SARS-CoV-2 RNA surveillance in large to small centralized wastewater treatment plants preceding the third COVID-19 resurgence in Bangkok, Thailand

The Science of The Total Environment, Год журнала: 2021, Номер 809, С. 151169 - 151169

Опубликована: Окт. 25, 2021

Wastewater surveillance for SARS-CoV-2 RNA has been a successful indicator of COVID-19 outbreaks in populations prior to clinical testing. However, this mostly conducted high-income countries, which means there is dearth performance investigations low- and middle-income countries with different socio-economic settings. This study evaluated the applicability monitoring wastewater (n = 132) inform infection city Bangkok, Thailand using CDC N1 N2 RT-qPCR assays. influents 112) effluents 20) were collected from 19 centralized treatment plants (WWTPs) comprising four large, medium, 11 small WWTPs during seven sampling events January April 2021 third resurgence that was officially declared 2021. The assay showed higher detection rates lower Ct values than N2. first detected at event when new reported cases low. Increased positive preceded an increase number newly increased over time incidence. (both viral loads) strongest correlation daily 22-24 days lag (Spearman's Rho 0.85-1.00). Large (serving 432,000-580,000 population) exhibited similar trends loads those all WWTPs, emphasizing routine large could provide sufficient information city-scale dynamics. Higher frequency fewer sites, i.e., representative therefore suggested especially subsiding period outbreak indicate prevalence infection, acting as early warning resurgence.

Язык: Английский

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Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples

Applied and Environmental Microbiology, Год журнала: 2022, Номер 88(8)

Опубликована: Апрель 5, 2022

Wastewater represents a pooled biological sample of the contributing community and thus resource for assessing health. Here, we show that emergence, spread, disappearance SARS-CoV-2 infections caused by variants concern are reflected in presence variant genomic RNA wastewater settled solids. This work highlights an important public health use case wastewater.

Язык: Английский

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Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater

The Science of The Total Environment, Год журнала: 2022, Номер 833, С. 155059 - 155059

Опубликована: Апрель 6, 2022

Язык: Английский

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SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance

The Science of The Total Environment, Год журнала: 2022, Номер 838, С. 155828 - 155828

Опубликована: Май 16, 2022

SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants concern (VOCs) emerge there also need to identify primary circulating community, accomplished date by sequencing clinical samples. Quantifying offers cost-effective means augment these efforts. In this study, N1 concentrations and daily loadings were determined compared data collected as part national programme determine validity monitor infection spread greater Dublin area. Further, samples was conducted lineages Dublin. Finally, digital PCR employed whether VOCs, Alpha Delta, quantifiable from wastewater. No lead or lag time observed between trends significantly correlated with notification confirmed cases through preceding collection 5-day average. This demonstrates that viral Dublin's mirrors community. Clinical sequence demonstrated increased during Ireland's third wave coincided introduction variant, while fourth Delta variant. Interestingly, variant detected prior first genome being sequenced samples, identified at same work infections highlights its effectiveness identifying may prove useful when capacity limited.

Язык: Английский

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Waterborne pathogens detection technologies: advances, challenges, and future perspectives

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Ноя. 23, 2023

The World Health Organization (WHO) estimated that pathogens like Escherichia coli, primarily linked to food and water contamination, are associated with 485,000 deaths from diarrheal diseases annually, translating a staggering worldwide economic loss of nearly 12 billion USD per annum. International organizations the WHO United Nations Children’s Fund (UNICEF) have established related guidelines criteria for pathogenic detection technologies driving search innovative efficient methods. This comprehensive review examines trajectory waterborne bacteria traditional techniques, i.e., culture-based methods, current methods including various forms polymerase chain reaction (PCR) techniques [qualitative real-time PCR, digital ELISA, loop-mediated isothermal amplification, next-generation sequencing (NGS)] emerging biosensors artificial intelligence (AI). scope paper focuses on recognized as human pathogens, posing tangible threats public health through waterborne. techniques’ merits, constraints, research gaps future perspectives critically discussed. Advancements in droplet NGS significantly improved sensitivity specificity, revolutionizing pathogen detection. Additionally, integration (AI) these has enhanced accuracy, enabling analysis large datasets. Molecular-based show promise quality monitoring, especially resource-constrained settings, but on-site practical implementation remains challenge. pairwise comparison metrics used this also offer valuable insights into quick evaluation advantages, limitations focusing their applicability field settings timely analyses. Future efforts should focus developing robust, cost-effective user-friendly routine ultimately safeguarding global supplies health, AI data playing crucial role advancing safer environment.

