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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM, Gibb K, Coventry K, Collignon P, Cassar S, Allerberger F, Begum A, Hossain ZZ, Worrell C, Vandenberg O, Pieters I, Victorien DT, Gutierrez ADS, Soria F, Grujić VR, Mazalica N, Rahube TO, Tagliati CA, Rodrigues D, Oliveira G, de Souza LCR, Ivanov I, Juste BI, Oumar T, Sopheak T, Vuthy Y, Ngandjio A, Nzouankeu A, Olivier ZAAJ, Yost CK, Kumar P, Brar SK, Tabo DA, Adell AD, Paredes-Osses E, Martinez MC, Cuadros-Orellana S, Ke C, Zheng H, Baisheng L, Lau LT, Chung T, Jiao X, Yu Y, JiaYong Z, Morales JFB, Valencia MF, Donado-Godoy P, Coulibaly KJ, Hrenovic J, Jergović M, Karpíšková R, Deogratias ZN, Elsborg B, Hansen LT, Jensen PE, Abouelnaga M, Salem MF, Koolmeister M, Legesse M, Eguale T, Heikinheimo A, Le Guyader S, Schaeffer J, Villacis JE, Sanneh B, Malania L, Nitsche A, Brinkmann A, Schubert S, Hesse S, Berendonk TU, Saba CKS, Mohammed J, Feglo PK, Banu RA, Kotzamanidis C, Lytras E, Lickes SA, Kocsis B, Solymosi N, Thorsteinsdottir TR, Hatha AM, Ballal M, Bangera SR, Fani F, Alebouyeh M, Morris D, O’Connor L, Cormican M, Moran-Gilad J, Battisti A, Diaconu EL, Corno G, Di Cesare A, Alba P, Hisatsune J, Yu L, Kuroda M, Sugai M, Kayama S, Shakenova Z, Kiiyukia C, Ng’eno E, Raka L, Jamil K, Fakhraldeen SA, Alaati T, Bērziņš A, Avsejenko J, Kokina K, Streikisa M, Bartkevics V, Matar GM, Daoud Z, Pereckienė A, Butrimaite-Ambrozeviciene C, Penny C, Bastaraud A, Rasolofoarison T, Collard JM, Samison LH, Andrianarivelo MR, Banda DL, Amin A, Rajandas H, Parimannan S, Spiteri D, Haber MV, Santchurn SJ, Vujacic A, Djurovic D, Bouchrif B, Karraouan B, Vubil DC, Pal P, Schmitt H, van Passel M, Jeunen GJ, Gemmell N, Chambers ST, Mendoza FP, Huete-Pιrez J, Vilchez S, Ahmed AO, Adisa IR, Odetokun IA, Fashae K, Sørgaard AM, Wester AL, Ryrfors P, Holmstad R, Mohsin M, Hasan R, Shakoor S, Gustafson NW, Schill CH, Rojas MLZ, Velasquez JE, Magtibay BB, Catangcatang K, Sibulo R, Yauce FC, Wasyl D, Manaia C, Rocha J, Martins J, Álvaro P, Di Yoong Wen D, Shin H, Hur HG, Yoon S, Bosevska G, Kochubovski M, Cojocaru R, Burduniuc O, Hong PY, Perry MR, Gassama A, Radosavljevic V, Tay MYF, Zuniga-Montanez R, Wuertz S, Gavačová D, Pastuchová K, Truska P, Trkov M, Keddy K, Esterhuyse K, Song MJ, Quintela-Baluja M, Lopez MG, Cerdà-Cuéllar M, Perera RRDP, Bandara NKBKRGW, Premasiri HI, Pathirage S, Charlemagne K, Rutgersson C, Norrgren L, Örn S, Boss R, Van der Heijden T, Hong YP, Kumburu HH, Mdegela RH, Hounmanou YMG, Chonsin K, Suthienkul O, Thamlikitkul V, de Roda Husman AM, Bidjada B, Njanpop-Lafourcade BM, Nikiema-Pessinaba SC, Levent B, Kurekci C, Ejobi F, Kalule JB, Thomsen J, Obaidi O, Jassim LM, Moore A, Leonard A, Graham DW, Bunce JT, Zhang L, Gaze WH, Lefor B, Capone D, Sozzi E, Brown J, Meschke JS, Sobsey MD, Davis M, Beck NK, Sukapanpatharam P, Truong P, Lilienthal R, Kang S, Wittum TE, Rigamonti N, Baklayan P, Van CD, Tran DMN, Do Phuc N, Kwenda G, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2023; 14:178. [PMID: 36635285 PMCID: PMC9837105 DOI: 10.1038/s41467-023-35890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick Munk
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christian Brinch
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N. Petersen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S. Hendriksen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S. Kjeldgaard
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - D. G. Joakim Larsson
- grid.8761.80000 0000 9919 9582Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- grid.5645.2000000040459992XDepartment of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- grid.4305.20000 0004 1936 7988Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M. Aarestrup
- grid.5170.30000 0001 2181 8870Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Álvaro P, Vilaça J, Ribeiro J, Silva M, Coelho N, Brôco N, Carvalho M, Santos R. Recovery of SARS-CoV-2 from large volumes of raw wastewater is enhanced with the inuvai R180 system. J Environ Manage 2022; 304:114296. [PMID: 34923418 PMCID: PMC8673751 DOI: 10.1016/j.jenvman.2021.114296] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 09/02/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 05/06/2023]
Abstract
Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a powerful tool to complement syndromic surveillance. Although detection of SARS-CoV-2 in raw wastewater may be prompted with good recoveries during periods of high community prevalence, in the early stages of population outbreaks concentration procedures are required to overcome low viral concentrations. Several methods have become available for the recovery of SARS-CoV-2 from raw wastewater, generally involving filtration. However, these methods are limited to small sample volumes, possibly missing the early stages of virus circulation, and restrained applicability across different water matrices. The aim of this study was thus to evaluate the performance of three methods enabling the concentration of SARS-CoV-2 from large volumes of wastewater: i) hollow fiber filtration using the inuvai R180, with an enhanced elution protocol and polyethylene glycol (PEG) precipitation; ii) PEG precipitation; and iii) skimmed milk flocculation. The performance of the three approaches was evaluated in wastewater from multiple wastewater treatment plants (WWTP) with distinct singularities, according to: i) effective volume; ii) percentage of recovery; iii) extraction efficiency; iv) inhibitory effect; and v) the limits of detection and quantification. The inuvai R180 system had the best performance, with detection of spiked control across all samples, with average recovery percentages of 68% for porcine epidemic diarrhea virus (PEDV), with low variability. Mean recoveries for PEG precipitation and skimmed milk flocculation were 9% and 14%, respectively. The inuvai R180 enables the scalability of volumes without negative impact on the costs, time for analysis, and recovery/inhibition. Moreover, hollow fiber ultrafilters favor the concentration of different microbial taxonomic groups. Such combined features make this technology attractive for usage in environmental waters monitoring.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research Into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews, KY16 9LZ, Scotland, UK; Centro de Estatística e Aplicações, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Eugénia Cardoso
- Águas Do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254, Lisboa, Portugal
| | - Pedro Álvaro
- Águas Do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254, Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356, Canidelo, Portugal
| | - Jorge Ribeiro
- SIMDOURO, ETAR de Gaia Litoral, 4400-356, Canidelo, Portugal
| | - Marco Silva
- Águas Do Norte, Lugar de Gaído, 4755-045, Barcelos, Portugal
| | - Norberta Coelho
- Águas Do Norte, Lugar de Gaído, 4755-045, Barcelos, Portugal
| | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421, Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421, Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Monteiro S, Rente D, Cunha MV, Gomes MC, Marques TA, Lourenço AB, Cardoso E, Álvaro P, Silva M, Coelho N, Vilaça J, Meireles F, Brôco N, Carvalho M, Santos R. A wastewater-based epidemiology tool for COVID-19 surveillance in Portugal. Sci Total Environ 2022; 804:150264. [PMID: 34798759 PMCID: PMC8432975 DOI: 10.1016/j.scitotenv.2021.150264] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 05/20/2023]
Abstract
The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater produced interest in its use for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three Coronavirus disease 2019 (COVID-19) reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. For the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing. This is the first study crossing several epidemiological stages highlighting the long-term use of WBE for SARS-CoV-2.
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Affiliation(s)
- Sílvia Monteiro
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Carmo Gomes
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland, United Kingdom; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Artur B Lourenço
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - Pedro Álvaro
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - Marco Silva
- Águas do Norte, Lugar de Gaído, 4755-045 Barcelos, Portugal
| | | | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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