Article
Engineering, Environmental
Adam L. Smith, Phillip Wang
Summary: Wastewater surveillance of antibiotic resistance genes (ARGs) provides valuable information on the prevalence and genetic characteristics of antibiotic-resistant bacteria. This study detected several variants of the mobile colistin-resistant (mcr) gene in Los Angeles County wastewater, and through further analysis, identified conserved gene cassettes and discovered novel plasmids carrying these genes. The findings highlight the importance of wastewater surveillance in understanding the transmission and dissemination of ARGs.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2023)
Review
Environmental Sciences
Xue Yu, Ying Zhang, Lu Tan, Chenglong Han, Haixiao Li, Lifang Zhai, Weiqi Ma, Chengtao Li, Xueqiang Lu
Summary: The study found that antibiotic resistance genes enriched on microplastics were more abundant than on inorganic substrates and natural water environments, but less abundant than on natural organic substrates. Microplastics in freshwater tended to have a higher degree of ARG enrichment than those in saline water and sewage.
ENVIRONMENTAL POLLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Hanseob Shin, Yongjin Kim, Seunggyun Han, Hor-Gil Hur
Summary: Since the discovery of antibiotics, the introduction of new antibiotics has led to the emergence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The rapid spread of ARB and ARGs in aquatic environments is a global concern, with transmission occurring via various routes. Most ARGs are found in Gammaproteobacteria class, including potential pathogens. Therefore, certain ARGs and mobile genetic elements have been proposed as indicators for contamination levels in aquatic environments. Active surveillance systems have been implemented globally due to the occurrence of critical pathogens in aquatic environments. However, there is still no clear strategy to address antibiotic resistance in these environments, highlighting the need for a strict framework for further research.
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Geosciences, Multidisciplinary
Yunxin Xie, Chenyang Zhu, Runshan Hu, Zhengwei Zhu
Summary: Lithology identification is crucial for reservoir exploration and petroleum engineering. Recent interest has been focused on using intelligent logging approaches for lithology classification, with machine learning emerging as a powerful tool in inferring lithology types. Challenges such as manual entry of logging parameters, borehole conditions, and tool calibrations have been addressed. This study proposes a unified framework utilizing outlier detection, multi-class classification, and an extremely randomized tree-based classifier for training a multi-class lithology classification model, demonstrating higher prediction accuracy in sandstones compared to other machine learning classifiers.
MATHEMATICAL GEOSCIENCES
(2021)
Article
Environmental Sciences
Hannah C. Lepper, Meghan R. Perry, Bryan A. Wee, David Wills, Hanne Nielsen, Saria Otani, Moray Simon, Frank M. Aarestrup, Mark E. J. Woolhouse, Bram A. D. van Bunnik
Summary: This study compares the resistome and microbiome of hospital, community, and mixed municipal wastewater and finds that the resistome in hospital wastewater is different from that in other locations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Environmental Sciences
Aemere Ogunlaja, Olumuyiwa O. Ogunlaja, Olumide D. Olukanni, Gloria O. Taylor, Chidinma G. Olorunnisola, Wassiyath Mousse, Despo Fatta-Kassinos, Titus A. M. Msagati, Emmanuel I. Unuabonah
Summary: This review summarizes the presence and distribution of antibiotic resistant bacteria and genes in African aquatic environments, revealing that larger economies in Africa have reports of ARB and ARGs while smaller economies lack such data. Common ARGs found in African aquatic environments include resistance to sulfonamide, tetracycline, beta-lactam, and macrolide classes of antibiotics.
ENVIRONMENTAL POLLUTION
(2022)
Article
Engineering, Environmental
Yuhao Fu, Fang Wang, Hongjie Sheng, Fang Hu, Ziquan Wang, Min Xu, Yongrong Bian, Xin Jiang, James M. Tiedje
Summary: The use of magnetic biochar/quaternary phosphonium salt (MBQ) significantly enhances the adsorption capacity of extracellular DNA, resulting in over 92.7% removal of antibiotic resistance genes (ARGs) from water. This approach effectively mitigates the spread of ARGs and reduces the risk of antimicrobial resistance propagation in aquatic environments.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Environmental Sciences
Atya Kapley, Mohammed Shahique Sheeraz, Sushrut Kukade, Aamir Ansari, Asifa Qureshi, Abhay Bajaj, Noor Afshan Khan, Shalini Tandon, Rachana Jain, Swapnil Dudhwadkar, Shubhi Sharma, Archana Bharadwaj Siva
Summary: The surge of Antibiotic Resistant Bacteria (ARB) in the environment is poised to be the next health threat, with developing countries being at a greater risk due to untreated wastewater and poor sanitation. This study conducted surveillance of sewage-carrying drains in four urban cities in India, revealing the presence of ARBs in the bacterial community against multiple classes of antibiotics. The report emphasizes the importance of routine sewage surveillance by state authorities.