Язык: Английский

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Recommendations for the use of metagenomics for routine monitoring of antibiotic resistance in wastewater and impacted aquatic environments

Critical Reviews in Environmental Science and Technology, Год журнала: 2023, Номер 53(19), С. 1731 - 1756

Опубликована: Март 1, 2023

Shotgun metagenomic sequencing of the collective genomic information carried across microbial communities is emerging as a powerful approach for monitoring antibiotic resistance in environmental matrices. Metagenomics advantageous that known and putative genes (ARGs) (i.e., resistome) can be screened simultaneously without priori selection targets. Additionally, new ARGs are discovered catalogued, stored data reanalyzed to assess prevalence or pathogens. However, best practices generation processing needed support comparability space time. To reproducible downstream analysis, guidance first with respect sampling design, sample preservation storage, DNA extraction, library preparation, depth, experimental controls. Here we conducted systematic review current application metagenomics AR profiling wastewater, recycled water, surface water offer recommendations collection, production, analysis resulting data. Based on integrated findings reported 95 articles identified, field benchtop workflow discussed optimizing representativeness generated Through reanalysis 1474 publicly-available metagenomes, appropriate depths per environment uniform normalization strategies provided. Further, there opportunity harness quantitative capacity more overtly through inclusion The will amplify overall value within between study comparisons, now future.

Язык: Английский

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Simultaneous detection of SARS-CoV-2, influenza A, respiratory syncytial virus, and measles in wastewater by multiplex RT-qPCR

The Science of The Total Environment, Год журнала: 2023, Номер 889, С. 164261 - 164261

Опубликована: Май 17, 2023

Язык: Английский

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Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage

FEMS Microbes, Год журнала: 2023, Номер 4

Опубликована: Янв. 1, 2023

Abstract The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development sensitive accurate detection quantification methods. Metagenomics quantitative PCR (qPCR) are amongst most used approaches. In this study, we aimed to evaluate compare performance these methods screen genes in animal faecal, wastewater, water samples. Water wastewater samples were from hospital effluent, different treatment stages two plants, receiving river at discharge point. pig chicken faeces. Antibiotic gene coverage, sensitivity, usefulness information analyzed discussed. While both able distinguish resistome profiles detect gradient stepwise mixtures faeces, qPCR presented higher sensitivity for a few water/wastewater. addition, comparison predicted observed quantifications unveiled accuracy qPCR. analyses, while less sensitive, provided markedly coverage compared complementarity importance selecting best method according study purpose

Язык: Английский

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Human norovirus (HuNoV) GII RNA in wastewater solids at 145 United States wastewater treatment plants: comparison to positivity rates of clinical specimens and modeled estimates of HuNoV GII shedders

Journal of Exposure Science & Environmental Epidemiology, Год журнала: 2023, Номер 34(3), С. 440 - 447

Опубликована: Авг. 7, 2023

Human norovirus (HuNoV) is a leading cause of disease globally, yet actual incidence unknown. HuNoV infections are not reportable in the United States, and surveillance limited to tracking severe illnesses or outbreaks. Wastewater monitoring for has been done previously results indicate it present wastewater influent concentrations associated with communities contributing wastewater. However, work mostly monthly samples liquid at one few treatment plants (WWTPs).

Язык: Английский

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Adsorption of Respiratory Syncytial Virus, Rhinovirus, SARS-CoV-2, and F+ Bacteriophage MS2 RNA onto Wastewater Solids from Raw Wastewater

Environmental Science & Technology, Год журнала: 2023, Номер 57(36), С. 13346 - 13355

Опубликована: Авг. 30, 2023

Despite the widespread adoption of wastewater surveillance, more research is needed to understand fate and transport viral genetic markers in wastewater. This information essential for optimizing monitoring strategies interpreting surveillance data. In this study, we examined solid–liquid partitioning behavior four viruses wastewater: SARS-CoV-2, respiratory syncytial virus (RSV), rhinovirus (RV), F+ coliphage/MS2. We used two approaches: (1) laboratory experiments using lab-grown (2) distribution endogenous raw Partition were conducted at 4 22 °C. Wastewater samples spiked with varying concentrations each virus, solids liquids separated via centrifugation, RNA quantified reverse-transcription-digital droplet PCR (RT-ddPCR). For experiments, collected from six treatment plants processed without spiking exogenous viruses; measured liquids. both higher solid fraction than liquid by approximately 3–4 orders magnitude. coefficients (KF) ranged 2000–270,000 mL·g–1 across temperature conditions. Distribution (Kd) consistent results experiments. Further how characteristics might influence

Язык: Английский

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