barcelona, Catalonia, Spain
| | - Rosa Maria Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.,Research Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921, Santa Coloma de Gramenet, Catalonia, Spain
| | - Josep Pueyo-Ros
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain
| | - Robert Sanfeliu
- Applied Artificial Intelligence Technological Unit, Eurecat, Centre Tecnològic de Catalunya, Science and Technology Park, H3, 25003, Lleida, Catalonia, Spain
| | - Joan Teichenné
- Technological Unit of Nutrition and Health, Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Avinguda Universitat 1, 43204, Reus, Catalonia, Spain
| | - Lluís Corominas
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain.,Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003, Girona, Catalonia, Spain. .,Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Catalonia, Spain.
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9
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Carcereny A, Garcia-Pedemonte D, Martínez-Velázquez A, Quer J, Garcia-Cehic D, Gregori J, Antón A, Andrés C, Pumarola T, Chacón-Villanueva C, Borrego CM, Bosch A, Guix S, Pintó RM. Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Environ Res 2022; 208:112720. [PMID: 35074352 PMCID: PMC8782736 DOI: 10.1016/j.envres.2022.112720] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/23/2021] [Revised: 01/02/2022] [Accepted: 01/08/2022] [Indexed: 05/25/2023]
Abstract
Wastewater based epidemiology (WBE) offers an overview of the SARS-CoV-2 variants circulating among the population thereby serving as a proper surveillance method. The variant of concern (VOC) Alpha was first identified in September 2020 in the United Kingdom, and rapidly became dominant across Europe. Our objective was to elucidate the Alpha VOC outcompetition rate and identify mutations in the spike glycoprotein (S) gene, indicative of the circulation of the Alpha VOC and/or other variants in the population through wastewater analysis. In the period covered by this study (November 2020-April 2021), forteen wastewater treatment plants (WWTPs) were weekly sampled. The total number of SARS-CoV-2 genome copies per L (GC/L) was determined with a Real-Time qPCR, targeting the N gene. Surveillance of the Alpha VOC circulation was ascertained using a duplex RT-qPCR, targeting and discriminating the S gene. Our results showed that in a period of 6 weeks the Alpha VOC was present in all the studied WWTPs, and became dominant in 11 weeks on average. The outcompetition rates of the Alpha VOC were estimated, and their relationship with different parameters statistically analyzed. The rapid spread of the Alpha VOC was influenced by its initial input and by the previous circulation of SARS-COV-2 in the population. This latter point could be explained by its higher transmissibility, particularly advantadgeous when a certain degree of herd immunity exists. Moreover, the presence of signature mutations of SARS-COV-2 variants were established by deep-sequencing of the complete S gene. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified.
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Affiliation(s)
- Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Adán Martínez-Velázquez
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Cristina Andrés
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | | | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
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10
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Cáliz J, Subirats J, Triadó-Margarit X, Borrego CM, Casamayor EO. Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions. Environ Int 2022; 160:107077. [PMID: 35016024 DOI: 10.1016/j.envint.2022.107077] [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: 09/26/2021] [Revised: 01/01/2022] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.
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Affiliation(s)
- Joan Cáliz
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona E-17003, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona E-17003, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona E-17003, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
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11
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Maganha de Almeida Kumlien AC, Pérez-Vega C, González-Villalobos E, Borrego CM, Balcázar JL. Genome analysis of a new Escherichia phage vB_EcoM_C2-3 with lytic activity against multidrug-resistant Escherichia coli. Virus Res 2022; 307:198623. [PMID: 34762992 DOI: 10.1016/j.virusres.2021.198623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022]
Abstract
In this study, we present the complete, annotated genome of a new member of the Tequatrovirus (T4-like) genus, Escherichia phage vB_EcoM_C2-3. This phage has an isometric head (92 nm in diameter) and a contractile tail (114 nm in length). Its genome consists of a linear, double-stranded DNA of 167,069bp with an average G+C content of 35.3%. There are 267 predicted genes, of which 125 encode functional proteins, including those for DNA replication, transcription and packaging, phage morphogenesis and cell lysis. Neither genes involved in the regulation of lysogeny nor antibiotic resistance genes were identified. Based on our results, its genomic features provide valuable insights into the use of a potential biocontrol agent, as Escherichia phage vB_EcoM_C2-3 exhibited lytic activity against E. coli, including multidrug-resistant strains.
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Affiliation(s)
| | - Clara Pérez-Vega
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona, Girona, Spain
| | | | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona, Girona, Spain.
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12
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Jarma D, Sánchez MI, Green AJ, Peralta-Sánchez JM, Hortas F, Sánchez-Melsió A, Borrego CM. Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use. Sci Total Environ 2021; 783:146872. [PMID: 33872913 DOI: 10.1016/j.scitotenv.2021.146872] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 01/05/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (blaTEM, blaKPC and blaNDM), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, blaTEM, and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (blaKPC) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.
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Affiliation(s)
- Dayana Jarma
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510 Puerto Real, Cádiz, Spain.
| | - Marta I Sánchez
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avda. de Reina Mercedes, 41012 Sevilla, Spain; Department of Wetland Ecology, Estación Biológica de Doñana EBD-CSIC, Américo Vespucio 26, 41092 Sevilla, Spain
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana EBD-CSIC, Américo Vespucio 26, 41092 Sevilla, Spain
| | - Juan Manuel Peralta-Sánchez
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avda. de Reina Mercedes, 41012 Sevilla, Spain
| | - Francisco Hortas
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510 Puerto Real, Cádiz, Spain
| | - Alexandre Sánchez-Melsió
- Water Quality, Institut Català de Recerca de l'Aigua (ICRA), Carrer Emili Grahit 101, E-17003 Girona, Spain
| | - Carles M Borrego
- Water Quality, Institut Català de Recerca de l'Aigua (ICRA), Carrer Emili Grahit 101, E-17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Campus de Montilivi, E-17003 Girona, Spain
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13
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Forés E, Bofill-Mas S, Itarte M, Martínez-Puchol S, Hundesa A, Calvo M, Borrego CM, Corominas LL, Girones R, Rusiñol M. Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater. Sci Total Environ 2021; 768:144786. [PMID: 33429117 PMCID: PMC7789912 DOI: 10.1016/j.scitotenv.2020.144786] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 11/01/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 05/18/2023]
Abstract
Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 103 GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.
