A5062071393- Pharmaceutical and Antibiotic Environmental Impacts
- SARS-CoV-2 detection and testing
- Biosensors and Analytical Detection
- Advanced biosensing and bioanalysis techniques
- Antibiotics Pharmacokinetics and Efficacy
- Antibiotic Resistance in Bacteria
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- Antibiotic Use and Resistance
- Innovative Microfluidic and Catalytic Techniques Innovation
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Bacterial Identification and Susceptibility Testing
- Water Treatment and Disinfection
- Wastewater Treatment and Reuse
- Gene expression and cancer classification
- Advanced oxidation water treatment
Rice University
2019-2024
Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based quasi-unique mutations. The benefits QuaID are three-fold: (i) provides up to 3-week earlier detection, (ii) accurate (>95% precision simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).
First investigation of ARG and MGE removal in an anaerobic membrane bioreactor co-treating real wastewater manure shows increased loading improves removal.
Abstract With the widespread use of last-resort antibiotics, carbapenems, clinical reports infections associated with carbapenem-resistant Enterobacterales (CRE) have increased. Clinical surveillance for CRE involves susceptibility testing and/or whole genome sequencing resistant isolates, which is laborious, resource intensive, and requires expertise. Wastewater can potentially complement CRE, population-level antibiotic resistance (AR) more broadly. In this study, we quantitatively...
To evaluate the threat of environmental dissemination antibiotic resistance associated with wastewater treatment plants (WWTPs), removal efficiency genes (ARGs) during needs to be assessed. The sample collection strategy is one factor that often overlooked in study design and most studies on ARGs perform grab sampling. Here, we hypothesized sampling (i.e., composite sampling) influences observed ARG concentrations calculated rates across WWTPs. We compared based two different methods for...
This study compares culture-based and ddPCR methods for quantifying carbapenem resistance in wastewater, revealing weak correlations. Nanopore sequencing clarifies mechanisms, emphasizing method selection integrated AR surveillance.
Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variants concern (VoC) in communities. Multiple recent studies support that wastewater-based detection circulating VoC precede cases by up to two weeks. Furthermore, based epidemiology enables wide population-based screening and study viral evolutionary dynamics. However, highly sensitive emerging remains a complex task due pooled nature environmental samples genetic...
Abstract Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced assembled via tiled sequencing. While computational tools design exist, they require downstream manual optimization both computationally experimentally, which is slow costly. Here we present Olivar, a first step towards fully automated, variant-aware amplicons pathogen genomes. Olivar...
Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 2 million complete SARS-CoV-2 genomes are now publicly available, most sequenced assembled via tiled sequencing. While computational tools design exist, they require downstream manual optimization both computationally experimentally, which is slow costly. Here we present Olivar, a first step towards fully automated, variant-aware amplicons pathogen genomes. Olivar converts each...
Abstract Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge selecting which analytical deploy measure risk indicators, such as genes (ARGs) and their respective bacterial hosts. Although metagenomics frequently used for analyzing ARGs, few studies have compared performance of long-read short-read identifying bacteria harbor ARGs wastewater. Furthermore, ARG host detection, untargeted has not been targeted methods...
Over the course of COVID-19 pandemic, variants SARS-CoV-2 have emerged that are more contagious and likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification analysis variants. However, when applied environmental samples such as wastewater, it remains unclear how sensitive this method detecting variant-associated mutations in samples. Here we directly compare targeted (using ARTIC v3; hereafter referred sequencing) with RT-ddPCR...
Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge selecting which analytical deploy measure risk indicators, such as genes (ARGs) and their respective bacterial hosts. Although metagenomics frequently used for analyzing ARGs, few studies have compared performance of long-read short-read identifying bacteria harbor ARGs wastewater. Furthermore, ARG host detection, untargeted has not been targeted methods epicPCR....
Over the course of COVID-19 pandemic, variants SARS-CoV-2 have emerged that are more contagious and likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification analysis variants. However, when applied environmental samples such as wastewater, it remains unclear how sensitive this method detecting variant-associated mutations in samples. Here we directly compare targeted (using ARTIC v3; hereafter referred sequencing) with RT-ddPCR...