ENVIRONMENTAL POLLUTION
(2023)
Review
Engineering, Environmental
Aleksandra Milobedzka, Catarina Ferreira, Ivone Vaz-Moreira, David Calderon-Franco, Adrian Gorecki, Sabina Purkrtova, Jan Bartacek, Lukasz Dziewit, Caitlin M. Singleton, Per Halkjaer Nielsen, David Gregory Weissbrodt, Celia M. Manaia
Summary: Antibiotic resistance (AR) is a global issue that requires international cooperation and coordinated action. Global monitoring of AR occurrence and dissemination paths must rely on comparable methods, while taking into account distinct needs and available resources. Despite the challenges posed by the diverse methodological approaches and variable features of monitored sites, fostering dialogue between different methods and producing action-oriented data is crucial.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Computer Science, Artificial Intelligence
Tullio Mancini, Hector Calvo-Pardo, Jose Olmo
Summary: This paper introduces a novel prediction model based on an ensemble of deep neural networks with extra randomness for improved accuracy and uncertainty computation. The method performs well in terms of mean square prediction error and accuracy of prediction intervals, outperforming state-of-the-art methods in experimental settings.
Review
Environmental Sciences
Benjamin C. C. Davis, Connor Brown, Suraj Gupta, Jeannette Calarco, Krista Liguori, Erin Milligan, Valerie J. J. Harwood, Amy Pruden, Ishi Keenum
Summary: Shotgun metagenomic sequencing is a powerful approach for monitoring antibiotic resistance in environmental samples. It allows for simultaneous screening of known and putative antibiotic resistance genes without prior target selection. This study presents recommendations for sampling design, DNA extraction, sequencing depth, and experimental controls to ensure comparability of metagenomic data. Through comprehensive analysis and reanalysis of publicly-available metagenomes, optimal sequencing depths and normalization strategies are provided. The implementation of these recommendations will enhance the overall value of metagenomic data in supporting future comparisons.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Article
Environmental Sciences
Anna Abramova, Thomas U. Berendonk, Johan Bengtsson-Palme
Summary: The environment plays a crucial role in the emergence and spread of antimicrobial resistance (AMR), yet monitoring efforts outside of clinical and veterinary settings have been limited. This is partly due to a lack of comprehensive reference data for most environments. To establish a baseline of AMR in various settings, a literature survey was conducted, identifying 150 papers with relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data, spanning from 2001 to 2020 and representing 1594 samples from 30 countries and 12 sample types, revealed that the abundances of most ARGs in human impacted environments fell within a range of 10-5 to 10-3 copies per 16S rRNA, approximately one ARG copy in a thousand bacteria. Overall, these findings provide a comprehensive overview of ARG occurrence and levels in different environments, contributing to the development of risk assessment models in AMR monitoring frameworks.
ENVIRONMENT INTERNATIONAL
(2023)
Review
Environmental Sciences
Hanlin Cui, Adam L. Smith
Summary: Nanoparticles and antibiotic resistance elements are commonly found in wastewater and have complex interactions that impact antibiotic resistance. Sub-lethal levels of engineered nanoparticles may contribute to selective pressure on antibiotic resistance genes, while emergent nanoparticles could naturally attenuate the dissemination of resistance genes.
ENVIRONMENTAL RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Ahmed I. Osman, Ali Ayati, Mohamed Farghali, Pavel Krivoshapkin, Bahareh Tanhaei, Hassan Karimi-Maleh, Elena Krivoshapkina, Parsana Taheri, Chantal Tracey, Ahmed Al-Fatesh, Ikko Ihara, David W. Rooney, Mika Sillanpaae
Summary: This article reviews advanced adsorption methods to remove pharmaceuticals from the environment, focusing on ibuprofen's occurrence, toxicity, adsorbents, kinetics, and adsorption isotherms. Carbon-based adsorbents show the highest adsorption capacity for ibuprofen, with activated carbon at 10.8-408 mg/g and biochar at 2.5-1033 mg/g. Metal-organic frameworks are also promising due to their high surface area and tunable properties and morphology.
