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Kalvaitienė G, Picazo Espinosa R, Vaičiūtė D, Kataržytė M. Diverse sources of fecal contamination in macroalgae wrack-affected environment adjacent to river outflow along the Baltic Sea coast. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124429. [PMID: 38925212 DOI: 10.1016/j.envpol.2024.124429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
We investigated the dynamics of feces-associated microorganisms in areas with wrack accumulation in the southeastern part of the Baltic Sea. Our study covered single-day (2021 ) and multi-day (2022) observations during the recreational season. We collected water, sand, and wrack samples and assessed the abundance of fecal indicator bacteria (FIB), as well metagenomic analysis was conducted to monitor changes in microbial composition. Based on metagenomic data we identified taxa associated with feces, sewage, and ruminant sources. Human-related fecal pollution based on genetic markers correlated with the presence of Lachnospiraceae, Prevotellaceae and Rickenellacea abundance. Higher abundance and diversity of feces-associated and ruminant-associated taxa and the presence of enteric pathogens were observed when wrack accumulated near the river outflow in 2021, suggesting a potential link with fecal pollution from the river. As a preventive measure, it is recommended to remove the wrack to reduce the risk of exposure to potential enteric pathogens if it is accumulated next to the river outflow.
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Affiliation(s)
- Greta Kalvaitienė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Rafael Picazo Espinosa
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Diana Vaičiūtė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
| | - Marija Kataržytė
- Klaipėda University, Marine Research Institute, University Avenue 17, 92295 Klaipėda, Lithuania.
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2
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Lazuardi M, Hestianah EP, Restiadi TI. Prototype for rapid test devices to detect residues of sulfonamides in chicken carcasses from traditional breeders in Surabaya, Indonesia. Vet World 2023; 16:1252-1259. [PMID: 37577197 PMCID: PMC10421549 DOI: 10.14202/vetworld.2023.1252-1259] [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: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 08/15/2023] Open
Abstract
Background and Aim Sulfadiazine, one of the sulfonamide group's active compounds, is widely used for therapeutic production against several diseases. Veterinary drug residues can have a significant impact on human health conditions. This study aimed to develop a prototype of rapid test devices (RTDs) for detecting sulfadiazine residues on chicken carcasses based on the color indication. Materials and Methods Seven samples of carcasses collected from traditional breeders in Surabaya-Indonesia were prepared and tested using RTDs. This sample represents the population considering that in the last report, the use of antibiotics was more than 40%, while the ability to monitor RTDs was estimated at 100. The standard color of purple by Hex code standard color or decimal code color was used to compare the positive samples. A light-emitting diode (LED) lamp was used to observe purple color. Analysis of sulfonamides resulting from RTDs was compared using a ultraviolet-visible spectrophotometer. Results Sulfonamides contamination levels of 50% and 100% were detected at concentrations of 0.472 μg/mL and 0.642 μg/mL, respectively. Sulfonamides contamination that was <0.395 μg/mL did not appear purple. Conclusion The study's findings showed that RTDs can be used to detect sulfonamides residues at a limit of detection 0.5 mg/mL after a 45 min exposure to an LED operating at a wavelength of 980 nm (p < 0.05). The limitation of RTDs was not being able to monitor the presence of residues bound in fat samples. Rapid test devices can be developed for commonly monitoring devices due to the limited technology available in the market.
