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Schmiege D, Haselhoff T, Thomas A, Kraiselburd I, Meyer F, Moebus S. Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review. Int J Hyg Environ Health 2024; 259:114379. [PMID: 38626689 DOI: 10.1016/j.ijheh.2024.114379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/25/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Wastewater analysis can serve as a source of public health information. In recent years, wastewater-based epidemiology (WBE) has emerged and proven useful for the detection of infectious diseases. However, insights from the wastewater treatment plant do not allow for the small-scale differentiation within the sewer system that is needed to analyze the target population under study in more detail. Small-scale WBE offers several advantages, but there has been no systematic overview of its application. The aim of this scoping review is to provide a comprehensive overview of the current state of knowledge on small-scale WBE for infectious diseases, including methodological considerations for its application. A systematic database search was conducted, considering only peer-reviewed articles. Data analyses included quantitative summary and qualitative narrative synthesis. Of 2130 articles, we included 278, most of which were published since 2020. The studies analyzed wastewater at the building level (n = 203), especially healthcare (n = 110) and educational facilities (n = 80), and at the neighborhood scale (n = 86). The main analytical parameters were viruses (n = 178), notably SARS-CoV-2 (n = 161), and antibiotic resistance (ABR) biomarkers (n = 99), often analyzed by polymerase chain reaction (PCR), with DNA sequencing techniques being less common. In terms of sampling techniques, active sampling dominated. The frequent lack of detailed information on the specification of selection criteria and the characterization of the small-scale sampling sites was identified as a concern. In conclusion, based on the large number of studies, we identified several methodological considerations and overarching strategic aspects for small-scale WBE. An enabling environment for small-scale WBE requires inter- and transdisciplinary knowledge sharing across countries. Promoting the adoption of small-scale WBE will benefit from a common international conceptualization of the approach, including standardized and internationally accepted terminology. In particular, the development of good WBE practices for different aspects of small-scale WBE is warranted. This includes the establishment of guidelines for a comprehensive characterization of the local sewer system and its sub-sewersheds, and transparent reporting to ensure comparability of small-scale WBE results.
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Affiliation(s)
- Dennis Schmiege
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130, Essen, Germany.
| | - Timo Haselhoff
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130, Essen, Germany
| | - Alexander Thomas
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131, Essen, Germany
| | - Ivana Kraiselburd
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131, Essen, Germany
| | - Folker Meyer
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131, Essen, Germany
| | - Susanne Moebus
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130, Essen, Germany
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2
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Philo SE, De León KB, Noble RT, Zhou NA, Alghafri R, Bar-Or I, Darling A, D'Souza N, Hachimi O, Kaya D, Kim S, Gaardbo Kuhn K, Layton BA, Mansfeldt C, Oceguera B, Radniecki TS, Ram JL, Saunders LP, Shrestha A, Stadler LB, Steele JA, Stevenson BS, Vogel JR, Bibby K, Boehm AB, Halden RU, Delgado Vela J. Wastewater surveillance for bacterial targets: current challenges and future goals. Appl Environ Microbiol 2024; 90:e0142823. [PMID: 38099657 PMCID: PMC10807411 DOI: 10.1128/aem.01428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Wastewater-based epidemiology (WBE) expanded rapidly in response to the COVID-19 pandemic. As the public health emergency has ended, researchers and practitioners are looking to shift the focus of existing wastewater surveillance programs to other targets, including bacteria. Bacterial targets may pose some unique challenges for WBE applications. To explore the current state of the field, the National Science Foundation-funded Research Coordination Network (RCN) on Wastewater Based Epidemiology for SARS-CoV-2 and Emerging Public Health Threats held a workshop in April 2023 to discuss the challenges and needs for wastewater bacterial surveillance. The targets and methods used in existing programs were diverse, with twelve different targets and nine different methods listed. Discussions during the workshop highlighted the challenges in adapting existing programs and identified research gaps in four key areas: choosing new targets, relating bacterial wastewater data to human disease incidence and prevalence, developing methods, and normalizing results. To help with these challenges and research gaps, the authors identified steps the larger community can take to improve bacteria wastewater surveillance. This includes developing data reporting standards and method optimization and validation for bacterial programs. Additionally, more work is needed to understand shedding patterns for potential bacterial targets to better relate wastewater data to human infections. Wastewater surveillance for bacteria can help provide insight into the underlying prevalence in communities, but much work is needed to establish these methods.IMPORTANCEWastewater surveillance was a useful tool to elucidate the burden and spread of SARS-CoV-2 during the pandemic. Public health officials and researchers are interested in expanding these surveillance programs to include bacterial targets, but many questions remain. The NSF-funded Research Coordination Network for Wastewater Surveillance of SARS-CoV-2 and Emerging Public Health Threats held a workshop to identify barriers and research gaps to implementing bacterial wastewater surveillance programs.