ENVIRONMENTAL CHEMISTRY LETTERS
(2023)
Review
Microbiology
Daniel Basiry, Nooshin Entezari Heravi, Cansu Uluseker, Krista Michelle Kaster, Roald Kommedal, Ilke Pala-Ozkok
Summary: The outbreak of the SARS-CoV-2 pandemic has increased the use of disinfectants and antiseptics, resulting in higher concentrations of these compounds in wastewaters and water bodies. This can lead to the development of resistance against these compounds and also promote antibiotic resistance among bacteria. This review provides an overview of the structure and modes of action of disinfectants and antiseptics, discusses effective treatment techniques for their removal from wastewater, and addresses their impact on antibiotic resistance and occurrence in aquatic systems.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Wei Wang, Asifur Rahman, Qishen Huang, Peter J. Vikesland
Summary: An improved understanding of bacterial inactivation mechanisms was obtained by evaluating bacterial response to different inactivation methods using surface-enhanced Raman spectroscopy (SERS). The results showed that changes in the SERS signal were closely related to cellular disruption, and the changes in cellular morphology after inactivation cannot be ignored. Different methods, such as heat treatment, UV254 treatment, and UV254/chlorine treatment, led to severe membrane disruption, resulting in increased peak intensities. However, ethanol treatment resulted in intact cell morphologies and minimal changes in the SERS spectra. The main changes observed during inactivation were related to nucleic acids, and the peaks associated with nucleic acids showed significant variations. Carbohydrates and proteins on the cell membrane were denatured or lost after chlorine treatment, leading to a decrease in related peak intensities. The method was also found to be applicable to different bacterial strains and water matrices.
Article
Chemistry, Multidisciplinary
Asifur Rahman, Seju Kang, Sean McGinnis, Peter J. Vikesland
Summary: This study compared the environmental impacts of FeOx-NPs produced through seven common synthesis routes using a cradle-to-gate life cycle assessment. The results showed that physical and biological synthesis routes had higher environmental impacts, while chemical synthesis routes had lower impacts, except for the thermal decomposition method.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Engineering, Environmental
Qishen Huang, Peter J. Vikesland
Summary: This study demonstrates the use of flash-freeze surface-enhanced Raman spectroscopy (SERS) to characterize the pH of micrometer-sized droplets generated from low solute concentration environmental water samples. The flash-freeze SERS approach preserves the initial droplet properties and provides greater sensitivity compared to pH paper. The results show that droplet and bulk pH were generally comparable for most environmental samples, except for one rainwater sample with a higher droplet pH. This indicates the potential influence of droplet composition on droplet pH.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
Review
Environmental Sciences
Asifur Rahman, Wei Wang, Divyapriya Govindaraj, Seju Kang, Peter J. Vikesland
Summary: Cellulose nanomaterials are advantageous due to their low cost, biocompatibility, and high stability and specific surface area. They can be combined with metal nanoparticles, organic polymers, and metal-organic frameworks to produce nanocomposites with various applications in environmental science and engineering.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Article
Engineering, Environmental
Maria Virginia Prieto Riquelme, Emily Garner, Suraj Gupta, Jake Metch, Ni Zhu, Matthew F. Blair, Gustavo Arango-Argoty, Ayella Maile-Moskowitz, An-dong Li, Carl-Fredrik Flach, Diana S. Aga, Indumathi M. Nambi, D. G. Joakim Larsson, Helmut Buergmann, Tong Zhang, Amy Pruden, Peter J. Vikesland
Summary: This study presents a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage. The results show that there are shared antibiotic resistance genes (ARGs) across different regions/communities, and certain ARGs can be used as discriminatory markers to differentiate Asian and European/US resistomes. The study also reveals discrepancies between measured antibiotic concentrations and public sales data, suggesting that wastewater-based surveillance (WBS) can capture additional antibiotic uses that are not accounted for. The WBS approach demonstrated in this study is sensitive to local/regional factors and can provide comparable results across different sites.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Correction
Green & Sustainable Science & Technology
Shantanu V. Bhide, Stanley B. Grant, Emily A. Parker, Megan A. Rippy, Adil N. Godrej, Sujay Kaushal, Greg Prelewicz, Niffy Saji, Shannon Curtis, Peter Vikesland, Ayella Maile-Moskowitz, Marc Edwards, Kathryn G. Lopez, Thomas A. Birkland, Todd Schenk
NATURE SUSTAINABILITY
(2023)
Article
Biotechnology & Applied Microbiology
Connor L. Brown, James Mullet, Fadi Hindi, James E. Stoll, Suraj Gupta, Minyoung Choi, Ishi Keenum, Peter Vikesland, Amy Pruden, Liqing Zhang
Summary: This study provides a comprehensive analysis of bacterial mobile genetic elements (MGEs) and presents a database, mobileOG-db, containing over 6,000 protein families for the annotation and analysis of MGEs. The database offers a multilevel classification scheme, allowing for the annotation of plasmids, phages, integrative elements, and transposable elements.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Wei Wang, Seju Kang, Wei Zhou, Peter J. Vikesland
Summary: Many emerging infectious diseases are caused by viruses, which can be transmitted through various environmental matrices. The development of nanosensors based on unique properties of nanomaterials offers great potential for rapid and sensitive virus detection in the environment. These nanosensors can generate detectable signals through interactions between viruses and nanomaterials, providing fast response times, high sensitivity, and specificity.