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Affiliation(s)
- E Forés
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain; The Water Institute of the University of Barcelona, Spain
| | - S Bofill-Mas
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain; The Water Institute of the University of Barcelona, Spain
| | - M Itarte
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain; The Water Institute of the University of Barcelona, Spain
| | - S Martínez-Puchol
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain; The Water Institute of the University of Barcelona, Spain
| | - A Hundesa
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - M Calvo
- Section of Statistics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - C M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, E-17003 Girona, Spain
| | - L L Corominas
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain; University of Girona, E-17003 Girona, Spain
| | - R Girones
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain; The Water Institute of the University of Barcelona, Spain
| | - M Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain.
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14
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Ávila C, García-Galán MJ, Borrego CM, Rodríguez-Mozaz S, García J, Barceló D. New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands. Sci Total Environ 2021; 755:142554. [PMID: 33059136 DOI: 10.1016/j.scitotenv.2020.142554] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 05/14/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m2 each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, blaTEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for blaTEM.
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Affiliation(s)
- Cristina Ávila
- Catalan Institute for Water Research (ICRA), C/Emili Grahit 101, E-17003 Girona, Spain; Universitat de Girona. Girona, Spain; AIMEN Technology Center, c/ Relva, 27 A - Torneiros, E-36410 Porriño, Pontevedra, Spain
| | - María J García-Galán
- GEMMA-Group of Environmental Engineering and Microbiology. Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona, 1-3, Building D1, E-08034 Barcelona, Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), C/Emili Grahit 101, E-17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA), C/Emili Grahit 101, E-17003 Girona, Spain; Universitat de Girona. Girona, Spain
| | - Joan García
- GEMMA-Group of Environmental Engineering and Microbiology. Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona, 1-3, Building D1, E-08034 Barcelona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA), C/Emili Grahit 101, E-17003 Girona, Spain; Universitat de Girona. Girona, Spain; Department of Environmental Chemistry, IDAEA-CSIC, C/ Jordi Girona 18-26, E-08034 Barcelona, Spain
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15
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Maganha de Almeida Kumlien AC, Borrego CM, Balcázar JL. Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection. Trends Microbiol 2021; 29:517-527. [PMID: 33500192 DOI: 10.1016/j.tim.2020.12.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/23/2022]
Abstract
This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens but they are also known to withstand common disinfection treatments deployed to produce safe drinking/reclaimed water. Recent studies also suggest that phages have the potential to become an additional footprint to monitor water safety. A precautionary approach should therefore include phages in surveillance programs aimed at monitoring antimicrobial resistance (AMR) in the urban water cycle. This article argues that phages ought to be used to assess the efficiency of disinfection treatments (both classical and novel) on reducing the risk associated with antibiotic resistance. Finally, this article discusses contributions to the advancement of AMR stewardship in aquatic settings and is relevant for researchers and water industry practitioners.
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Affiliation(s)
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003 Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain; University of Girona, 17004 Girona, Spain
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16
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Oliveira BB, Veigas B, Carlos FF, Sánchez-Melsió A, Balcázar JL, Borrego CM, Baptista PV. Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach. Sci Total Environ 2020; 741:140447. [PMID: 32887010 DOI: 10.1016/j.scitotenv.2020.140447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/25/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.
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Affiliation(s)
- Beatriz B Oliveira
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal; i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Fábio Ferreira Carlos
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Alexandre Sánchez-Melsió
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain)
| | - José Luís Balcázar
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain)
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, (Spain); Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, M. Aurèlia Capmany 40, E-17003, Girona, (Spain)
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
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17
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Compte-Port S, Fillol M, Gich F, Borrego CM. Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. PLoS One 2020; 15:e0231238. [PMID: 32267873 PMCID: PMC7141681 DOI: 10.1371/journal.pone.0231238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.
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Affiliation(s)
- Sergi Compte-Port
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M. Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
- * E-mail:
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18
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Subirats J, Di Cesare A, Varela Della Giustina S, Fiorentino A, Eckert EM, Rodriguez-Mozaz S, Borrego CM, Corno G. High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance. Water Res 2019; 167:114895. [PMID: 31553931 DOI: 10.1016/j.watres.2019.114895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 02/13/2019] [Revised: 06/25/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.
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Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Andrea Di Cesare
- Microbial Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
| | - Saulo Varela Della Giustina
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Antonino Fiorentino
- Microbial Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
| | - Ester M Eckert
- Microbial Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
| | - Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Gianluca Corno
- Microbial Ecology Group, Water Research Institute, National Research Council of Italy (CNR-IRSA), Verbania, Italy
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19
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Gros M, Marti E, Balcázar JL, Boy-Roura M, Busquets A, Colón J, Sànchez-Melsió A, Lekunberri I, Borrego CM, Ponsá S, Petrovic M. Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant. J Hazard Mater 2019; 378:120716. [PMID: 31279253 DOI: 10.1016/j.jhazmat.2019.05.109] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 03/02/2019] [Revised: 05/23/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.
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Affiliation(s)
- Meritxell Gros
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona, Girona, Spain.
| | - Elisabet Marti
- Beta Technological Centre (TECNIO Network), University of Vic-Central University of Catalonia, Vic, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona, Girona, Spain
| | - Mercè Boy-Roura
- Beta Technological Centre (TECNIO Network), University of Vic-Central University of Catalonia, Vic, Spain
| | - Anna Busquets
- Beta Technological Centre (TECNIO Network), University of Vic-Central University of Catalonia, Vic, Spain
| | - Joan Colón
- Beta Technological Centre (TECNIO Network), University of Vic-Central University of Catalonia, Vic, Spain
| | | | - Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sergio Ponsá
- Beta Technological Centre (TECNIO Network), University of Vic-Central University of Catalonia, Vic, Spain
| | - Mira Petrovic
- Catalan Institute for Water Research (ICRA), Girona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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20
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Subirats J, Timoner X, Sànchez-Melsió A, Balcázar JL, Acuña V, Sabater S, Borrego CM. Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities. Water Res 2018; 138:77-85. [PMID: 29573631 DOI: 10.1016/j.watres.2018.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [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: 10/11/2017] [Revised: 03/01/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L-1 of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on the maintenance and spread of antibiotic resistance genes in streambed biofilms under controlled conditions. Our results also highlight that nutrients could enhance the effect of emerging contaminants on the dissemination of antibiotic resistance.
