Destination Area: Global Systems Science (GSS)

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https://hdl.handle.net/10919/78630

GSS fosters transdisciplinary study of the dynamic interplay between natural and social systems. Faculty in this area collaborate to discover creative solutions to critical social problems emergent from human activity and environmental change, in areas such as freshwater and coastal water systems, rural environments, infectious disease, and food production and safety. Work in this area also embraces equity in the human condition by seeking the equitable distribution and availability of physical safety and well-being, psychological well-being, respect for human dignity, and access to crucial material and social resources throughout the world’s diverse communities.

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2021 GAP Report Launch: Strengthening the Climate For Sustainable Agricultural Growth
Steensland, Ann (Virginia Tech College of Agriculture and Life Sciences, 2021-10-20)
During the launch of the 2021 Global Agricultural Productivity Report (GAP Report), the newest data on agricultural productivity across the globe was revealed to be well below the Global Agricultural Productivity Index target. Through a solution-oriented discussion, experts across the globe discuss what we can do now to address the looming crisis.
Addressing the Contribution of Indirect Potable Reuse to Inland Freshwater Salinization
Bhide, Shantanu V.; Grant, Stanley B.; Parker, Emily A.; Rippy, Megan A.; Godrej, Adil N.; Kaushal, Sujay S.; Prelewicz, Gregory; Saji, Niffy; Curtis, Shannon; Vikesland, Peter J.; Maile-Moskowitz, Ayella; Edwards, Marc A.; Lopez, Kathryn; Birkland, Thomas A.; Schenk, Todd (2021-02-02)
Inland freshwater salinity is rising worldwide, a phenomenon called the freshwater salinization syndrome (FSS). We investigate a potential conflict between managing the FSS and indirect potable reuse, the practice of augmenting water supplies through the addition of reclaimed wastewater to surface waters and groundwaters. From time-series data collected over 25 years, we quantify the contributions of three salinity sources—a wastewater reclamation facility and two rapidly urbanizing watersheds—to the rising concentration of sodium (a major ion associated with the FSS) in a regionally important drinking water reservoir in the Mid-Atlantic United States. Sodium mass loading to the reservoir is primarily from watershed runoff during wet weather and reclaimed wastewater during dry weather. Across all timescales evaluated, sodium concentration in the reclaimed wastewater is higher than in outflow from the two watersheds. Sodium in reclaimed wastewater originates from chemicals added during wastewater treatment, industrial and commercial discharges, human excretion, and down-drain disposal of drinking water and sodium-rich household products. Thus, numerous opportunities exist to reduce the contribution of indirect potable reuse to sodium pollution at this site, and the FSS more generally. These efforts will require deliberative engagement with a diverse community of watershed stakeholders and careful consideration of the local political, social, and environmental context.
Advanced sequencing approaches detected insertions of viral and human origin in the viral genome of chronic hepatitis E virus patients
Papp, C-Patrick; Biedermann, Paula; Harms, Dominik; Wang, Bo; Kebelmann, Marianne; Choi, Mira; Helmuth, Johannes; Corman, Victor M.; Thuermer, Andrea; Altmann, Britta; Klink, Patrycja; Hofmann, Joerg; Bock, C-Thomas (Nature Portfolio, 2022-02-02)
The awareness of hepatitis E virus (HEV) increased significantly in the last decade due to its unexpectedly high prevalence in high-income countries. There, infections with HEV-genotype 3 (HEV-3) are predominant which can progress to chronicity in immunocompromised individuals. Persistent infection and antiviral therapy can select HEV-3 variants; however, the spectrum and occurrence of HEV-3 variants is underreported. To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. Using this new approach, we not only identified several insertions of human (AHNAK, RPL18) and viral origin (RdRp-derived) in the HVR-region isolated from an exemplary sample but detected a variant containing two different insertions simultaneously (AHNAK- and RdRp-derived). This finding is the first HEV-variant recognized as such showing various insertions in the HVR-domain. Thus, this molecular approach will add incrementally to our current knowledge of the HEV-genome organization and pathogenesis in chronic hepatitis E.