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Affiliation(s)
- Mochamad Lazuardi
- Sub-Division of Veterinary Pharmacy, Faculty of Veterinary Medicine, Universitas Airlangga, Mulyorejo Rd, 60115, Surabaya, Indonesia
| | - Eka Pramyrtha Hestianah
- Division of Histology, Faculty of Veterinary Medicine, Universitas Airlangga, Mulyorejo Rd, 60115, Surabaya, Indonesia
| | - Tjuk Imam Restiadi
- Division of Reproduction, Faculty of Veterinary Medicine, Universitas Airlangga, Mulyorejo Rd, 60115, Surabaya, Indonesia
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3
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Clokey JE, Hawker DW, Verhagen R, Ghorbani Gorji S, Knight ER, Thomas KV, Kaserzon SL. Calibration of a microporous polyethylene tube passive sampler for polar organic compounds in wastewater effluent. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162497. [PMID: 36863593 DOI: 10.1016/j.scitotenv.2023.162497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Water resources are vulnerable to contamination from polar organic compounds (POCs) originating from sources such as wastewater effluent. Two configurations of a microporous polyethylene tube (MPT) passive sampler were investigated for the time-integrative detection and quantification of POCs in effluent. One configuration contained the polymeric reversed phase sorbent Strata-X (SX) and the other Strata-X suspended in agarose gel (SX-Gel). These were deployed for up to 29 days and analysed for forty-nine POCs including pesticides, pharmaceuticals and personal care products (PPCPs) together with illicit drugs. Complementary composite samples were collected on days 6, 12, 20 and 26 representing the previous 24 h. Thirty-eight contaminants were detected in composite samples and MPT extracts, with MPT sampling rates (Rs) for 11 pesticides and 9 PPCPs/drugs ranging from 0.81 to 10.32 mL d-1 in SX and 1.35-32.83 mL d-1 in SX-Gel. Half-times to equilibrium of contaminants with the SX and SX-Gel equipped samplers ranged from two days to >29 days. MPT (SX) samplers were also deployed at 10 wastewater treatment effluent discharge sites across Australia for 7 days (again with complementary composite samples), to validate the sampler performance under varying conditions. Extracts from these MPTs detected 48 contaminants in comparison with 46 in composite samples, with concentrations ranging from 0.1 to 138 ng mL-1. An advantage of the MPT was preconcentration of contaminants, resulting in extract levels often markedly above instrument analytical detection limits. The validation study demonstrated a high correlation between accumulated contaminant mass in the MPTs and wastewater concentrations from composite samples (r2 > 0.70, where concentrations in composite samples were > 3× LOD). The MPT sampler shows promise as a sensitive tool for detecting POCs at trace levels in wastewater effluent and also quantifying these levels if temporal concentration variations are not significant.
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Affiliation(s)
- Joseph E Clokey
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia.
| | - Darryl W Hawker
- Griffith University, School of Environment and Science, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Rory Verhagen
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Sara Ghorbani Gorji
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Emma R Knight
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Sarit L Kaserzon
- The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
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Aunins AA, Mueller SJ, Fike JA, Cornman RS. Assessing arthropod diversity metrics derived from stream environmental DNA: spatiotemporal variation and paired comparisons with manual sampling. PeerJ 2023; 11:e15163. [PMID: 37020852 PMCID: PMC10069422 DOI: 10.7717/peerj.15163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Background
Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods.
Methods
We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment.
Results
Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.
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Affiliation(s)
- Aaron A. Aunins
- Eastern Ecological Research Center, U.S. Geological Survey, Kearneysville, West Virginia, United States
| | - Sara J. Mueller
- Wildlife and Fisheries Sciences Program, The Pennsylvania State College, State College, Pennsylvania, United States
| | - Jennifer A. Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
| | - Robert S. Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, United States
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Hendricks A, Mackie CM, Luy E, Sonnichsen C, Smith J, Grundke I, Tavasoli M, Furlong A, Beiko RG, LaRoche J, Sieben V. Compact and automated eDNA sampler for in situ monitoring of marine environments. Sci Rep 2023; 13:5210. [PMID: 36997631 PMCID: PMC10063616 DOI: 10.1038/s41598-023-32310-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/25/2023] [Indexed: 04/01/2023] Open
Abstract
Using environmental DNA (eDNA) to monitor biodiversity in aquatic environments is becoming an efficient and cost-effective alternative to other methods such as visual and acoustic identification. Until recently, eDNA sampling was accomplished primarily through manual sampling methods; however, with technological advances, automated samplers are being developed to make sampling easier and more accessible. This paper describes a new eDNA sampler capable of self-cleaning and multi-sample capture and preservation, all within a single unit capable of being deployed by a single person. The first in-field test of this sampler took place in the Bedford Basin, Nova Scotia, Canada alongside parallel samples taken using the typical Niskin bottle collection and post-collection filtration method. Both methods were able to capture the same aquatic microbial community and counts of representative DNA sequences were well correlated between methods with R[Formula: see text] values ranging from 0.71-0.93. The two collection methods returned the same top 10 families in near identical relative abundance, demonstrating that the sampler was able to capture the same community composition of common microbes as the Niskin. The presented eDNA sampler provides a robust alternative to manual sampling methods, is amenable to autonomous vehicle payload constraints, and will facilitate persistent monitoring of remote and inaccessible sites.