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Affiliation(s)
- Sarah E. Philo
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kara B. De León
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Rachel T. Noble
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, North Carolina, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police, Dubai, UAE
| | - Itay Bar-Or
- Israel Ministry of Health, Jerusalem, Israel
| | - Amanda Darling
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Oumaima Hachimi
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Devrim Kaya
- School of Public Health, San Diego State University, San Diego, California, USA
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California, USA
| | - Katrin Gaardbo Kuhn
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Cresten Mansfeldt
- Environmental Engineering Program, University of Colorado Boulder, Boulder, Colorado, USA
| | - Bethany Oceguera
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Tyler S. Radniecki
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Jeffrey L. Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | | | - Abhilasha Shrestha
- Environmental and Occupational Health Sciences Division, University of Illinois Chicago School of Public Health, Chicago, Illinois, USA
| | - Lauren B. Stadler
- Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Joshua A. Steele
- Department of Microbiology, Southern California Coastal Research Project, Costa Mesa, California, USA
| | | | - Jason R. Vogel
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Rolf U. Halden
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina, USA
- Department of Civil and Environmental Engineering, Howard University, Washington, District of Columbia, USA
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3
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Xu X, Deng Y, Ding J, Shi X, Zheng X, Wang D, Yang Y, Liu L, Wang C, Li S, Gu H, Poon LLM, Zhang T. Refining detection methods for emerging SARS-CoV-2 mutants in wastewater: A case study on the Omicron variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166215. [PMID: 37591380 DOI: 10.1016/j.scitotenv.2023.166215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
COVID-19 is an ongoing public health threat worldwide driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wastewater surveillance has emerged as a complementary tool to clinical surveillance to control the COVID-19 pandemic. With the emergence of new variants of SARS-CoV-2, accumulated mutations that occurred in the SARS-CoV-2 genome raise new challenges for RT-qPCR diagnosis used in wastewater surveillance. There is a pressing need to develop refined methods for modifying primer/probes to better detect these emerging variants in wastewater. Here, we exemplified this process by focusing on the Omicron variants, for which we have developed and validated a modified detection method. We first modified the primers/probe mismatches of three assays commonly used in wastewater surveillance according to in silico analysis results for the mutations of 882 sequences collected during the fifth-wave outbreak in Hong Kong, and then evaluated them alongside the seven original assays. The results showed that five of seven original assays had better sensitivity for detecting Omicron variants, with the limits of detection (LoDs) ranging from 1.53 to 2.76 copies/μL. UCDC-N1 and Charité-E sets had poor performances, having LoDs higher than 10 copies/μL and false-positive/false-negative results in wastewater testing, probably due to the mismatch and demonstrating the need for modification of primer/probe sequences. The modified assays exhibited higher sensitivity and specificity, along with better reproducibility in detecting 81 wastewater samples. In addition, the sequencing results of six wastewater samples by Illumina also validated the presence of mismatches in the primer/probe binding sites of the three assays. This study highlights the importance of re-configuration of the primer-probe sets and refinements for the sequences to ensure the diagnostic effectiveness of RT-qPCR detection.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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4
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Xu X, Deng Y, Ding J, Zheng X, Wang C, Wang D, Liu L, Gu H, Peiris M, Poon LLM, Zhang T. Wastewater genomic sequencing for SARS-CoV-2 variants surveillance in wastewater-based epidemiology applications. WATER RESEARCH 2023; 244:120444. [PMID: 37579567 DOI: 10.1016/j.watres.2023.120444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely used as a complementary approach to SARS-CoV-2 clinical surveillance. Wastewater genomic sequencing could provide valuable information on the genomic diversity of SARS-CoV-2 in the surveyed population. However, reliable detection and quantification of variants or mutations remain challenging. In this study, we used mock wastewater samples created by spiking SARS-CoV-2 variant standard RNA into wastewater RNA to evaluate the impacts of sequencing throughput on various aspects such as genome coverage, mutation detection, and SARS-CoV-2 variant deconvolution. We found that wastewater datasets with sequencing throughput greater than 0.5 Gb yielded reliable results in genomic analysis. In addition, using in silico mock datasets, we evaluated the performance of the adopted pipeline for variant deconvolution. By sequencing 86 wastewater samples covering more than 6 million people over 7 months, we presented two use cases of wastewater genomic sequencing for surveying COVID-19 in Hong Kong in WBE applications, including the replacement of Delta variants by Omicron variants, and the prevalence and development trends of three Omicron sublineages. Importantly, the wastewater genomic sequencing data were able to reveal the variant trends 16 days before the clinical data did. By investigating mutations of the spike (S) gene of the SARS-CoV-2 virus, we also showed the potential of wastewater genomic sequencing in identifying novel mutations and unique alleles. Overall, our study demonstrated the crucial role of wastewater genomic surveillance in providing valuable insights into the emergence and monitoring of new SARS-CoV-2 variants and laid a solid foundation for the development of genomic analysis methodologies for WBE of other novel emerging viruses in the future.