Advances in Ecohydrology for Water Resources Optimization in Arid and Semi-Arid Areas
Castellini, Mirko; Di Prima, Simone; Stewart, Ryan D.; Biddoccu, Marcella; Rahmati, Mehdi; Alagna, Vincenzo (MDPI, 2022-06-07)
Conserving water resources is a current challenge that will become increasingly urgent in future due to climate change. The arid and semi-arid areas of the globe are expected to be particularly affected by changes in water availability. Consequently, advances in ecohydrology sciences, i.e., the interplay between ecological and hydrological processes, are necessary to enhance the understanding of the critical zone, optimize water resources’ usage in arid and semi-arid areas, and mitigate climate change. This Special Issue (SI) collected 10 original contributions on sustainable land management and the optimization of water resources in fragile environments that are at elevated risk due to climate change. In this context, the topics mainly concern transpiration, evapotranspiration, groundwater recharge, deep percolation, and related issues. The collection of manuscripts presented in this SI represents knowledge of ecohydrology. It is expected that ecohydrology will have increasing applications in the future. Therefore, it is realistic to assume that efforts to increase environmental sustainability and socio-economic development, with water as a central theme, will have a greater chance of success.
Advancing the Global Land Grant Institution: Creating a Virtual Environment to Re-envision Extension and Advance GSS-related Research, Education, and Collaboration
Hall, Ralph P.; Polys, Nicholas F.; Sforza, Peter M.; Eubank, Stephen D.; Lewis, Bryan L.; Krometis, Leigh-Anne H.; Pollyea, Ryan M.; Schoenholtz, Stephen H.; Sridhar, Venkataramana; Crowder, Van; Lipsey, John; Christie, Maria Elisa; Glasson, George E.; Scherer, Hannah H.; Davis, A. Jack; Dunay, Robert J.; King, Nathan T.; Muelenaer, Andre A.; Muelenaer, Penelope; Rist, Cassidy; Wenzel, Sophie (Virginia Tech, 2017-05-15)
The vision for this project has emerged from several years of research, teaching, and service in Africa and holds the potential to internationalize education at Virginia Tech and in our partner institutions in Malawi. The vision is simple, to develop a state-of-the-art, data rich, virtual decision-support and learning environment that enables local-, regional-, and national-level actors in developed and developing regions to make decisions that improve resilience and sustainability. Achieving these objectives will require a system that can combine biogeophysical and sociocultural data in a way that enables actors to understand and leverage these data to enhance decision-making at various levels. The project will begin by focusing on water, agricultural, and health systems in Malawi, and can be expanded over time to include any sector or system in any country. The core ideas are inherently scalable...
Age influences the thermal suitability of Plasmodium falciparum transmission in the Asian malaria vector Anopheles stephensi
Miazgowicz, K. L.; Shocket, M. S.; Ryan, Sadie J.; Villena, O. C.; Hall, R. J.; Owen, J.; Adanlawo, T.; Balaji, K.; Johnson, Leah R.; Mordecai, Erin A.; Murdock, Courtney C. (2020-07-29)
Models predicting disease transmission are vital tools for long-term planning of malaria reduction efforts, particularly for mitigating impacts of climate change. We compared temperature-dependent malaria transmission models when mosquito life-history traits were estimated from a truncated portion of the lifespan (a common practice) versus traits measured across the full lifespan. We conducted an experiment on adult femaleAnopheles stephensi, the Asian urban malaria mosquito, to generate daily per capita values for mortality, egg production and biting rate at six constant temperatures. Both temperature and age significantly affected trait values. Further, we found quantitative and qualitative differences between temperature-trait relationships estimated from truncated data versus observed lifetime values. Incorporating these temperature-trait relationships into an expression governing the thermal suitability of transmission, relativeR(0)(T), resulted in minor differences in the breadth of suitable temperatures forPlasmodium falciparumtransmission between the two models constructed from onlyAn. stephensitrait data. However, we found a substantial increase in thermal niche breadth compared with a previously published model consisting of trait data from multipleAnophelesmosquito species. Overall, this work highlights the importance of considering how mosquito trait values vary with mosquito age and mosquito species when generating temperature-based suitability predictions of transmission.