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Affiliation(s)
- Andre Hendricks
- Department of Electrical and Computer Engineering, Dalhousie University, Halifax, NS, Canada
| | | | - Edward Luy
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
| | - Colin Sonnichsen
- Department of Electrical and Computer Engineering, Dalhousie University, Halifax, NS, Canada
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
| | - James Smith
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
| | - Iain Grundke
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
| | - Mahtab Tavasoli
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | | | - Robert G Beiko
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Julie LaRoche
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Vincent Sieben
- Department of Electrical and Computer Engineering, Dalhousie University, Halifax, NS, Canada.
- Dartmouth Ocean Technologies Inc, Dartmouth, NS, Canada.
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Quality Assessment of Burdekin Plum ( Pleiogynium timoriense) during Ambient Storage. Molecules 2023; 28:molecules28041608. [PMID: 36838596 PMCID: PMC9958931 DOI: 10.3390/molecules28041608] [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: 12/03/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
Pleiogynium timoriense, commonly known as Burdekin plum (BP), is among many Australian native plants traditionally used by Indigenous people. However, only limited information is available on the nutritional and sensory quality of BP grown in Australia as well as its changes during storage. Therefore, this study evaluated the quality of BP during one week of ambient storage (temperature 21 °C, humidity 69%). Proximate analysis revealed a relatively high dietary fiber content in BP (7-10 g/100 g FW). A significant reduction in fruit weight and firmness (15-30% and 60-90%, respectively) with distinguishable changes in flesh color (ΔE > 3) and an increase in total soluble solids (from 11 to 21 °Brix) could be observed during storage. The vitamin C and folate contents in BP ranged from 29 to 59 mg/100g FW and 0.3 to 5.9 μg/100g FW, respectively, after harvesting. A total phenolic content of up to 20 mg GAE/g FW and ferric reducing antioxidant power of up to 400 μmol Fe2+/g FW in BP indicate a strong antioxidant capacity. In total, 34 individual phenolic compounds were tentatively identified in BP including cyanidin 3-galactoside, ellagic acid and gallotannins as the main phenolics. Principle component analysis (PCA) of the quantified phenolics indicated that tree to tree variation had a bigger impact on the phenolic composition of BP than ambient storage. Sensory evaluation also revealed the diversity in aroma, appearance, texture, flavor and aftertaste of BP. The results of this study provide crucial information for consumers, growers and food processors.
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Cantillon D, Roberts AP. Development and evaluation of TaqMan-based, one-step, real-time RT-PCR assays for pepper mild mottle virus detection for near source tracking and wastewater-based epidemiology validation. PLoS One 2022; 17:e0278784. [PMID: 36534927 PMCID: PMC9762892 DOI: 10.1371/journal.pone.0278784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Emergence of novel human pathogens pose significant challenges to human health as highlighted by the SARS-CoV-2 pandemic. Wastewater based epidemiology (WBE) has previously been employed to identify viral pathogens and outbreaks by testing samples from regional wastewater treatment plants. Near source tracking (NST) allows for more targeted WBE by analysing samples from individual buildings such as schools or even individual floors such as in multi-floor office buildings. Despite the public health advantages of WBE, few strategies exist for optimising NST sampling methodologies. Therefore, we developed a protocol to evaluate virus detection in NST sampling using Pepper Mild Mottle Virus (PMMoV) as a proxy for RNA viruses. PMMoV is the most abundant enteric human associated RNA virus and is present in peppers/pepper-containing foods. Two bespoke TaqMan RT-PCR assays were developed to detect a PMMoV genomic 5' region and a capsid associated gene. To evaluate the protocol against field samples, pepper homogenates were flushed down an in-use toilet (Liverpool School of Tropical Medicine, UK) to spike wastewater with PMMoV on multiple days, and samples collected from two sewage access points to validate NST samplers. These wastewater samples were assessed for PMMoV based on Ct values and results compared to pepper and Tabasco derived PMMoV positive controls. Positive detection of PMMoV was comparable and consistent in ten independent samples across two NST samplers regardless of pepper homogenate spiking. We have developed two novel one step TaqMan assays that amplify both PMMoV targets in viral RNA extractions from peppers, Tabasco, and wastewater samples with cDNA synthesis through to RT-PCR results taking approximately 30 minutes. Pepper homogenate flushing was not required to detect PMMoV in our wastewater samples, however this strategy of flushing PMMoV containing materials outlined here could be valuable in assessing and validating NST in buildings with no previous or current sewage flow.
