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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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Kim LH, Mikolaityte V, Kim S. Establishment of wastewater-based SARS-CoV-2 monitoring system over two years: Case studies in South Korea. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110289. [PMID: 37292384 PMCID: PMC10240911 DOI: 10.1016/j.jece.2023.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023]
Abstract
With the global COVID-19 pandemic, wastewater surveillance has received a considerable attention as a method for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater treatment plant (WWTP) and sewer systems. For the first time in Korea, this study utilized the wastewater surveillance technique to monitor the COVID-19 outbreak. Sampling efforts were carried out at the WWTPs in the capital city of Korea, Seoul, and Daegu the place where the first severe outbreak was reported. The RNA of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been extracted from the collected wastewater influent and primary sewage sludge samples. The outcomes were contrasted with the COVID-19 cases in the WWTPs served area. Additionally, whole transcriptome sequencing was used to compare the microbial community alterations before and after the COVID-19 outbreak and SARS-CoV-2 variations. The results demonstrated that the changes in SARS-CoV-2 RNA concentrations in the influent and sludge matched the trends of reported COVID-19 cases, especially sludge showed high-resolution data, which is well-matched when fewer COVID-19 cases (0-250) are reported. Interestingly, one month before the clinical report, we found that the SARS-CoV-2 Beta variant (South Africa, B.1.351) in the wastewater. In addition, the Aeromonas bacterial species was dominated (21.2%) among other bacterial species in wastewater after the COVID-19 outbreak, suggesting a potential indirect microbial indicator of the COVID-19 outbreak.
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Affiliation(s)
- Lan Hee Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Viktorija Mikolaityte
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Sungpyo Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
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Itani T, Chalapa V, Semenov A, Sergeev A. Laboratory diagnosis of nonpolio enteroviruses: A review of the current literature. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Faleye TOC, Elyaderani A, Skidmore P, Adhikari S, Smith A, Kaiser N, Sandrolini H, Finnerty S, Halden RU, Varsani A, Scotch M. Surveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotype. Influenza Other Respir Viruses 2022; 17:e13057. [PMID: 36168937 PMCID: PMC9835438 DOI: 10.1111/irv.13057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 01/31/2023] Open
Abstract
We determine the presence and diversity of rhinoviruses in nasopharyngeal swab samples from 248 individuals who presented with influenza-like illness (ILI) at a university clinic in the Southwest United States between October 1, 2020 and March 31, 2021. We identify at least 13 rhinovirus genotypes (A11, A22, A23, A25, A67, A101, B6, B79, C1, C17, C36, and C56, as well a new genotype [AZ88**]) and 16 variants that contributed to the burden of ILI in the community. We also describe the complete capsid protein gene of a member (AZ88**) of an unassigned rhinovirus A genotype.
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Affiliation(s)
- Temitope O. C. Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Amir Elyaderani
- College of Health SolutionsArizona State UniversityTempeArizonaUSA
| | - Peter Skidmore
- College of Health SolutionsArizona State UniversityTempeArizonaUSA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign InstituteArizona State UniversityTempeArizonaUSA,School of Sustainable Engineering and the Built EnvironmentArizona State UniversityTempeArizonaUSA
| | - Abriana Smith
- College of Health SolutionsArizona State UniversityTempeArizonaUSA
| | - Nicole Kaiser
- College of Health SolutionsArizona State UniversityTempeArizonaUSA
| | | | | | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, Biodesign InstituteArizona State UniversityTempeArizonaUSA,School of Sustainable Engineering and the Built EnvironmentArizona State UniversityTempeArizonaUSA,OneWaterOneHealthNonprofit Project of the Arizona State University FoundationTempeArizonaUSA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign InstituteArizona State UniversityTempeArizonaUSA,College of Health SolutionsArizona State UniversityTempeArizonaUSA
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Faleye TO, Skidmore PT, Elyaderani A, Smith A, Kaiser N, Adhikari S, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021. INFECTION, GENETICS AND EVOLUTION 2022; 103:105315. [PMID: 35714764 PMCID: PMC9482372 DOI: 10.1016/j.meegid.2022.105315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/07/2022]
Abstract
Virus surveillance by wastewater-based epidemiology (WBE) in two Arizona municipalities in Maricopa County, USA (~700,000 people), revealed the presence of six canine picornavirus (CanPV) variants: five in 2019 and one in 2021. Phylogenetic analysis suggests these viruses might be from domestic dog breeds living within or around the area. Phylogenetic and pairwise identity analyses suggest over 15 years of likely enzootic circulation of multiple lineages of CanPV in the USA and possibly globally. Considering <10 CanPV sequences are publicly available in GenBank as of June 2, 2022, the results provided here constitute an increase of current knowledge on CanPV diversity and highlight the need for increased surveillance.
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Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein. Microbiol Resour Announc 2022; 11:e0033722. [PMID: 36043869 PMCID: PMC9584320 DOI: 10.1128/mra.00337-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We describe the genome of Microvirus-AZ-2020, which was identified from wastewater in Arizona, USA, in October 2020. Microvirus-AZ-2020 belongs to subfamily Gokushovirinae and contains six (five known and one hypothetical) open reading frames (ORFs), each with >40 codons. HHPred analysis and Colabfold structure prediction suggest that the hypothetical ORF encodes a previously undescribed putative DNA-binding protein.