Agent-Based Simulation Framework for Epidemic Forecasting during Hajj Seasons in Saudi Arabia
Alshammari, Sultanah Mohammed; Ba-Aoum, Mohammed Hassan; Alganmi, Nofe Ateq; Allinjawi, Arwa AbdulAziz (MDPI, 2021-08-12)
The religious pilgrimage of Hajj is one of the largest annual gatherings in the world. Every year approximately three million pilgrims travel from all over the world to perform Hajj in Mecca in Saudi Arabia. The high population density of pilgrims in confined settings throughout the Hajj rituals can facilitate infectious disease transmission among the pilgrims and their contacts. Infected pilgrims may enter Mecca without being detected and potentially transmit the disease to other pilgrims. Upon returning home, infected international pilgrims may introduce the disease into their home countries, causing a further spread of the disease. Computational modeling and simulation of social mixing and disease transmission between pilgrims can enhance the prevention of potential epidemics. Computational epidemic models can help public health authorities predict the risk of disease outbreaks and implement necessary intervention measures before or during the Hajj season. In this study, we proposed a conceptual agent-based simulation framework that integrates agent-based modeling to simulate disease transmission during the Hajj season from the arrival of the international pilgrims to their departure. The epidemic forecasting system provides a simulation of the phases and rituals of Hajj following their actual sequence to capture and assess the impact of each stage in the Hajj on the disease dynamics. The proposed framework can also be used to evaluate the effectiveness of the different public health interventions that can be implemented during the Hajj, including size restriction and screening at entry points.
Agricultural Practices Influence Salmonella Contamination and Survival in Pre-harvest Tomato Production
Gu, Ganyu; Strawn, Laura K.; Oryang, David O.; Zheng, Jie; Reed, Elizabeth A.; Ottesen, Andrea R.; Bell, Rebecca L.; Chen, Yuhuan; Duret, Steven; Ingram, David T.; Reiter, Mark S.; Pfuntner, Rachel; Brown, Eric W.; Rideout, Steven L. (Frontiers, 2018-10-16)
Between 2000 and 2010 the Eastern Shore of Virginia was implicated in four Salmonella outbreaks associated with tomato. Therefore, a multi-year study (2012-2015) was performed to investigate presumptive factors associated with the contamination of Salmonella within tomato fields at Virginia Tech's Eastern Shore Agricultural Research and Extension Center. Factors including irrigation water sources (pond and well), type of soil amendment: fresh poultry litter (PL), PL ash, and a conventional fertilizer (triple superphosphate - TSP), and production practices: staked with plastic mulch (SP), staked without plastic mulch (SW), and non-staked without plastic mulch (NW), were evaluated by split-plot or complete-block design. All field experiments relied on naturally occurring Salmonella contamination, except one follow up experiment (worst-case scenario) which examined the potential for contamination in tomato fruits when Salmonella was applied through drip irrigation. Samples were collected from pond and well water; PL, PL ash, and TSP; and the rhizosphere, leaves, and fruits of tomato plants. Salmonella was quantified using a most probable number method and contamination ratios were calculated for each treatment. Salmonella serovar was determined by molecular serotyping. Salmonella populations varied significantly by year; however, similar trends were evident each year. Findings showed use of untreated pond water and raw PL amendment increased the likelihood of Salmonella detection in tomato plots. Salmonella Newport and Typhimurium were the most frequently detected serovars in pond water and PL amendment samples, respectively. Interestingly, while these factors increased the likelihood of Salmonella detection in tomato plots (rhizosphere and leaves), all tomato fruits sampled (n = 4800) from these plots were Salmonella negative. Contamination of tomato fruits was extremely low (< 1%) even when tomato plots were artificially inoculated with an attenuated Salmonella Newport strain (10(4) CFU/mL). Furthermore, Salmonella was not detected in tomato plots irrigated using well water and amended with PL ash or TSP. Production practices also influenced the likelihood of Salmonella detection in tomato plots. Salmonella detection was higher in tomato leaf samples for NW plots, compared to SP and SW plots. This study provides evidence that attention to agricultural inputs and production practices may help reduce the likelihood of Salmonella contamination in tomato fields.