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Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Xisca Timoner
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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21
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Kassotaki E, Pijuan M, Joss A, Borrego CM, Rodriguez-Roda I, Buttiglieri G. Unraveling the potential of a combined nitritation-anammox biomass towards the biodegradation of pharmaceutically active compounds. Sci Total Environ 2018; 624:722-731. [PMID: 29272841 DOI: 10.1016/j.scitotenv.2017.12.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 10/02/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
In the past few years, anaerobic ammonium oxidation-based processes have attracted a lot of attention for their implementation at the mainstream line of wastewater treatment plants, due to the possibility of leading to energy autarky if combined with anaerobic digestion. However, little is known about the potential degradation of micropollutants by the microbial groups responsible of these processes and the few results available are inconclusive. This study aimed to assess the degradation capability of biomass withdrawn from a combined nitritation/anaerobic ammonium oxidation (combined N/A) pilot plant towards five pharmaceutically active compounds (ibuprofen, sulfamethoxazole, metoprolol, venlafaxine and carbamazepine). Batch experiments were performed under different conditions by selectively activating or inhibiting different microbial groups: i) regular combined N/A operation, ii) aerobic (optimal for nitrifying bacteria), iii) aerobic with allylthiourea (an inhibitor of ammonia monooxygenase, enzyme of ammonia oxidizing bacteria), iv) anoxic (optimal for anaerobic ammonium oxidizing bacteria), v) aerobic with acetate (optimal for heterotrophic bacteria) and vi) anoxic with acetate (optimal for heterotrophic denitrifying bacteria). Ibuprofen was the most biodegradable compound being significantly degraded (49-100%) under any condition except heterotrophic denitrification. Sulfamethoxazole, exhibited the highest removal (70%) under optimal conditions for nitrifying bacteria but in the rest of the experiments anoxic conditions were found to be slightly more favorable (up to 58%). For metoprolol the highest performance was obtained under anoxic conditions favoring anammox bacteria (62%). Finally, carbamazepine and venlafaxine were hardly removed (≤10% in the majority of cases). Taken together, these results suggest the specificity of different microbial groups that in combination with alternating operational parameters can lead to enhanced removal of some micropollutants.
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Affiliation(s)
- Elissavet Kassotaki
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
| | - Maite Pijuan
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
| | - Adriano Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, 8600 Dübendorf, Switzerland.
| | - Carles M Borrego
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain.
| | - Ignasi Rodriguez-Roda
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain; LEQUiA, Laboratory of Chemical and Environmental Engineering, University of Girona, Campus Montilivi, 17071 Girona, Spain.
| | - Gianluigi Buttiglieri
- ICRA, Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, 17003 Girona, Spain.
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22
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Compte-Port S, Borrego CM, Moussard H, Jeanbille M, Restrepo-Ortiz CX, de Diego A, Rodriguez-Iruretagoiena A, Gredilla A, Fdez-Ortiz de Vallejuelo S, Galand PE, Kalenitchenko D, Rols JL, Pokrovsky OS, Gonzalez AG, Camarero L, Muñiz S, Navarro-Navarro E, Auguet JC. Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes. Environ Microbiol 2018; 20:2422-2437. [PMID: 29687572 DOI: 10.1111/1462-2920.14252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/22/2022]
Abstract
Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (105 to 109 copies g-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.
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Affiliation(s)
- Sergi Compte-Port
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain
| | - Carles M Borrego
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain.,Group of Molecular Microbial Ecology (gEMM), Institute of Aquatic Ecology, University of Girona (UdG), Girona, Spain
| | - Hélène Moussard
- Equipe Environnement et Microbiologie (IPREM-EEM), UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Mathilde Jeanbille
- Department of plant pathology and forest mycology Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
| | | | - Alberto de Diego
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Ainara Gredilla
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Dimitri Kalenitchenko
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Jean-Luc Rols
- EcoLab, UMR CNRS 5245, Observatory of Midi-Pyrénées, University Paul Sabatier, Toulouse, France
| | - Oleg S Pokrovsky
- Geosciences and Environment Toulouse, UMR 5563 CNRS, 14 Avenue Edouard Belin 31400, Toulouse, France.,BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk, Russia
| | - Aridane G Gonzalez
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Lluis Camarero
- Group of integrative freshwater ecology, Department of continental ecology, Center of advanced studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Selene Muñiz
- Pyrenean institute of ecology (IPE-CSIC), Zaragoza, Spain
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23
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Lekunberri I, Balcázar JL, Borrego CM. Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges. Environ Pollut 2018; 234:538-542. [PMID: 29220785 DOI: 10.1016/j.envpol.2017.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 09/19/2017] [Revised: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Mobile genetic elements (MGEs) are key agents in the spread of antibiotic resistance genes (ARGs) across environments. Here we used metagenomics to compare the river resistome (collection of all ARGs) and mobilome (e.g., integrases, transposases, integron integrases and insertion sequence common region "ISCR" elements) between samples collected upstream (n = 6) and downstream (n = 6) of an urban wastewater treatment plant (UWWTP). In comparison to upstream metagenomes, downstream metagenomes showed a drastic increase in the abundance of ARGs, as well as markers of MGEs, particularly integron integrases and ISCR elements. These changes were accompanied by a concomitant prevalence of 16S rRNA gene signatures of bacteria affiliated to families encompassing well-known human and animal pathogens. Our results confirm that chronic discharges of treated wastewater severely impact the river resistome affecting not only the abundance and diversity of ARGs but also their potential spread by enriching the river mobilome in a wide variety of MGEs.
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Affiliation(s)
- Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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24
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O'Flaherty E, Borrego CM, Balcázar JL, Cummins E. Human exposure assessment to antibiotic-resistant Escherichia coli through drinking water. Sci Total Environ 2018; 616-617:1356-1364. [PMID: 29126642 DOI: 10.1016/j.scitotenv.2017.10.180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 09/16/2017] [Revised: 10/17/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Antibiotic-resistant bacteria (ARB) are a potential threat to human health through drinking water with strong evidence of ARB presence in post treated tap water around the world. This study examines potential human exposure to antibiotic-resistant (AR) Escherichia coli (E. coli) through drinking water, the effect of different drinking water treatments on AR E. coli and the concentration of AR E. coli required in the source water for the EU Drinking Water Directive (DWD) (Council Directive 98/83/EC, 0CFU/100ml of E. coli in drinking water) to be exceeded. A number of scenarios were evaluated to examine different water treatment combinations and to reflect site specific conditions at a study site in Europe. A literature search was carried out to collate data on the effect of environmental conditions on AR E. coli, the effect of different water treatments on AR E. coli and typical human consumption levels of tap water. A human exposure assessment model was developed with probability distributions used to characterise uncertainty and variability in the input data. Overall results show the mean adult human exposure to AR E. coli from tap water consumption ranged between 3.44×10-7 and 2.95×10-1cfu/day for the scenarios tested and varied depending on the water treatments used. The level of AR E. coli required in the source water pre-treatment to exceed the DWD varied between 1 and 5logcfu/ml, depending on the water treatments used. This can be used to set possible monitoring criteria in pre-treated water for potential ARB exposure in drinking water.