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Affiliation(s)
- Daire Cantillon
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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8
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Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [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]
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9
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Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
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Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
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Kmush BL, Monk D, Green H, Sachs† DA, Zeng T, Larsen DA. Comparability of 24-hour composite and grab samples for detection of SARS-2-CoV RNA in wastewater. FEMS MICROBES 2022; 3:xtac017. [PMID: 37332496 PMCID: PMC10117866 DOI: 10.1093/femsmc/xtac017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 08/22/2023] Open
Abstract
Wastewater surveillance is a cost-effective way to monitor pathogen prevalence and transmission patterns in the entire community. Here, we compare 24-hour composite and grab samples collected during September 2020 from several municipalities in New York State to detect SARS-CoV-2. A total of 45 paired samples (90 total samples) from three counties and 14 wastewater treatment plants were available for analysis. The categorical comparison (SARS-CoV-2 genetic material detected and quantifiable, genetic material detected but below the limits of quantification, and genetic material not detected) between the grab and composite samples was quite strong, with 91.1% agreement (kappa P-value < .001). The correlations among the quantifiable grab and composite samples were statistically significant yet modest for SARS2-CoV RNA (Pearson correlation = 0.44, P = .02), crAssphage cDNA (Pearson correlation = 0.36, P = .02), and crAssphage DNA (Pearson correlation = 0.46, P = .002). We found good comparison between grab and 24-hour composite samples for detecting SARS-CoV-2 RNA from municipal wastewater treatment plants. Grab sampling is an efficient and cost-effective method to monitor for the presence of SARS-CoV-2 in the entire community.
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Affiliation(s)
- Brittany L Kmush
- Department of Public Health, Syracuse University, Suite 444 White Hall, Syracuse, NY 13244, United States
| | - David Monk
- Arcadis, 110 W Fayette St, Syracuse, NY 13202, United States
| | - Hyatt Green
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, NY 13210, United States
| | - Darcy A Sachs†
- Arcadis, 110 W Fayette St, Syracuse, NY 13202, United States
| | - Teng Zeng
- Department of Civil and Environmental Engineering, Syracuse University, 151 Link Hall, Syracuse, NY 13244, United States
| | - David A Larsen
- Department of Public Health, Syracuse University, Suite 444 White Hall, Syracuse, NY 13244, United States
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Centralized and decentralized wastewater-based epidemiology to infer COVID-19 transmission - A brief review. One Health 2022; 15:100405. [PMID: 35664497 PMCID: PMC9150914 DOI: 10.1016/j.onehlt.2022.100405] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022] Open
Abstract
Wastewater-based epidemiology has shown to be a promising and innovative approach to measure a wide variety of illicit drugs that are consumed in the communities. In the same way as for illicit drugs, wastewater-based epidemiology is a promising approach to understand the prevalence of viruses in a community-level. The ongoing coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on public health and diagnostic laboratories all over the world because of the need for massive laboratory testing. Many studies have shown the applicability of a centralized wastewater-based epidemiology (WBE) approach, where samples are collected at WWTPs. A more recent concept is a decentralized approach for WBE where samples are collected at different points of the sewer system and at polluted water bodies. The second being particularly important in countries where there are insufficient connections from houses to municipal sewage pipelines and thus untreated wastewater is discharged directly in environmental waters. A decentralized approach can be used to focus the value of diagnostic tests in what we call targeted-WBE, by monitoring wastewater in parts of the population where an outbreak is likely to happen, such as student dorms, retirement homes and hospitals. A combination of centralized and decentralized WBE should be considered for an affordable, sustainable, and successful WBE implementation in high-, middle- and low-income countries.