Air Quality in Southeast Brazil during COVID-19 Lockdown: A Combined Satellite and Ground-Based Data Analysis
Brandao, Rayssa; Foroutan, Hosein (MDPI, 2021-05-01)
With the current COVID-19 pandemic being spread all over the world, lockdown measures are being implemented, making air pollution levels go down in several countries. In this context, the air quality changes in the highly populated and trafficked Brazilian states of São Paulo (SP) and Rio de Janeiro (RJ) were addressed using a combination of satellite and ground-based daily data analysis. We explored nitrogen dioxide (NO2) and fine particulate matter (PM2.5) daily levels for the month of May from 2015–2020. Daily measurements of NO2 column concentrations from the Ozone Monitoring Instrument (OMI) aboard NASA’s Aura satellite were analyzed and decreases of 42% and 49.6% were found for SP and RJ, respectively, during the year 2020 compared to the 2015–2019 average. Besides NO2 column retrievals, ground-based data measured by the Brazilian States Environmental Institutions were analyzed and correlated with satellite retrievals. Correlation coefficients between year-to-year changes in satellite column and ground-based concentrations were 77% and 53% in SP and RJ, respectively. Ground-based data showed 13.3% and 18.8% decrease in NO2 levels for SP and RJ, respectively, in 2020 compared to 2019. In SP, no significant change in PM2.5 was observed in 2020 compared to 2019. To further isolate the effect of emissions reduction due to the lockdown, meteorological data and number of wildfire hotspots were analyzed. NO2 concentrations showed negative and positive correlations with wind speed and temperature, respectively. PM2.5 concentration distributions suggested an influence by the wildfires in the southeast region of the country. Synergistic analyses of satellite retrievals, surface level concentrations, and weather data provide a more complete picture of changes to pollutant levels.
Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2
Azouz, N. P.; Klingler, A. M.; Callahan, Victoria; Akhrymuk, Ivan V.; Elez, K.; Raich, L.; Henry, B. M.; Benoit, J. L.; Benoit, S. W.; Noé, F.; Kehn-Hall, Kylene; Rothenberg, M. E. (2021-01-01)
Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein priming, an important step for binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) receptor before cell entry. Methods: We developed a cell-based assay to identify TMPRSS2 inhibitors. Inhibitory activity was established in SARS-CoV-2 viral load systems. Results: We identified the human extracellular serine protease inhibitor (serpin) alpha 1 anti-trypsin (A1AT) as a novel TMPRSS2 inhibitor. Structural modeling revealed that A1AT docked to an extracellular domain of TMPRSS2 in a conformation that is suitable for catalysis, resembling similar serine protease inhibitor complexes. Inhibitory activity of A1AT was established in a SARS-CoV-2 viral load system. Notably, plasma A1AT levels were associated with COVID-19 disease severity. Conclusions: Our data support the key role of extracellular serine proteases in SARS CoV-2 infections and indicate that treatment with serpins, particularly the FDA-approved drug A1AT, may be effective in limiting SARS-CoV-2 dissemination by affecting the surface of the host cells.
Altered toxicological endpoints in humans from common quaternary ammonium compound disinfectant exposure
Hrubec, Terry C.; Seguin, Ryan P.; Xu, L.; Cortopassi, G. A.; Datta, S.; Hanlon, Alexandra L.; Lozano, A. J.; McDonald, V. A.; Healy, C. A.; Anderson, T. C.; Musse, N. A.; Williams, R. T. (Elsevier, 2021-01-01)
Humans are frequently exposed to Quaternary Ammonium Compounds (QACs). QACs are ubiquitously used in medical settings, restaurants, and homes as cleaners and disinfectants. Despite their prevalence, nothing is known about the health effects associated with chronic low-level exposure. Chronic QAC toxicity, only recently identified in mice, resulted in developmental, reproductive, and immune dysfunction. Cell based studies indicate increased inflammation, decreased mitochondrial function, and disruption of cholesterol synthesis. If these findings translate to human toxicity, multiple physiological processes could be affected. This study tested whether QAC concentrations could be detected in the blood of 43 human volunteers, and whether QAC concentrations influenced markers of inflammation, mitochondrial function, and cholesterol synthesis. QAC concentrations were detected in 80 % of study participants. Blood QACs were associated with increase in inflammatory cytokines, decreased mitochondrial function, and disruption of cholesterol homeostasis in a dose dependent manner. This is the first study to measure QACs in human blood, and also the first to demonstrate statistically significant relationships between blood QAC and meaningful health related biomarkers. Additionally, the results are timely in light of the increased QAC disinfectant exposure occurring due to the SARS-CoV-2 pandemic. Main Findings: This study found that 80 % of study participants contained QACs in their blood; and that markers of inflammation, mitochondrial function, and sterol homeostasis varied with blood QAC concentration.