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Affiliation(s)
- Xiaoqing Xu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiahui Ding
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiawan Zheng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Haogao Gu
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Malik Peiris
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- Li Ka Shing Faculty of Medicine, School of Public Health, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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5
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Liguori K, Calarco J, Maldonado Rivera G, Kurowski A, Keenum I, Davis BC, Harwood VJ, Pruden A. Comparison of Cefotaxime-Resistant Escherichia coli and sul1 and intI1 by qPCR for Monitoring of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water. Antibiotics (Basel) 2023; 12:1252. [PMID: 37627672 PMCID: PMC10451376 DOI: 10.3390/antibiotics12081252] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Awareness of the need for surveillance of antimicrobial resistance (AMR) in water environments is growing, but there is uncertainty regarding appropriate monitoring targets. Adapting culture-based fecal indicator monitoring to include antibiotics in the media provides a potentially low-tech and accessible option, while quantitative polymerase chain reaction (qPCR) targeting key genes of interest provides a broad, quantitative measure across the microbial community. The purpose of this study was to compare findings obtained from the culture of cefotaxime-resistant (cefR) Escherichia coli with two qPCR methods for quantification of antibiotic resistance genes across wastewater, recycled water, and surface waters. The culture method was a modification of US EPA Method 1603 for E. coli, in which cefotaxime is included in the medium to capture cefR strains, while qPCR methods quantified sul1 and intI1. A common standard operating procedure for each target was applied to samples collected by six water utilities across the United States and processed by two laboratories. The methods performed consistently, and all three measures reflected the same overarching trends across water types. The qPCR detection of sul1 yielded the widest dynamic range of measurement as an AMR indicator (7-log versus 3.5-log for cefR E. coli), while intI1 was the most frequently detected target (99% versus 96.5% and 50.8% for sul1 and cefR E. coli, respectively). All methods produced comparable measurements between labs (p < 0.05, Kruskal-Wallis). Further study is needed to consider how relevant each measure is to capturing hot spots for the evolution and dissemination of AMR in the environment and as indicators of AMR-associated human health risk.
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Affiliation(s)
- Krista Liguori
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA (V.J.H.)
| | - Gabriel Maldonado Rivera
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Anna Kurowski
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Ishi Keenum
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Benjamin C. Davis
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA (V.J.H.)
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
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6
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Amman F, Markt R, Endler L, Hupfauf S, Agerer B, Schedl A, Richter L, Zechmeister M, Bicher M, Heiler G, Triska P, Thornton M, Penz T, Senekowitsch M, Laine J, Keszei Z, Klimek P, Nägele F, Mayr M, Daleiden B, Steinlechner M, Niederstätter H, Heidinger P, Rauch W, Scheffknecht C, Vogl G, Weichlinger G, Wagner AO, Slipko K, Masseron A, Radu E, Allerberger F, Popper N, Bock C, Schmid D, Oberacher H, Kreuzinger N, Insam H, Bergthaler A. Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale. Nat Biotechnol 2022; 40:1814-1822. [PMID: 35851376 DOI: 10.1038/s41587-022-01387-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/07/2022] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.