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Affiliation(s)
- E O'Flaherty
- University College Dublin, School of Biosystems and Food Engineering, Belfield, Dublin 4, Ireland.
| | - C M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - J L Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - E Cummins
- University College Dublin, School of Biosystems and Food Engineering, Belfield, Dublin 4, Ireland
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25
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Auguet O, Pijuan M, Borrego CM, Rodriguez-Mozaz S, Triadó-Margarit X, Giustina SVD, Gutierrez O. Sewers as potential reservoirs of antibiotic resistance. Sci Total Environ 2017; 605-606:1047-1054. [PMID: 28709370 DOI: 10.1016/j.scitotenv.2017.06.153] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 06/06/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
Wastewater transport along sewers favors the colonization of inner pipe surfaces by wastewater-derived microorganisms that grow forming biofilms. These biofilms are composed of rich and diverse microbial communities that are continuously exposed to antibiotic residues and antibiotic resistant bacteria (ARB) from urban wastewater. Sewer biofilms thus appear as an optimal habitat for the dispersal and accumulation of antibiotic resistance genes (ARGs). In this study, the concentration of antibiotics, integron (intI1) and antibiotic resistance genes (qnrS, sul1, sul2, blaTEM, blaKPC, ermB, tetM and tetW), and potential bacterial pathogens were analyzed in wastewater and biofilm samples collected at the inlet and outlet sections of a pressurized sewer pipe. The most abundant ARGs detected in both wastewater and biofilm samples were sul1 and sul2 with roughly 1 resistance gene for each 10 copies of 16s RNA gene. Significant differences in the relative abundance of gene intI1 and genes conferring resistance to fluoroquinolones (qnrS), sulfonamides (sul1 and sul2) and betalactams (blaTEM) were only measured between inlet and outlet biofilm samples. Composition of bacterial communities also showed spatial differences in biofilms and a higher prevalence of Operational Taxonomic Units (OTUs) with high sequence identity (>98%) to well-known human pathogens was observed in biofilms collected at the inlet pipe section. Our study highlights the role of sewer biofilms as source and sink of ARB and ARGs and supports the idea that community composition rather than antibiotic concentration is the main factor driving the diversity of the sewage resistome.
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Affiliation(s)
- Olga Auguet
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Xavier Triadó-Margarit
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain; Integrative Freshwater Ecology Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Saulo Varela Della Giustina
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Oriol Gutierrez
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain.
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26
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Lekunberri I, Villagrasa M, Balcázar JL, Borrego CM. Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges. Sci Total Environ 2017; 601-602:206-209. [PMID: 28551539 DOI: 10.1016/j.scitotenv.2017.05.174] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 03/20/2017] [Revised: 05/16/2017] [Accepted: 05/19/2017] [Indexed: 05/25/2023]
Abstract
In this study, we quantified eleven antibiotic compounds and nine antibiotic resistance genes (ARGs) in water samples collected upstream and downstream of the discharge point from a municipal wastewater treatment plant (WWTP) into the Ter River. Antibiotics were analyzed by liquid chromatography coupled to mass spectrometry, whereas the concentration of ARGs in bacterial, phage and plasmid DNA fractions was determined by real-time PCR to explore their contribution to environmental antibiotic resistance. WWTP discharges resulted in higher concentrations of antibiotic residues as well as ARGs in water samples collected downstream the impact point. Specifically, genes conferring resistance to macrolides (ermB), fluoroquinolones (qnrS) and tetracyclines (tetW) showed significant differences (p<0.05) between upstream and downstream sites in the three DNA fractions (i.e. bacteria, plasmids and phages). Interestingly, genes conferring resistance to β-lactams (blaTEM, blaNDM and blaKPC) and glycopeptides (vanA) only showed significant differences (p<0.05) between upstream and downstream sites in phage and plasmid DNA but not in the bacterial DNA fraction. Our results show for the first time the extent to which phages and plasmids contribute to the mobilization of ARGs in an aquatic environment exposed to chronic antibiotic pollution via WWTP discharges. Accordingly, these mobile genetic elements should be included in further studies to get a global view of the spread of antibiotic resistance.
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Affiliation(s)
- Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Marta Villagrasa
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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27
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Lekunberri I, Balcázar JL, Borrego CM. Detection and quantification of the plasmid-mediated mcr-1 gene conferring colistin resistance in wastewater. Int J Antimicrob Agents 2017; 50:734-736. [DOI: 10.1016/j.ijantimicag.2017.08.018] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/21/2017] [Accepted: 08/15/2017] [Indexed: 10/19/2022]
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28
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Compte-Port S, Subirats J, Fillol M, Sànchez-Melsió A, Marcé R, Rivas-Ruiz P, Rosell-Melé A, Borrego CM. Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula. Microb Ecol 2017; 74:776-787. [PMID: 28508926 DOI: 10.1007/s00248-017-0989-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 01/10/2017] [Accepted: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.
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Affiliation(s)
- Sergi Compte-Port
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Rafael Marcé
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Pedro Rivas-Ruiz
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Rosell-Melé
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain.
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29
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Nasri E, Subirats J, Sànchez-Melsió A, Mansour HB, Borrego CM, Balcázar JL. Abundance of carbapenemase genes (bla KPC, bla NDM and bla OXA-48) in wastewater effluents from Tunisian hospitals. Environ Pollut 2017; 229:371-374. [PMID: 28614760 DOI: 10.1016/j.envpol.2017.05.095] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 02/21/2017] [Revised: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 05/29/2023]
Abstract
Carbapenems are β-lactam antibiotics with a broad spectrum of activity and are usually considered the last resort for the treatment of severe infections caused by multidrug-resistant pathogens. The clinically most significant carbapenemases are KPC, NDM, and OXA-48-like enzymes, whose genes have been increasingly reported worldwide in members of the family Enterobacteriaceae. In this study, we quantified the abundance of these genes in wastewater effluents from different Tunisian hospitals. The blaNDM and blaOXA-48-like genes were detected at similar concentrations in all hospital wastewater effluents. In contrast, the blaKPC gene was detected at lower concentration than other genes and it was only detected in three of the seven effluents analyzed. To the best of our knowledge, this study quantified for the first time the abundance of blaKPC, blaNDM, and blaOXA-48-like genes in wastewater effluents from Tunisian hospitals, highlighting the widespread distribution of these carbapenemase genes.
