Gigabyte, Journal Year: 2024, Volume and Issue: 2024
Published: Aug. 31, 2024
Next-generation sequencing for microbial communities has become a standard technique. However, the computational analysis remains resource-intensive. With declining costs and growing adoption of sequencing-based methods in many fields, validated, fully automated, reproducible flexible pipelines are increasingly essential various scientific fields.
Language: Английский
International Journal of Hygiene and Environmental Health, Journal Year: 2024, Volume and Issue: 259, P. 114379 - 114379
Published: April 15, 2024
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 infectious diseases. However, insights from wastewater treatment plant do not allow small-scale differentiation within sewer system that is needed to analyze target population under study in more detail. Small-scale WBE offers several advantages, but there been no systematic overview its application. The aim this scoping review provide comprehensive current state knowledge on diseases, including methodological considerations A database search was conducted, considering only peer-reviewed articles. Data analyses included quantitative summary qualitative narrative synthesis. Of 2130 articles, we 278, most which were published since 2020. studies analyzed at building level (n = 203), especially healthcare 110) educational facilities 80), neighborhood scale 86). main analytical parameters viruses 178), notably SARS-CoV-2 161), antibiotic resistance (ABR) biomarkers 99), often by polymerase chain reaction (PCR), with DNA sequencing techniques being less common. terms sampling techniques, active dominated. frequent lack detailed information specification selection criteria characterization sites identified concern. conclusion, based large number studies, overarching strategic aspects WBE. An enabling environment requires inter- transdisciplinary sharing across countries. Promoting adoption will benefit common international conceptualization approach, standardized internationally accepted terminology. particular, development good practices different warranted. This includes establishment guidelines local sub-sewersheds, transparent reporting ensure comparability results.
Language: Английский
Citations
7
The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 967, P. 178767 - 178767
Published: Feb. 12, 2025
Wastewater-based epidemiology (WBE) is a promising approach for assessing population-level exposures to toxicants and lifestyle factors. Our pilot investigated the spatial variability of biomarkers indicating exposure nicotine endocrine disrupting chemicals in municipal wastewater, taking into account important covariates, i.e. physicochemical wastewater parameters sewershed characteristics. We also tested normalization by an endogenous population marker. Twenty-four-hour composite samples (n = 24) were collected volume-proportional manner using automated samplers from four treatment plants Essen, Germany, over three weeks late 2023. Substances public health concern, previously already quantified expected be present high concentrations, analyzed SPE-LC-HRMS. Concentrations normalized reported (de jure) daily mass load catecholamine metabolite vanillylmandelic acid (VMA) as proxy de facto population. Spatial variations multiple linear regression. Nicotine metabolites (cotinine, hydroxycotinine) industrial chemical Bisphenol A (BPA) quantifiable all samples. The population-normalized (median range: 0.6-1.6 g/d/1000 inh) BPA (2.5-4.0 varied between WWTPs, but observed variation disappeared when adjusting temperature (nicotine) pH (BPA). Normalization VMA resulted different patterns increased variance considerably. findings highlight importance characteristics analyzing community-wide differences factors via ensure accurate interpretations underlying drivers these differences.
Language: Английский
Citations
0
The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 970, P. 179007 - 179007
Published: March 1, 2025
Wastewater-based surveillance (WBS) of SARS-CoV-2 is increasingly recognized as a valuable complement to clinical reporting for estimating COVID-19 infection rates. This acceptance stems from the strong correlation found between wastewater and case data during early stages pandemic. However, cessation restrictions, changes in testing requirements by late 2021, widespread use take-home antigen tests have diminished reliability volume clinically reported counts. study explores dynamics cases wastewater-based results period transition, focusing on student residential areas within university campus. We analyzed 13 sub-sewersheds, serving populations 300 4000 individuals, three times weekly December 2021 June 2022. The analysis revealed two spikes this time, whereas reports indicated at most single surge infections across communities. Further, first surge, plateaued sooner than trends and, second either lagged or were completely absent. Correlations concentrations 3-day rolling average weak smaller communities (≤1000 people) but improved with larger community sizes (>1000 people). Normalization PMMoV did not enhance these correlations. Given challenges executing accurate mass testing, our findings advocate efficacy WBS reliably forecasting surges, even less populous settings, thereby facilitating swift, informed public health interventions.
Language: Английский
Citations
0
Viruses, Journal Year: 2025, Volume and Issue: 17(4), P. 477 - 477
Published: March 27, 2025
In December 2021, an outbreak of the SARS-CoV-2 B.1.640.2 variant, potentially originating from Cameroon, was investigated among schoolchildren in Germany. The index case, adult who had recently returned a three-week stay Republic Congo, introduced variant into school setting via their children, resulting subsequent transmission within and ultimately to hospital ward. Whole-genome sequencing viral samples identified both B.1.640.1 lineages. This highlights unpredictable nature emerging variants emphasizes importance early detection containment mitigate high-risk populations. Notably, wastewater surveillance detected during study peri-od, reinforcing utility wastewater-based epidemiology as complementary tool for warning novel variants. These findings underline critical need timely research adherence quarantine measures enhance control efforts.
Language: Английский
Citations
0
BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)
Published: June 28, 2024
Abstract Background At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for long period of time, with first reports variants concern (VOCs) late 2020. Subsequently, genome sequencing has become an indispensable tool characterizing ongoing pandemic, particularly typing samples obtained from patients or environmental surveillance. For such typing, various vitro and silico workflows exist, yet to date, no systematic cross-platform validation been reported. Results In this work, we present comprehensive evaluation workflows. The relies on dataset 54 patient-derived sequenced several different approaches all relevant state-of-the-art platforms. Moreover, UnCoVar, robust, production-grade reproducible workflow that outperforms other tested terms precision recall. Conclusions many ways, pandemic accelerated development techniques analytical approaches. We believe can serve as blueprint dealing future pandemics. Accordingly, UnCoVar is easily generalizable towards viral pathogens fully automated assembles genomes patient samples, identifies existing lineages, provides high-resolution insights into individual mutations. includes extensive quality control automatically generates interactive visual reports. implemented Snakemake workflow. open-source code available under BSD 2-clause license at github.com/IKIM-Essen/uncovar .
Language: Английский
Citations
2
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 8, 2024
Abstract Background Next-generation sequencing for assaying microbial communities has become a standard technique in recent years. However, the initial investment required into in-silico analytics is still quite significant, especially facilities not focused on bioinformatics. With rapid decline costs and growing adoption of sequencing-based methods number fields, validated, fully automated, reproducible yet flexible pipelines will play greater role various scientific fields future. Results We present RiboSnake, QIIME2-based analysis pipeline implemented Snakemake computational 16S rRNA gene amplicon data. The comes with pre-packaged validated parameter sets, optimized different sample types. sets range from complex environmental samples to patient configuration packages can be easily adapted shared, requiring minimal user input. Conclusion RiboSnake new alternative researchers employing looking customizable user-friendly microbiome in-vitro settings. complete generated automated based types significant improvement existing methods. workflow repository found GitHub ( https://github.com/IKIM-Essen/RiboSnake ).
Language: Английский
Citations
0
Gigabyte, Journal Year: 2024, Volume and Issue: 2024
Published: Aug. 31, 2024
Next-generation sequencing for microbial communities has become a standard technique. However, the computational analysis remains resource-intensive. With declining costs and growing adoption of sequencing-based methods in many fields, validated, fully automated, reproducible flexible pipelines are increasingly essential various scientific fields.
Language: Английский
Citations
0