Biology subjects

Raskin, L.

Publications and source records attributed to Raskin, L..

4 recordsLinked to original sources

bioRxiv2024

Source-to-Tap Investigation of the Occurrence of Nontuberculous Mycobacteria in a Full-Scale Chloraminated Drinking Water System

Nontuberculous mycobacteria (NTM) in drinking water are a significant public health concern. However, an incomplete understanding of the factors that influence the occurrence of NTM in drinking water limits our ability to characterize risk and prevent infection. This study sought to evaluate the influence of season and water treatment, distribution, and stagnation on NTM in drinking water. Samples were collected source-to-tap in a full-scale, chloraminated drinking water system approximately monthly from December 2019 to November 2020. NTM were characterized using culture-dependent (plate culture with matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS] isolate analysis) and culture-independent methods (quantitative PCR and genome resolved metagenomics). Sampling locations included source waters, three locations within the treatment plant, and five buildings receiving water from the distribution system. Building plumbing samples consisted of first draw, five-minute flush, and full flush cold-water samples. As the study took place during the COVID-19 pandemic, the influence of reduced water usage in three of the five buildings was also investigated. The highest concentrations of NTM source-to-tap were found in the summer first draw building water samples (107 gene copies/L), which also had the lowest chloramine concentrations. Flushing was found to be effective for reducing NTM and restoring disinfectant residuals, though flush times necessary to improve water quality varied by building. Clinically-relevant NTM species, including Mycobacterium avium, were recovered via plate culture, with increased occurrence observed in buildings with higher water age. Four of five NTM metagenome-assembled genomes were identified to the species level and matched identified isolates. ImportanceNTM infections are increasing in prevalence, difficult to treat, and associated with high mortality rates. Our lack of understanding of the factors that influence NTM occurrence in drinking water limits our ability to prevent infections, accurately characterize risk, and focus remediation efforts. In this study, we comprehensively evaluated NTM in a full-scale drinking water system, showing that various steps in treatment and distribution influence NTM presence. Stagnant building water contained the highest NTM concentrations source-to-tap and was associated with low disinfectant residuals. We illustrated the differences in NTM detection and characterization obtained from culture-based and culture-independent methods, highlighting the complementarity between these approaches. We demonstrated that focusing NTM mitigation efforts in building plumbing systems, which have the highest NTM concentrations source-to-tap, has potential for immediate positive effects. We also identified steps during treatment that increase NTM levels, which provides beneficial information for utilities seeking to reduce NTM in finished water.

microbiology↗

bioRxiv2023

Simulating Rumen Conditions using an Anaerobic Dynamic Membrane Bioreactor to Enhance Hydrolysis of Lignocellulosic Biomass

An anaerobic dynamic membrane bioreactor (AnDMBR) was used to mimic rumen conditions to enhance the hydrolysis of lignocellulosic materials and the production of volatile fatty acids (VFA) when treating food waste. The AnDMBR was inoculated with cow rumen content and operated at a 0.5-day hydraulic retention time, 2 to 4-day solids retention time, a temperature of 39 {degrees}C, and a pH of 6.3, characteristics similar to those of a rumen. An operational strategy of repeating settle-permeate-mix cycles was utilized to simulate the regurgitation of ruminant animals. Removal rates of neutral detergent fiber (NDF) and acid detergent fiber (ADF) of 58.9 {+/-} 8.4 % and 69.0 {+/-} 8.6 %, respectively, and a VFA yield of 0.55 {+/-} 0.12 g VFA/g CODfed were observed when operating at an organic loading rate of 18 {+/-} 2 kg VS/m3/day. Sequencing results of both 16S rRNA gene and 16S rRNA revealed that a microbial community resistant to both disruption and reinoculation developed six weeks after inoculation. Up to 66.7 {+/-} 5.7 % of the active microbial populations (based on 16S rRNA sequence data) and 51.0 {+/-} 7.0 % of the total microbial populations (based on 16S rRNA gene sequence data) present in the rumen-mimicking AnDMBR originated from the rumen inoculum. This study offers a reliable strategy to leverage the unique features of a rumen; the rumen-mimicking AnDMBR achieved high hydrolysis and acidogenesis rates even when treating substrates drastically different from those fed to ruminants.

bioengineering↗

bioRxiv2021

A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use

Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.

microbiology↗

bioRxiv2020

Predictive modeling of virus inactivation by UV

Disinfection strategies are commonly applied to inactivate pathogenic viruses in water, food, air, and on surfaces to prevent the spread of infectious diseases. Determining how quickly viruses are inactivated to mitigate health risks is not always feasible due to biosafety restrictions or difficulties with virus culturability. Therefore, methods that would rapidly predict kinetics of virus inactivation by UV254 would be valuable, particularly for emerging and difficult-to-culture viruses. We conducted a rapid systematic literature review to collect high-quality inactivation rate constants for a wide range of viruses. Using these data and basic virus information (e.g., genome sequence attributes), we developed and evaluated four different model classes, including linear and non-linear approaches, to find the top performing prediction model. For both the (+) ssRNA and dsDNA virus types, multiple linear regressions were the top performing model classes. In both cases, the cross-validated root mean squared relative prediction errors were similar to those associated with experimental rate constants. We tested the models by predicting and measuring inactivation rate constants for two viruses that were not identified in our systematic review, including a (+) ssRNA mouse coronavirus and a dsDNA marine bacteriophage; the predicted rate constants were within 7% and 71% of the experimental rate constants, respectively. Finally, we applied our models to predict the UV254 rate constants of several viruses for which high-quality UV254 inactivation data are not available. Our models will be valuable for predicting inactivation kinetics of emerging or difficult-to-culture viruses.

microbiology↗