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Bowes DA, Driver EM, Halden RU. A framework for wastewater sample collection from a sewage cleanout to inform building-scale wastewater-based epidemiology studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155576. [PMID: 35504397 DOI: 10.1016/j.scitotenv.2022.155576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Wastewater-based epidemiology (WBE) is a public health tool utilized for drug surveillance, and more recently, infectious disease monitoring of SARS-CoV-2. Sample collection is historically performed at a wastewater treatment plant, however, at this spatial resolution, much information related to actionable and contextually relevant community health data may be lost. Sampling from within the sewer collection system is now being employed more widely, bringing unique challenges, including health and safety concerns related to sample collection. As proof of concept, we tested the efficacy of sampling at the building-level from a sewer cleanout at an undisclosed location in Greater Phoenix, AZ, USA, to (i) test the feasibility of wastewater sample collection from this alternative access point, (ii) assess the advantages and limitations experienced for both maintenance-hole and cleanout-level sampling, (iii) screen for chemical analytes to evaluate detectability, and (iv) create a sampling framework for future near-source WBE investigations. Results indicate that use of a sewer cleanout compared to a maintenance hole is cost-effective, practical, and safe, while still preserving the anonymity and privacy for the contributing population. Additionally, of the 37 biomarkers screened over two sampling events, 20 were detected that cover a wide range of human behavior, exposure, and activity, indicating use of a sewer cleanout to be entirely feasible for downstream analysis. This reported success of sewer cleanout sampling for WBE and corresponding framework may allow practitioners to isolate specific complexes or buildings of interest, while avoiding challenges that can arise from maintenance hole sampling, thus allowing for widescale implementation of WBE for public health purposes.
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Affiliation(s)
- Devin A Bowes
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, AZ 85287-8101, USA; School for Engineering of Matter, Transport, and Energy, Arizona State University, 1001 S. McAllister Ave, AZ 85287-8101, USA
| | - Erin M Driver
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, AZ 85287-8101, USA
| | - Rolf U Halden
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave, AZ 85287-8101, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, 1001 S. McAllister Ave, AZ 85287-8101, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85281, USA; Global Futures Laboratory, Arizona State University, 800 S. Cady Mall, Tempe, AZ 85281, USA.
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Adhikari S, Halden RU. Opportunities and limits of wastewater-based epidemiology for tracking global health and attainment of UN sustainable development goals. ENVIRONMENT INTERNATIONAL 2022; 163:107217. [PMID: 35395576 PMCID: PMC9815123 DOI: 10.1016/j.envint.2022.107217] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 05/11/2023]
Abstract
Wastewater-based epidemiology (WBE) emerged as a powerful, actionable health management tool during the COVID-19 pandemic. Hypothesizing future uses, we explored its potential for real-time, tracking of progress in attaining United Nations Sustainable Development Goals (SDGs) globally as a non-expensive method using existing infrastructure. We inventoried (i) literature-documented sewerage infrastructure, (ii) demographics of populations served, and (iii) WBE markers informative of 9 SDGs. Among the 17 different sustainable development goals listed by the UN 2030 agenda, more than half of these may be monitored by using WBE monitoring at centralized treatment infrastructure as tabulated in this study. Driven mainly by COVID-19, WBE currently is practiced in at least 55 countries, reaching about 300 million people. Expansion of WBE to 109,000 + treatment plants inventoried in 129 countries would increase global coverage 9-fold to 34.7% or 2.7 billion, leaving out 5 billion people not served by centralized sewerage systems. Associations between population demographics and present-day infrastructure are explored, and geospatial regions particularly vulnerable to infectious disease outbreaks are identified. The results suggest that difference in the differential outcomes in well-being is an outcome of the sanitation infrastructure inequalities and lack of sanitation infrastructure creates doubly disadvantaged populations at risk of poor hygiene and cut off from the early-warning benefits of conventional WBE. This is the first study to explore the feasibility and potential barriers to the use of WBE for tracking the attainment of SDGs globally with at least 9 out of 17 SDGs.
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Affiliation(s)
- Sangeet Adhikari
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Environmental Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U Halden
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Environmental Engineering, Arizona State University, Tempe, AZ 85287, USA; OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, Tempe, AZ 85287, USA; Global Futures Laboratory, Arizona State University, 800 S. Cady Mall, Tempe, AZ 85281, USA.
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Keeren K, Böttcher S, Diedrich S. Enterovirus Surveillance (EVSurv) in Germany. Microorganisms 2021; 9:2005. [PMID: 34683328 PMCID: PMC8538599 DOI: 10.3390/microorganisms9102005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
The major aim of the enterovirus surveillance (EVSurv) in Germany is to prove the absence of poliovirus circulation in the framework of the Global Polio Eradication Program (GPEI). Therefore, a free-of-charge enterovirus diagnostic is offered to all hospitals for patients with symptoms compatible with a polio infection. Within the quality proven laboratory network for enterovirus diagnostic (LaNED), stool and cerebrospinal fluid (CSF) samples from patients with suspected aseptic meningitis/encephalitis or acute flaccid paralysis (AFP) are screened for enterovirus (EV), typing is performed in all EV positive sample to exclude poliovirus infections. Since 2006, ≈200 hospitals from all 16 German federal states have participated annually. On average, 2500 samples (70% stool, 28% CSF) were tested every year. Overall, the majority of the patients studied are children <15 years. During the 15-year period, 53 different EV serotypes were detected. While EV-A71 was most frequently detected in infants, E30 dominated in older children and adults. Polioviruses were not detected. The German enterovirus surveillance allows monitoring of the circulation of clinically relevant serotypes resulting in continuous data about non-polio enterovirus epidemiology.
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Affiliation(s)
- Kathrin Keeren
- Secretary of the National Commission for Polio Eradication in Germany, Robert Koch Institute, 13353 Berlin, Germany;
| | - Sindy Böttcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | | | - Sabine Diedrich
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
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Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020. Viruses 2021; 13:v13091803. [PMID: 34578384 PMCID: PMC8472758 DOI: 10.3390/v13091803] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022] Open
Abstract
We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900-2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.
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