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Augusto MR, Claro ICM, Siqueira AK, Sousa GS, Caldereiro CR, Duran AFA, de Miranda TB, Bomediano Camillo LDM, Cabral AD, de Freitas Bueno R. Sampling strategies for wastewater surveillance: Evaluating the variability of SARS-COV-2 RNA concentration in composite and grab samples. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2022; 10:107478. [PMID: 35251931 PMCID: PMC8882035 DOI: 10.1016/j.jece.2022.107478] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/28/2022] [Accepted: 02/25/2022] [Indexed: 05/06/2023]
Abstract
The shedding of SARS-CoV-2 RNA titers by infected individuals, even asymptomatic and oligosymptomatic ones, allows the use of wastewater monitoring to track the COVID-19 spread in a community. This approach is interesting especially for emerging countries with limited clinical testing capabilities. However, there are still important methodological aspects that need validation so that wastewater monitoring data become more representative and useful for public health. This study evaluated the between-day and within-day variability of SARS-CoV-2 RNA concentrations in 24-hour composite and grab samples from three different sampling points, including two wastewater treatment plants (WTTP) and a sewer manhole. In the between-day evaluation (17 weeks of monitoring), a good agreement between the SARS-CoV-2 RNA concentration of each sampling method was observed. There were no significant differences between the mean concentrations of the grab and composite samples (p-value > 0.05), considering N1 and N2 gene assays. The strong relationship between composite and grab samples was proven by correlation coefficients: Pearson's r of 0.83 and Spearman's rho of 0.78 (p-value < 0.05). In within-day evaluation, 24-hour cycles were analyzed and low variability in hourly viral concentrations was observed for three sampling points. The coefficient of variation (CV) values ranged from 3.0% to 11.5%. Overall, 24-hour profiles showed that viral RNA concentrations had less variability and greater agreement with the mean values between 8 a.m. and 10 a.m, the recommended time for grab sampling. Therefore, this study provides important information on wastewater sampling techniques for COVID-19 surveillance. Wastewater monitoring information will only be useful to public health and decision-makers if we ensure data quality through best practices.
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Affiliation(s)
- Matheus Ribeiro Augusto
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Ieda Carolina Mantovani Claro
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Aline Kaori Siqueira
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Guilherme Santos Sousa
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Cláudio Roberto Caldereiro
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Adriana Feliciano Alves Duran
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Taís Browne de Miranda
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Lívia de Moraes Bomediano Camillo
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
| | - Aline Diniz Cabral
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
- Federal University of Uberlândia (UFU), Faculty of Veterinary Medicine, Uberlândia, Minas Gerais 38402-018, Brazil
| | - Rodrigo de Freitas Bueno
- Federal University of ABC (UFABC), Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo 09210-580, Brazil
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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150264. [PMID: 34798759 PMCID: PMC8432975 DOI: 10.1016/j.scitotenv.2021.150264] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [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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Cornman RS, McKenna JE, Fike JA. Composition and distribution of fish environmental DNA in an Adirondack watershed. PeerJ 2021; 9:e10539. [PMID: 33680576 PMCID: PMC7919543 DOI: 10.7717/peerj.10539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/19/2020] [Indexed: 11/24/2022] Open
Abstract
Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Affiliation(s)
- Robert S Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - James E McKenna
- U.S. Geological Survey, Great Lakes Science Center, Cortland, NY, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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Wang S, Yan Z, Hänfling B, Zheng X, Wang P, Fan J, Li J. Methodology of fish eDNA and its applications in ecology and environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142622. [PMID: 33059148 DOI: 10.1016/j.scitotenv.2020.142622] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Fish environmental DNA (eDNA) studies have made substantial progress during the past decade, and significant advances in monitoring fishes have been gained by taking advantage of this technology. Although a number of reviews concerning eDNA are available and some recent fish eDNA reviews focused on fisheries or standard method have been published, a systematic review of methodology of fish eDNA and its applications in ecology and environment has not yet been published. To our knowledge, this is the first review of fish eDNA for