Annual water residence time effects on thermal structure: A potential lake restoration measure?
Olsson, Freya; Mackay, Eleanor B.; Moore, Tadhg N.; Barker, Phil; Davies, Sian; Hall, Ruth; Spears, Bryan; Wilkinson, Jayne; Jones, Ian D. (Academic Press - Elsevier, 2022-07-15)
Innovative methods to combat internal loading issues in eutrophic lakes are urgently needed to speed recovery and restore systems within legislative deadlines. In stratifying lakes, internal phosphorus loading is particularly problematic during the summer stratified period when anoxia persists in the hypolimnion, promoting phos-phorus release from the sediment. A novel method to inhibit stratification by reducing residence times is pro-posed as a way of controlling the length of the hypolimnetic anoxic period, thus reducing the loading of nutrients from the sediments into the water column. However, residence time effects on stratification length in natural lakes are not well understood. We used a systematic modelling approach to investigate the viability of changes to annual water residence time in affecting lake stratification and thermal dynamics in Elterwater, a small strati-fying eutrophic lake in the northwest of England. We found that reducing annual water residence times shortened and weakened summer stratification. Based on finer-scale dynamics of lake heat fluxes and water column sta-bility we propose seasonal or sub-seasonal management of water residence time is needed for the method to be most effective at reducing stratification as a means of controlling internal nutrient loading.
Antibiotic resistance genes in the faeces of dairy cows following short-term therapeutic and prophylactic antibiotic administration
Feng, Xin; Chambers, Lindsey R.; Knowlton, Katharine F. (2019-12-06)
The objective of the research was to quantify three antibiotic resistance genes (tetQ, cfxA and mefA) in the faeces of dairy cows following therapeutic and prophylactic antibiotic treatments. Manure collected from dairy cows treated with either no antibiotic, pirlimycin hydrochloride (PIRL), ceftiofur crystalline free acid (CCFA) or cephapirin benzathine (CEPH) were submitted to quantitative PCR analysis. No treatment effects on the abundance of the tetQ and cfxA were observed. There was a trend for the abundance of the mefA to be increased in cows treated with PIRL (P = 0.07). Overall, the results showed no difference of measured three ARGs from cows receiving different antibiotics. Considering the limited scope of our investigation, further investigation is needed to provide more information on ARGs excretion from cows that received therapeutic and prophylactic antibiotic treatment.
Antibiotic Use on Goat Farms: An Investigation of Knowledge, Attitudes, and Behaviors of Missouri Goat Farmers
Landfried, Lauren K.; Barnidge, Ellen K.; Pithua, Patrick; Lewis, Roger D.; Jacoby, Jonathan A.; King, Christopher C.; Baskin, Carole R. (MDPI, 2018-11-01)
Use of low dose, prophylactic antibiotics contributes to the emergence of antibiotic resistant bacteria. In one study, goat meat in Missouri was found to have a higher percentage of antibiotic residues at slaughter than the national average, so we attempted to identify factors related to goat production that may contribute to this issue. Using the knowledge, attitude, and behavior (KAB) model, we interviewed 11 Missouri goat farmers about factors affecting antibiotic use. Most of the farmers did not have specific protocols for managing illnesses and only relied on veterinarians for major health issues. Many felt veterinarians lacked knowledge about goat medicine so instead relied on other farmers’ or their own experiences for treatment modalities. While most agreed that antibiotic resistance was a concern, only 4 of the 11 indicated that they only used antibiotics when prescribed by the veterinarian. Veterinarians should be relied on and valued for their medical expertise, but they are not always being utilized in this manner. Therefore, veterinary education should emphasize goat health management to a greater extent than it currently does, and soft skills to build collaborative relationships with farmers should be taught to promote preventative health measures and more judicious use of antibiotics.