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Affiliation(s)
- Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Hupfauf
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lukas Richter
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - Martin Bicher
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Georg Heiler
- Complexity Science Hub, Vienna, Austria.,Institute of Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Petr Triska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Matthew Thornton
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Klimek
- Complexity Science Hub, Vienna, Austria.,Section for Science of Complex Systems, Medical University of Vienna, Vienna, Austria
| | - Fabiana Nägele
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Beatrice Daleiden
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
| | - Wolfgang Rauch
- Department of Infrastructure, Universität Innsbruck, Innsbruck, Austria
| | | | - Gunther Vogl
- Institut für Lebensmittelsicherheit, Veterinärmedizin und Umwelt des Landes Kärnten, Klagenfurt am Wörthersee, Austria
| | - Günther Weichlinger
- Abteilung 12 - Wasserwirtschaft, Amt der Kärntner Landesregierung, Klagenfurt am Wörthersee, Austria
| | | | - Katarzyna Slipko
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Elena Radu
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria.,Ştefan S. Nicolau Institute of Virology, Bucharest, Romania
| | | | - Niki Popper
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Heribert Insam
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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7
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Prieto Riquelme M, Garner E, Gupta S, Metch J, Zhu N, Blair MF, Arango-Argoty G, Maile-Moskowitz A, Li AD, Flach CF, Aga DS, Nambi IM, Larsson DGJ, Bürgmann H, Zhang T, Pruden A, Vikesland PJ. Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14982-14993. [PMID: 35759608 PMCID: PMC9631994 DOI: 10.1021/acs.est.1c08673] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.
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Affiliation(s)
| | - Emily Garner
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- Department
of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia26506, United States
| | - Suraj Gupta
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- The
Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational
Biology, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Jake Metch
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ni Zhu
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Matthew F. Blair
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Gustavo Arango-Argoty
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - An-dong Li
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Carl-Fredrik Flach
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Diana S. Aga
- Department
of Chemistry, University at Buffalo, Buffalo, New York14260, United States
| | - Indumathi M. Nambi
- Department
of Civil Engineering, Indian Institute of
Technology, Madras,
Chennai600036, India
| | - D. G. Joakim Larsson
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Helmut Bürgmann
- Eawag:
Swiss Federal Institute of Aquatic Science and Technology, CH-6047Kastanienbaum, Switzerland
| | - Tong Zhang
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
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8
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Sapoval N, Liu Y, Lou EG, Hopkins L, Ensor KB, Schneider R, Stadler LB, Treangen TJ. QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.09.08.21263279. [PMID: 35898338 PMCID: PMC9327636 DOI: 10.1101/2021.09.08.21263279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variants of concern (VoC) in communities. Multiple recent studies support that wastewater-based SARS-CoV-2 detection of circulating VoC can precede clinical cases by up to two weeks. Furthermore, wastewater based epidemiology enables wide population-based screening and study of viral evolutionary dynamics. However, highly sensitive detection of emerging variants remains a complex task due to the pooled nature of environmental samples and genetic material degradation. In this paper we propose quasi-unique mutations for VoC identification, implemented in a novel bioinformatics tool (QuaID) for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3 week earlier VoC detection compared to existing approaches, (ii) enables more sensitive VoC detection, which is shown to be tolerant of >50% mutation drop-out, and (iii) leverages all mutational signatures, including insertions & deletions.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Yunxi Liu
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Katherine B Ensor
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | | | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
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9
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Hyllestad S, Myrmel M, Lomba JAB, Jordhøy F, Schipper SK, Amato E. Effectiveness of environmental surveillance of SARS-CoV-2 as an early warning system during the first year of the COVID-19 pandemic: a systematic review. JOURNAL OF WATER AND HEALTH 2022; 20:1223-1242. [PMID: 36044191 DOI: 10.2166/wh.2022.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since infected persons shed SARS-CoV-2 in faeces before symptoms appear, environmental surveillance (ES) may serve as an early warning system (EWS) for COVID-19 and new variants of concern. The ES of SARS-CoV-2 has been widely reviewed; however, its effectiveness as an EWS for SARS-CoV-2 in terms of timeliness, sensitivity and specificity has not been systematically assessed. We conducted a systematic review to identify and synthesise evidence on the ES of SARS-CoV-2 as an EWS to evaluate the added value for public health. Of 1,014 studies identified, we considered 29 for a qualitative synthesis of the timeliness of ES as an EWS for COVID-19, while six studies were assessed for the ability to detect new variants and two for both aims. The synthesis indicates ES may serve as an EWS of 1-2 weeks. ES could complement clinical surveillance for SARS-CoV-2; however, its cost-benefit value for public health decisions needs to be assessed based on the stage of the pandemic and resources available. Studies focusing methodological knowledge gaps as well as how to use and interpret ES signals for public health actions are needed, as is the sharing of knowledge within countries/areas with long experience of such surveillance.
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Affiliation(s)
- Susanne Hyllestad
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jose Antonio Baz Lomba
- Department of Environmental Chemistry and Technology, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Fredrik Jordhøy
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Svanhild Kjørsvik Schipper
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Ettore Amato
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
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