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Affiliation(s)
- Emna Nasri
- Research Unit of Analysis and Process Applied to the Environmental - APAE Higher Institute of Applied Sciences and Technology Mahdia, University of Monastir, Monastir, Tunisia; Faculty of Sciences, University of Tunis El Manar, University Campus, Tunis, Tunisia
| | - Jessica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of The University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of The University of Girona, Girona, Spain
| | - Hedi Ben Mansour
- Research Unit of Analysis and Process Applied to the Environmental - APAE Higher Institute of Applied Sciences and Technology Mahdia, University of Monastir, Monastir, Tunisia
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of The University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of The University of Girona, Girona, Spain.
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30
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Subirats J, Triadó-Margarit X, Mandaric L, Acuña V, Balcázar JL, Sabater S, Borrego CM. Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments. Mol Ecol 2017; 26:5567-5581. [DOI: 10.1111/mec.14288] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/19/2017] [Accepted: 06/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group; Centre d'Estudis Avançats de Blanes; CEAB-CSIC; Blanes Girona Spain
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
| | - Ladislav Mandaric
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
- GRECO; Institute of Aquatic Ecology; University of Girona; Girona Spain
| | - Carles M. Borrego
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
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31
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Subirats J, Royo E, Balcázar JL, Borrego CM. Real-time PCR assays for the detection and quantification of carbapenemase genes (bla KPC, bla NDM, and bla OXA-48) in environmental samples. Environ Sci Pollut Res Int 2017; 24:6710-6714. [PMID: 28084599 DOI: 10.1007/s11356-017-8426-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
In this study, we have developed real-time PCR assays using SYBR Green chemistry to detect all known alleles of bla KPC, bla NDM, and bla OXA-48-like carbapenemase genes in water, sediment, and biofilm samples collected from hospital and wastewater treatment plant (WWTP) effluents and rivers receiving chronic WWTP discharges. The amplification of bla KPC, bla NDM, and bla OXA-48 DNA was linear over 7 log dilutions (R 2 between 0.995 and 0.997) and showing efficiencies ranging from 92.6% to 100.3%. The analytical sensitivity indicated that the reaction for bla KPC, bla NDM, and bla OXA-48-like genes was able to detect 35, 16, and 19 copy numbers per assay, respectively. The three carbapenemase genes were detected in hospital effluents, whereas only the bla KPC and bla NDM genes were detected in biofilm and sediment samples collected from wastewater-impacted rivers. The detection of bla KPC, bla NDM, and bla OXA-48-like genes in different matrices suggests that carbapenem-resistant bacteria occur in both planktonic and benthic habitats thus expanding the range of resistance reservoirs for last-resort antibiotics. We believe that these real-time PCR assays would be a powerful tool for the rapid detection and quantification of bla KPC, bla NDM, and bla OXA-48-like genes in complex environmental samples.
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Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Elena Royo
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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32
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Lekunberri I, Subirats J, Borrego CM, Balcázar JL. Exploring the contribution of bacteriophages to antibiotic resistance. Environ Pollut 2017; 220:981-984. [PMID: 27890586 DOI: 10.1016/j.envpol.2016.11.059] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [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: 07/28/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved. Here, we carry out a comprehensive analysis of thirty-three viromes from different habitats to investigate whether phages harbor ARGs. Our results demonstrate that while human-associated viromes do not or rarely carry ARGs, viromes from non-human sources (e.g. pig feces, raw sewage, and freshwater and marine environments) contain a large reservoir of ARGs, thus pointing out that phages could play a part on the spread of antibiotic resistance. Given this, the role of phages should not be underestimated and it should be considered when designing strategies to tackle the global crisis of antibiotic resistance.
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Affiliation(s)
- Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
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33
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Rafraf ID, Lekunberri I, Sànchez-Melsió A, Aouni M, Borrego CM, Balcázar JL. Abundance of antibiotic resistance genes in five municipal wastewater treatment plants in the Monastir Governorate, Tunisia. Environ Pollut 2016; 219:353-358. [PMID: 27814552 DOI: 10.1016/j.envpol.2016.10.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [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: 07/25/2016] [Revised: 09/30/2016] [Accepted: 10/21/2016] [Indexed: 05/23/2023]
Abstract
Antimicrobial resistance is a growing and significant threat to global public health, requiring better understanding of the sources and mechanisms involved in its emergence and spread. We investigated the abundance of antibiotic resistance genes (ARGs) before and after treatment in five wastewater treatment plants (WWTPs) located in different areas of the Monastir Governorate (Tunisia). Three of these WWTPs (Frina, Sahline and Zaouiet) use a conventional activated sludge process as secondary treatment, whereas the WWTP located in Beni Hassen applies an ultraviolet disinfection step after the activated sludge process and the WWTP located in Moknine treats wastewater using naturally aerated lagoons as a secondary treatment process. The abundance of six ARGs (blaCTX-M, blaTEM, qnrA, qnrS, sul I and ermB) and the class 1 integron-integrase gene (intI1) were determined by quantitative PCR. All ARGs and the intI1 gene were detected in the wastewater samples, except the blaCTX-M gene, which was not detected in both influent and effluent samples from Sahline and Beni Hassen WWTPs, and the qnrS gene, which was not detected neither in the WWTP influent in Moknine nor in the WWTP effluent in Beni Hassen. Although the relative concentration of ARGs was generally found to be similar between samples collected before and after the wastewater treatment, the abundance of blaCTX-M, blaTEM, and qnrS genes was higher in the effluent of the Frina WWTP which, unlike other WWTPs, not only receives domestic or industrial sewage but also untreated hospital waste. To the best of our knowledge, this study quantified for the first time the abundance of ARGs in different Tunisian WWTPs, and the results agree with previous studies suggesting that conventional wastewater treatment does not efficiently reduce ARGs. Therefore, these findings could be useful to improve the design or operation of WWTPs.