Antibiotics in Agroecosystems: Introduction to the Special Section
Franklin, Alison M.; Aga, Diana S.; Cytryn, Eddie; Durso, Lisa M.; McLain, Jean E.; Pruden, Amy; Roberts, Marilyn C.; Rothrock, Michael J. Jr.; Snow, Daniel D.; Watson, John E.; Dungan, Robert S. (2016-03)
The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper.
Anticipating and adapting to the future impacts of climate change on the health, security and welfare of low elevation coastal zone (LECZ) communities in Southeastern USA
Allen, Thomas; Behr, Joshua; Bukvic, Anamaria; Calder, Ryan S. D.; Caruson, Kiki; Connor, Charles; D'Elia, Christopher; Dismukes, David; Ersing, Robin; Franklin, Rima; Goldstein, Jesse; Goodall, Jonathon; Hemmerling, Scott; Irish, Jennifer L.; Lazarus, Steven; Loftis, Derek; Luther, Mark; McCallister, Leigh; McGlathery, Karen; Mitchell, Molly; Moore, William B.; Nichols, C. Reid; Nunez, Karinna; Reidenbach, Matthew; Shortridge, Julie; Weisberg, Robert; Weiss, Robert; Donelson Wright, Lynn; Xia, Meng; Xu, Kehui; Young, Donald; Zarillo, Gary; Zinnert, Julie C. (MDPI, 2021-10-29)
Low elevation coastal zones (LECZ) are extensive throughout the southeastern United States. LECZ communities are threatened by inundation from sea level rise, storm surge, wetland degradation, land subsidence, and hydrological flooding. Communication among scientists, stakeholders, policy makers and minority and poor residents must improve. We must predict processes spanning the ecological, physical, social, and health sciences. Communities need to address linkages of (1) human and socioeconomic vulnerabilities; (2) public health and safety; (3) economic concerns; (4) land loss; (5) wetland threats; and (6) coastal inundation. Essential capabilities must include a network to assemble and distribute data and model code to assess risk and its causes, support adaptive management, and improve the resiliency of communities. Better communication of information and understanding among residents and officials is essential. Here we review recent background literature on these matters and offer recommendations for integrating natural and social sciences. We advocate for a cyber-network of scientists, modelers, engineers, educators, and stakeholders from academia, federal state and local agencies, non-governmental organizations, residents, and the private sector. Our vision is to enhance future resilience of LECZ communities by offering approaches to mitigate hazards to human health, safety and welfare and reduce impacts to coastal residents and industries.
Antimicrobial Resistance Mitigation [ARM] Concept Paper
Vikesland, Peter J.; Alexander, Kathleen A.; Badgley, Brian D.; Krometis, Leigh-Anne H.; Knowlton, Katharine F.; Gohlke, Julia M.; Hall, Ralph P.; Hawley, Dana M.; Heath, Lenwood S.; Hession, W. Cully; Hull, Robert Bruce IV; Moeltner, Klaus; Ponder, Monica A.; Pruden, Amy; Schoenholtz, Stephen H.; Wu, Xiaowei; Xia, Kang; Zhang, Liqing (Virginia Tech, 2017-05-15)
The development of viable solutions to the global threat of antimicrobial resistance requires a transdisciplinary approach that simultaneously considers the clinical, biological, social, economic, and environmental drivers responsible for this emerging threat. The vision of the Antimicrobial Resistance Mitigation (ARM) group is to build upon and leverage the present strengths of Virginia Tech in ARM research and education using a multifaceted systems approach. Such a framework will empower our group to recognize the interconnectedness and interdependent nature of this threat and enable the delineation, development, and testing of resilient approaches for its mitigation. We seek to develop innovative and sustainable approaches that radically advance detection, characterization, and prevention of antimicrobial resistance emergence and dissemination in human-dominated and natural settings...