ENVIRONMENTAL SCIENCE-NANO
(2023)
Article
Chemistry, Analytical
Wei Wang, Asifur Rahman, Seju Kang, Peter J. Vikesland
Summary: Label-free surface-enhanced Raman spectroscopy (SERS) is a promising technique for bacterial detection. This study evaluated the impact of storage conditions on label-free SERS spectra of Pseudomonas syringae samples stored in phosphate buffered saline. The results showed that storage conditions can significantly affect bacterial SERS signals and should be considered when detecting bacteria or evaluating bacterial response to stress stimuli.
ANALYTICAL CHEMISTRY
(2023)
Article
Microbiology
Andrea J. J. French, Alexandra K. K. Longest, Jin Pan, Peter J. J. Vikesland, Nisha K. K. Duggal, Linsey C. C. Marr, Seema S. S. Lakdawala
Summary: Efficient spread of respiratory viruses requires the virus to maintain infectivity in the environment. Our study measured the impact of initial droplet volume and relative humidity on the stability of influenza A virus, bacteriophage Phi6, and SARS-CoV-2. Virus decay rates differed between the wet and dry phases, and there were differences in virus decay characteristics by droplet size and virus. This study suggests that virus decay in media is related to droplet evaporation, which is controlled by relative humidity.
Article
Chemistry, Multidisciplinary
Aditya Garg, Wonil Nam, Wei Wang, Peter Vikesland, Wei Zhou
Summary: This study demonstrates the in situ spatiotemporal characterization and multivariate analysis of Pseudomonas syringae biofilms using surface-enhanced Raman spectroscopy (SERS) and nanolaminate plasmonic crystal SERS devices. The results show the potential of this method for monitoring the dynamic evolution of biofilms and their response to viral infection, offering insights for anti-biofilm therapy and viral detection.
Article
Engineering, Environmental
Wei Wang, Peter J. Vikesland
Summary: In this study, surface-enhanced Raman spectroscopy (SERS) was used to monitor the bioactive metabolites produced by ampicillin-resistant Pseudomonas aeruginosa strains and investigate the mechanisms underlying antibiotic resistance. The results showed that the blue-green pigment pyocyanin (PYO) dominated the metabolite signals and was significantly enhanced in the presence of subminimal inhibitory concentrations of ampicillin. The SERS spectra also revealed minimal impact on the production of intermediate substances and consistent nutrient consumption. Furthermore, exogenously added PYO enhanced the tolerance of ampicillin-susceptible Escherichia coli to some extent, indicating that PYO mediates antibiotic resistance in both the parent species and cocultured bacterial strains. The metabolic SERS signal provides new insights into antibiotic resistance and has promising applications in environmental monitoring and rapid clinical detection.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Editorial Material
Engineering, Environmental
Peter Vikesland
ACS ENVIRONMENTAL AU
(2023)
Article
Chemistry, Analytical
Wei Wang, Peter J. Vikesland
Summary: This study incorporates gold nanoparticles into a hydrogel ink for 3D printing and culturing of cells, enabling the use of surface-enhanced Raman spectroscopy (SERS) for cell imaging. A random forest binary classifier is developed to accurately distinguish cell signals from the background. The results show that SERS signals provide information about cellular components.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
Wei Wang, Peter J. Vikesland
Summary: This study demonstrates the use of surface-enhanced Raman spectroscopy (SERS) to monitor the metabolites produced by ampicillin-resistant Pseudomonas aeruginosa strains and identify the mechanisms underlying antibiotic resistance. The results indicate that the blue-green pigment pyocyanin (PYO) dominates the metabolite signals and is significantly enhanced by exposure to subminimal inhibitory concentrations of ampicillin. These findings provide new insights into antibiotic resistance.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)