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Affiliation(s)
- Ikbel Denden Rafraf
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia; Higher Institute of Biotechnology of Monastir, Monastir, Tunisia
| | - Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
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Auguet O, Pijuan M, Borrego CM, Gutierrez O. Control of sulfide and methane production in anaerobic sewer systems by means of Downstream Nitrite Dosage. Sci Total Environ 2016; 550:1116-1125. [PMID: 26871557 DOI: 10.1016/j.scitotenv.2016.01.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/21/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Bioproduction of hydrogen sulfide (H2S) and methane (CH4) under anaerobic conditions in sewer pipes causes detrimental effects on both sewer facilities and surrounding environment. Among the strategies used to mitigate the production of both compounds, the addition of nitrite (NO2(-)) has shown a greater long-term inhibitory effect compared with other oxidants such as nitrate or oxygen. The aim of this study was to determine the effectiveness of a new method, the Downstream Nitrite Dosage strategy (DNO2D), to control H2S and CH4 emissions in sewers. Treatment effectiveness was assessed on H2S and CH4 abatement on the effluent of a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer. The experiment was divided in three different periods: system setup (period 1), nitrite addition (period 2) and system recovery (period 3). Different process and molecular methods were combined to investigate the impact of NO2(-) addition on H2S and CH4 production. Results showed that H2S load was reduced completely during nitrite addition when compared to period 1 due to H2S oxidation but increased immediately after nitrite addition stopped. The H2S overproduction during recovery period was associated with the bacterial reduction of different sulfur species (elemental sulfur/thiosulfate/sulfite) accumulated within the sewer biofilm matrix. Oxidation of CH4 was also detected during period 2 but, contrary to sulfide production, re-establishment of methanogenesis was not immediate after stopping nitrite dosing. The analysis of bulk and active microbial communities along experimental treatment showed compositional changes that agreed with the observed dynamics of chemical processes. Results of this study show that DNO2D strategy could significantly reduce H2S and CH4 emissions from sewers during the addition period but also suggest that microbial agents involved in such processes show a high resilience towards chemical stressors, thus favoring the re-establishment of H2S and CH4 production after stopping nitrite addition.
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Affiliation(s)
- Olga Auguet
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park UdG, Girona, Spain.
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park UdG, Girona, Spain.
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park UdG, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain.
| | - Oriol Gutierrez
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park UdG, Girona, Spain.
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Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. Microb Ecol 2016; 71:566-574. [PMID: 26552395 DOI: 10.1007/s00248-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.
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Affiliation(s)
- Tomàs Llorens-Marès
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Carles M Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain.
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Proia L, von Schiller D, Sànchez-Melsió A, Sabater S, Borrego CM, Rodríguez-Mozaz S, Balcázar JL. Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers. Environ Pollut 2016; 210:121-8. [PMID: 26708766 DOI: 10.1016/j.envpol.2015.11.035] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [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: 09/24/2015] [Revised: 11/10/2015] [Accepted: 11/20/2015] [Indexed: 05/28/2023]
Abstract
The extensive use of antibiotics in human and veterinary medicine and their subsequent release into the environment may have direct consequences for autochthonous bacterial communities, especially in freshwater ecosystems. In small streams and rivers, local inputs of wastewater treatment plants (WWTPs) may become important sources of organic matter, nutrients and emerging pollutants, such as antibiotic resistance genes (ARGs). In this study, we evaluated the effect of WWTP effluents as a source of ARGs in river biofilms. The prevalence of genes conferring resistance to main antibiotic families, such as beta-lactams (blaCTX-M), fluoroquinolones (qnrS), sulfonamides (sul I), and macrolides (ermB), was determined using quantitative PCR (qPCR) in biofilm samples collected upstream and downstream WWTPs discharge points in four low-order streams. Our results showed that the WWTP effluents strongly modified the hydrology, physico-chemistry and biological characteristics of the receiving streams and favoured the persistence and spread of antibiotic resistance in microbial benthic communities. It was also shown that the magnitude of effects depended on the relative contribution of each WWTP to the receiving system. Specifically, low concentrations of ARGs were detected at sites located upstream of the WWTPs, while a significant increase of their concentrations was observed in biofilms collected downstream of the WWTP discharge points (particularly ermB and sul I genes). These findings suggest that WWTP discharges may favour the increase and spread of antibiotic resistance among streambed biofilms. The present study also showed that the presence of ARGs in biofilms was noticeable far downstream of the WWTP discharge (up to 1 km). It is therefore reasonable to assume that biofilms may represent an ideal setting for the acquisition and spread of antibiotic resistance determinants and thus be considered suitable biological indicators of anthropogenic pollution by active pharmaceutical compounds.
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Affiliation(s)
- Lorenzo Proia
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Institute of Aquatic Ecology, GRECO, University of Girona, Girona, Spain.
| | - Daniel von Schiller
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Institute of Aquatic Ecology, GRECO, University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
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Balcázar JL, Subirats J, Borrego CM. The role of biofilms as environmental reservoirs of antibiotic resistance. Front Microbiol 2015; 6:1216. [PMID: 26583011 PMCID: PMC4628128 DOI: 10.3389/fmicb.2015.01216] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds.
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Affiliation(s)
| | | | - Carles M Borrego
- Catalan Institute for Water Research Girona, Spain ; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona Girona, Spain
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Noguerola I, Picazo A, Llirós M, Camacho A, Borrego CM. Diversity of freshwaterEpsilonproteobacteriaand dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake. FEMS Microbiol Ecol 2015. [PMID: 26195601 DOI: 10.1093/femsec/fiv086] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Imma Noguerola
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Marc Llirós
- Université Catholique de Louvain, Institut des Sciences de la Vie, Place Croix du Sud, 4/5 L07.07.06, B-1348 Louvain-La-Neuve, Belgium
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Edificio de Investigación 'Jeroni Muñoz', Campus de Burjassot, Universitat de Valencia, E-46100, Burjassot, Valencia, Spain
| | - Carles M Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, E-17003 Girona, Spain
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Fauteux L, Cottrell MT, Kirchman DL, Borrego CM, Garcia-Chaves MC, del Giorgio PA. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes. PLoS One 2015; 10:e0124035. [PMID: 25927833 PMCID: PMC4415779 DOI: 10.1371/journal.pone.0124035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.