Antimicrobial Resistance Prediction in PATRIC and RAST
Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; Kenyon, Ronald W.; Mao, Chunhong; Olson, Robert D.; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R.; Will, Rebecca; Xia, Fangfang; Stevens, Rick L. (Springer Nature, 2016-06-14)
The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned by their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii, methicillin resistance in Staphylococcus aureus, and beta-lactam and co-trimoxazole resistance in Streptococcus pneumoniae with accuracies ranging from 88-99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis, achieving accuracies ranging from 71-88%. This set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.
Approximating Community Water System Service Areas to Explore the Demographics of SDWA Compliance in Virginia
Marcillo, Cristina; Krometis, Leigh-Anne H.; Krometis, Justin (MDPI, 2021-12-16)
Although the United States Safe Drinking Water Act (SDWA) theoretically ensures drinking water quality, recent studies have questioned the reliability and equity associated with community water system (CWS) service. This study aimed to identify SDWA violation differences (i.e., monitoring and reporting (MR) and health-based (HB)) between Virginia CWSs given associated service demographics, rurality, and system characteristics. A novel geospatial methodology delineated CWS service areas at the zip code scale to connect 2000 US Census demographics with 2006–2016 SDWA violations, with significant associations determined via negative binomial regression. The proportion of Black Americans within a service area was positively associated with the likelihood of HB violations. This effort supports the need for further investigation of racial and socioeconomic disparities in access to safe drinking water within the United States in particular and offers a geospatial strategy to explore demographics in other settings where data on infrastructure extents are limited. Further interdisciplinary efforts at multiple scales are necessary to identify the entwined causes for differential risks in adverse drinking water quality exposures and would be substantially strengthened by the mapping of official CWS service boundaries.
Are nitrogen and carbon cycle processes impacted by common stream antibiotics? A comparative assessment of single vs. mixture exposures
Gray, Austin D.; Bernhardt, Emily S. (PLoS, 2022-01-05)
A variety of antibiotics are ubiquitous in all freshwater ecosystems that receive wastewater. A wide variety of antibiotics have been developed to kill problematic bacteria and fungi through targeted application, and their use has contributed significantly to public health and livestock management. Unfortunately, a substantial fraction of the antibiotics applied to humans, pets and livestock end up in wastewater, and ultimately many of these chemicals enter freshwater ecosystems. The effect of adding chemicals that are intentionally designed to kill microbes, on freshwater microbial communities remains poorly understood. There are reasons to be concerned, as microbes play an essential role in nutrient uptake, carbon fixation and denitrification in freshwater ecosystems. Chemicals that reduce or alter freshwater microbial communities might reduce their capacity to degrade the excess nutrients and organic matter that characterize wastewater. We performed a laboratory experiment in which we exposed microbial community from unexposed stream sediments to three commonly detected antibiotics found in urban wastewater and urban streams (sulfamethoxazole, danofloxacin, and erythromycin). We assessed how the form and concentration of inorganic nitrogen, microbial carbon, and nitrogen cycling processes changed in response to environmentally relevant doses (10 μg/L) of each of these antibiotics individually and in combination. We expected to find that all antibiotics suppressed rates of microbial mineralization and nitrogen transformations and we anticipated that this suppression of microbial activity would be greatest in the combined treatment. Contrary to our expectations we measured few significant changes in microbially mediated functions in response to our experimental antibiotic dosing. We found no difference in functional gene abundance of key nitrogen cycling genes nosZ, mcrA, nirK, and amoA genes, and we measured no treatment effects on NO3- uptake or N2O, N2, CH4, CO2 production over the course of our seven-day experiment. In the mixture treatment, we measured significant increases in NH4+ concentrations over the first 24 hours of the experiment, which were indistinguishable from controls within six hours. Our results suggest remarkable community resistance to pressure antibiotic exposure poses on naïve stream sediments.

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