solving ecological and environmental issues. First, the most comprehensive literature analysis of fish eDNA was presented and analyzed. Then, we systematically discuss the relevant experiments and analyses of fish eDNA, and infers that standard workflow is on the way to consensus. We additionally provide reference sequence databases and the primers used to amplify the reference sequences or detecting fish eDNA. The abiotic and biotic conditions affecting fish eDNA persistence are also summarized in a schematic diagram. Subsequently, we focus on the major achievements of fish eDNA in ecology and environment. We additionally highlight the exciting new tools, including in situ autonomous monitoring devices, CRISPR nucleic acid detection technology, and meta-omics technology for fish eDNA detection in future. Ultimately, methodology of fish eDNA will provide a wholly new paradigm for conservation actions of fishes, ecological and environmental management at a global scale.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Bernd Hänfling
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jianlong Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
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Saawarn B, Hait S. Occurrence, fate and removal of SARS-CoV-2 in wastewater: Current knowledge and future perspectives. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:104870. [PMID: 33282675 PMCID: PMC7706426 DOI: 10.1016/j.jece.2020.104870] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/12/2020] [Accepted: 11/29/2020] [Indexed: 05/03/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a pandemic of global concern, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, many studies have documented the detection of SARS-CoV-2 in human excreta and wastewater. The presence of SARS-CoV-2 in human excreta and wastewater poses serious implications for wastewater treatment. Thus, this review aims to understand the fate of SARS-CoV-2 in the urban water cycle and its inactivation in different stages of treatment in wastewater treatment plants (WWTPs) for effective control to prevent any recurrence of the outbreak. The viral load of SARS-CoV-2 in feces of individuals tested positive has been reported to be in the range of 104-108 copies/L depending on the infection stages. In the wastewater, dilution of feces results in the decrease of the viral load in the range of 102-106.5 copies/L. Monitoring of SARS-CoV-2 in WWTP samples following the wastewater-based epidemiology (WBE) can complement real epidemiological data from clinical testing to help to monitor disease outbreaks in a community. Though promising, high uncertainty involved with the WBE technique warrants further research for reliable and quantitative information. Inactivation of SARS-CoV-2 in WWTPs depends on the operational parameters and is generally enhanced by the tertiary treatment and disinfection techniques with a higher dosage. However, the risk of SARS-CoV-2 dissemination by the treated effluent intended to be disposed of or reused in the urban water cycle needs to be assessed with respect to the extent of viral infectivity.
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Affiliation(s)
- Bhavini Saawarn
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
| | - Subrata Hait
- Department of Civil and Environmental Engineering, Indian Institute of Technology Patna, Bihar 801 106, India
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Polo D, Quintela-Baluja M, Corbishley A, Jones DL, Singer AC, Graham DW, Romalde JL. Making waves: Wastewater-based epidemiology for COVID-19 - approaches and challenges for surveillance and prediction. WATER RESEARCH 2020; 186:116404. [PMID: 32942178 PMCID: PMC7480445 DOI: 10.1016/j.watres.2020.116404] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/13/2020] [Accepted: 09/06/2020] [Indexed: 05/17/2023]
Abstract
The presence of SARS-CoV-2 in the feces of infected patients and wastewater has drawn attention, not only to the possibility of fecal-oral transmission but also to the use of wastewater as an epidemiological tool. The COVID-19 pandemic has highlighted problems in evaluating the epidemiological scope of the disease using classical surveillance approaches, due to a lack of diagnostic capacity, and their application to only a small proportion of the population. As in previous pandemics, statistics, particularly the proportion of the population infected, are believed to be widely underestimated. Furthermore, analysis of only clinical samples cannot predict outbreaks in a timely manner or easily capture asymptomatic carriers. Threfore, community-scale surveillance, including wastewater-based epidemiology, can bridge the broader community and the clinic, becoming a valuable indirect epidemiological prediction tool for SARS-CoV-2 and other pandemic viruses. This article summarizes current knowledge and discusses the critical factors for implementing wastewater-based epidemiology of COVID-19.
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Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology. Wallingford, Oxfordshire, OX10 8BB, United Kingdom
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
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