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Affiliation(s)
- Lisa Fauteux
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Matthew T. Cottrell
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - David L. Kirchman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - Carles M. Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, E-17071, Girona, Spain
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Paul A. del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
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Fillol M, Sànchez-Melsió A, Gich F, M. Borrego C. Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats. FEMS Microbiol Ecol 2015; 91:fiv020. [DOI: 10.1093/femsec/fiv020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
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Rodriguez-Mozaz S, Chamorro S, Marti E, Huerta B, Gros M, Sànchez-Melsió A, Borrego CM, Barceló D, Balcázar JL. Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river. Water Res 2015; 69:234-242. [PMID: 25482914 DOI: 10.1016/j.watres.2014.11.021] [Citation(s) in RCA: 801] [Impact Index Per Article: 89.0] [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: 06/14/2014] [Revised: 11/14/2014] [Accepted: 11/15/2014] [Indexed: 05/17/2023]
Abstract
Antibiotic resistance has become a major health concern; thus, there is a growing interest in exploring the occurrence of antibiotic resistance genes (ARGs) in the environment as well as the factors that contribute to their emergence. Aquatic ecosystems provide an ideal setting for the acquisition and spread of ARGs due to the continuous pollution by antimicrobial compounds derived from anthropogenic activities. We investigated, therefore, the pollution level of a broad range of antibiotics and ARGs released from hospital and urban wastewaters, their removal through a wastewater treatment plant (WWTP) and their presence in the receiving river. Several antimicrobial compounds were detected in all water samples collected. Among antibiotic families, fluoroquinolones were detected at the highest concentration, especially in hospital effluent samples. Although good removal efficiency by treatment processes was observed for several antimicrobial compounds, most antibiotics were still present in WWTP effluents. The results also revealed that copy numbers of ARGs, such as blaTEM (resistance to β-lactams), qnrS (reduced susceptibility to fluoroquinolones), ermB (resistance to macrolides), sulI (resistance to sulfonamides) and tetW (resistance to tetracyclines), were detected at the highest concentrations in hospital effluent and WWTP influent samples. Although there was a significant reduction in copy numbers of these ARGs in WWTP effluent samples, this reduction was not uniform across analyzed ARGs. Relative concentration of ermB and tetW genes decreased as a result of wastewater treatment, whereas increased in the case of blaTEM, sulI and qnrS genes. The incomplete removal of antibiotics and ARGs in WWTP severely affected the receiving river, where both types of emerging pollutants were found at higher concentration in downstream waters than in samples collected upstream from the discharge point. Taken together, our findings demonstrate a widespread occurrence of antibiotics and ARGs in urban and hospital wastewater and how these effluents, even after treatment, contribute to the spread of these emerging pollutants in the aquatic environment.
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Affiliation(s)
- Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Sara Chamorro
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Elisabet Marti
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Belinda Huerta
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Spain
| | - Jose Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
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Auguet O, Pijuan M, Guasch-Balcells H, Borrego CM, Gutierrez O. Implications of Downstream Nitrate Dosage in anaerobic sewers to control sulfide and methane emissions. Water Res 2015; 68:522-532. [PMID: 25462758 DOI: 10.1016/j.watres.2014.09.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/18/2014] [Accepted: 09/24/2014] [Indexed: 06/04/2023]
Abstract
Nitrate (NO₃⁻) is commonly dosed in sewer systems to reduce sulfide (H₂S) and methane (CH₄) produced in anaerobic rising main pipes. However, anoxic conditions along the whole rising pipes are difficult and costly to maintain since nitrate is added at the upstream sections of the sewer. In this study we tested the effects of the Downstream Nitrate Dosage strategy (DND) in anaerobic pipes in a specially designed laboratory-scale systems that mimics a real rising main. Effectiveness of the strategy was assessed on H₂S and CH₄ abatement on the effluent of the lab sewer system. A combination of process (Normal Functioning monitoring and batch tests) and molecular (by 454-pyrosequencing) methods were used to investigate the impacts and microbial activities related to the nitrate addition. Results showed a complete abatement of H₂S generated, with a fraction transformed to elemental sulfur (S⁰). Methane discharged was reduced to 50% while nitrate was added, due to the CH₄ oxidation in the anoxic conditions established at the end of the pipe. Both sulfidogenic and methanogenic activities resumed upon cessation of NO₃⁻ dosage. An increase of microorganisms of the genera Simplicispira, Comamonas, Azonexus and Thauera was detected during nitrate addition. Regarding anoxic methane oxidation, only one Operational Taxonomic Unit (OTU) was identified, which is likely related with this metabolism. Obtained results are relevant for the optimal management of nitrate dosage strategies in sewer systems.
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Affiliation(s)
- Olga Auguet
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park UdG, Girona, Spain.
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Romaní AM, Borrego CM, Díaz-Villanueva V, Freixa A, Gich F, Ylla I. Shifts in microbial community structure and function in light- and dark-grown biofilms driven by warming. Environ Microbiol 2014; 16:2550-67. [DOI: 10.1111/1462-2920.12428] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 02/09/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Anna M. Romaní
- Group of Continental Aquatic Ecology; University of Girona; Girona Spain
| | - Carles M. Borrego
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
- Water Quality and Microbial Diversity; Catalan Institute for Water Research (ICRA); Girona Spain
| | | | - Anna Freixa
- Group of Continental Aquatic Ecology; University of Girona; Girona Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
| | - Irene Ylla
- Group of Continental Aquatic Ecology; University of Girona; Girona Spain
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Plasencia A, Gich F, Fillol M, Borrego CM. Phylogenetic characterization and quantification of ammonia-oxidizing archaea and bacteria from Lake Kivu in a long-term microcosm incubation. Int Microbiol 2014; 16:177-89. [PMID: 24568033 DOI: 10.2436/20.1501.01.192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A microcosm cultivation-based method was set up to investigate the growth of ammonia-oxidizing archaea (AOA), isolated from a water sample acquired at a depth of 50 m from the northern basin of Lake Kivu. For this purpose, both CARD-FISH and qPCR targeting of archaeal 16S rRNA and amoA genes were used. Archaeal cell growth at the end of the 246-day microcosm experiment accounted for 35% of the SybrGold-stained cells, which corresponded to 6.61 x 10(6) cells/ml and 1.76 +/- 0.09 x 10(6) archaeal 16S rRNA gene copies/ml. Clone libraries and DGGE fingerprinting confirmed the dominance of AOA phylotypes in the archaeal community microcosm. The majority of the identified archaeal 16S rRNA gene sequences in the clone libraries were affiliated with Thaumarchaeota Marine Group 1 .1a. Subsequent cultivation of the AOA community on deep-well microtiter plates in medium containing different carbon sources to stimulate archaeal growth failed to show significant differences in archaeal abundance (ANOVA t14 = -1.058, P = 0.308 and ANOVA t14= 1.584, P = 0.135 for yeast extract and simple organic acids, respectively). The lack of growth stimulation by organic compounds is in concordance with the oligotrophic status of Lake Kivu. Finally, the addition of antibiotics to the growth medium resulted in archaeal cell counts that were significantly lower than those obtained from cultures in antibiotic-free medium (ANOVA t14 = 12.12, P < 0.001).
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Affiliation(s)
- Anna Plasencia
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Mireia Fillol
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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Ferrera I, Borrego CM, Salazar G, Gasol JM. Marked seasonality of aerobic anoxygenic phototrophic bacteria in the coastal NW Mediterranean Sea as revealed by cell abundance, pigment concentration and pyrosequencing of pufM gene. Environ Microbiol 2013; 16:2953-65. [PMID: 24131493 DOI: 10.1111/1462-2920.12278] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 09/01/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
Abstract
The abundance and diversity of aerobic anoxygenic phototrophs (AAPs) were studied for a year cycle at the Blanes Bay Microbial Observatory (NW Mediterranean) and their potential links to an array of environmental variables were explored. Cell numbers were low in winter and peaked in summer, showing a marked seasonality that positively correlated with day length and light at the surface. Bacteriochlorophyll a concentration, their light-harvesting pigment, was only detected between April and October, and pigment cell quota showed large variations during this period. Pyrosequencing analysis of the pufM gene revealed that the most abundant operational taxonomic units (OTUs) were affiliated to phylogroup K (Gammaproteobacteria) and uncultured phylogroup C, although they were outnumbered by alphaproteobacterial OTUs in spring. Overall, richness was higher in winter than in summer, showing an opposite trend to abundance and day length. Clustering of samples by multivariate analyses showed a clear seasonality that suggests a succession of different AAP subpopulations over time. Temperature, chlorophyll a and day length were the environmental drivers that best explained the distribution of AAP assemblages. These results indicate that AAP bacteria are highly dynamic and undergo seasonal variations in diversity and abundance mostly dictated by environmental conditions as exemplified by light availability.
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Affiliation(s)
- Isabel Ferrera
- Department de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
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Llirós M, Alonso-Sáez L, Gich F, Plasencia A, Auguet O, Casamayor EO, Borrego CM. Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon. FEMS Microbiol Ecol 2011; 77:370-84. [DOI: 10.1111/j.1574-6941.2011.01117.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Bañeras L, Ros-Ponsatí M, Cristina XP, Garcia-Gil JL, Borrego CM. Phosphorus deficiency and kinetics of alkaline phosphatase in isolates and natural populations of phototrophic sulphur bacteria. FEMS Microbiol Ecol 2010; 73:243-53. [DOI: 10.1111/j.1574-6941.2010.00895.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Saccà A, Borrego CM, Renda R, Triadó-Margarit X, Bruni V, Guglielmo L. Predation impact of ciliated and flagellated protozoa during a summer bloom of brown sulfur bacteria in a meromictic coastal lake. FEMS Microbiol Ecol 2009; 70:42-53. [PMID: 19622068 DOI: 10.1111/j.1574-6941.2009.00735.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Anaerobic phagotrophic protozoa may play an important role in the carbon flux of chemically stratified environments, especially when phototrophic sulfur bacteria account for a high proportion of the primary production. To test this assumption, we investigated the vertical and temporal distribution of microbial heterotrophs and of autotrophic picoplankton throughout the water column of the meromictic coastal lake Faro (Sicily, Italy), in the summer of 2004, coinciding with a bloom of brown-colored green sulfur bacteria. We also assessed the grazing impact of ciliated and flagellated protozoa within the sulfur bacteria plate using a modification of the fluorescently labeled bacteria uptake approach, attempting to minimize the biases intrinsic to the technique and to preserve the in situ anoxic conditions. Significant correlations were observed between ciliate biomass and bacteriochlorophyll e concentration, and between heterotrophic nanoflagellate biomass and chlorophyll a concentration in the water column. The major predators of anaerobic picoplankton were pleuronematine ciliates and cryptomonad flagellates, with clearances of 26.6 and 9.5 nL per cell h(-1), respectively, and a cumulative impact on the picoplankton gross growth rate ranging between 36% and 72%. We concluded that protozoan grazing channels a large proportion of anaerobic picoplankton production to higher trophic levels without restraining photosynthetic bacteria productivity.
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Affiliation(s)
- Alessandro Saccà
- Department of Animal Biology and Marine Ecology, University of Messina, Messina, Italy.
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Bañeras L, Gich F, Martinez-Medina M, Miller M, Abella CA, Borrego CM. New phylotypes of mesophilic filamentous anoxygenic phototrophic bacteria enriched from sulfide-containing environments. Environ Microbiol Rep 2009; 1:86-93. [PMID: 23765724 DOI: 10.1111/j.1758-2229.2008.00009.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Agar-based solid media with increasing concentrations of organic matter were used to isolate new members of the Chloroflexaceae (phylum Chloroflexi) from mesophilic environments containing sulfide. Inorganic media yielded less than 10% positive enrichments, which were not able to be maintained after repetitive inoculations in fresh medium. The use of casaminoacids and complex organic acid mixtures increased the number of positive enrichments (up to 45%) from both water and sediment samples. Two different green filamentous bacteria, SisoF2 and SalF, could be stably maintained as co-cultures for long periods and their phylogeny inferred from the analysis of complete sequences of the 16S rRNA gene. Ribotype SalF showed a high homology (95-98%) to previously isolated Oscillochloris trichoides strains. The 16S rRNA gene sequence retrieved from culture SisoF2 was largely divergent (< 92% similarity) from any sequence derived from either cultured representatives or environmental samples, suggesting that ribotype SisoF2 may constitute a new genus within the phylum. The presence of the new morphotypes in the environment from where they were enriched was analysed by high-resolution phylogenetic fingerprinting.
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Affiliation(s)
- L Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology and Department of Biology, University of Girona, Campus Montilivi, E-17071, Girona, Spain. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark
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Auguet JC, Borrego CM, Bañeras L, Casamayor EO. Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark. Environ Microbiol 2008; 10:2527-36. [PMID: 18557770 DOI: 10.1111/j.1462-2920.2008.01677.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.
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Affiliation(s)
- Jean-Christophe Auguet
- Group of Limnology-Department of Continental Ecology. Centre d'Estudis Avançats de Blanes, CEAB-CSIC. Accés Cala Sant Francesc, 14. 17300 Blanes, Girona, Spain
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