Browsing by Author "Wind, Lauren L."

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    AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
    Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
    Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
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    Fecal Indicator Bacteria and Antibiotic Resistance Genes in Storm Runoff from Dairy Manure and Compost-Amended Vegetable Plots
    Jacobs, Kyle; Wind, Lauren L.; Krometis, Leigh-Anne H.; Hession, W. Cully; Pruden, Amy (American Society for Agronomy, 2019-07-01)
    Given the presence of antibiotics and resistant bacteria in livestock manures, it is important to identify the key pathways by which land-applied manure-derived soil amendments potentially spread resistance. The goal of this field-scale study was to identify the effects of different types of soil amendments (raw manure from cows treated with cephapirin and pirlimycin, compost from antibiotic-treated or antibiotic-free cows, or chemical fertilizer only) and crop type (lettuce [Lactuca sativa L.] or radish [Raphanus sativus L.]) on the transport of two antibiotic resistance genes (ARGs; sul1 and ermB) via storm runoff from six naturally occurring storms. Concurrent quantification of sediment and fecal indicator bacteria (FIB; Escherichia coli and enterococci) in runoff permitted comparison to traditional agricultural water quality targets that may be driving factors of ARG presence. Storm characteristics (total rainfall volume, storm duration, etc.) significantly influenced FIB concentration (two-way ANOVA, p < 0.05), although both effects from individual storm events (Kruskal-Wallis, p < 0.05) and vegetative cover influenced sediment levels. Composted and raw manure-amended plots both yielded significantly higher sul1 and ermB levels in runoff for early storms, at least 8 wk following initial planting, relative to fertilizer-only or unamended barren plots. There was no significant difference between sul1 or ermB levels in runoff from plots treated with compost derived from antibiotic-treated versus antibiotic-free dairy cattle. Our findings indicate that agricultural fields receiving manure-derived amendments release higher quantities of these two “indicator” ARGs in runoff, particularly during the early stages of the growing season, and that composting did not reduce effects of ARG loading in runoff.
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    Finding What Is Inaccessible: Antimicrobial Resistance Language Use among the One Health Domains
    Wind, Lauren L.; Briganti, Jonathan; Brown, Anne M.; Neher, Timothy P.; Davis, Meghan F.; Durso, Lisa M.; Spicer, Tanner; Lansing, Stephanie (MDPI, 2021-04-03)
    The success of a One Health approach to combating antimicrobial resistance (AMR) requires effective data sharing across the three One Health domains (human, animal, and environment). To investigate if there are differences in language use across the One Health domains, we examined the peer-reviewed literature using a combination of text data mining and natural language processing techniques on 20,000 open-access articles related to AMR and One Health. Evaluating AMR key term frequency from the European PubMed Collection published between 1990 and 2019 showed distinct AMR language usage within each domain and incongruent language usage across domains, with significant differences in key term usage frequencies when articles were grouped by the One Health sub-specialties (2-way ANOVA; p < 0.001). Over the 29-year period, “antibiotic resistance” and “AR” were used 18 times more than “antimicrobial resistance” and “AMR”. The discord of language use across One Health potentially weakens the effectiveness of interdisciplinary research by creating accessibility issues for researchers using search engines. This research was the first to quantify this disparate language use within One Health, which inhibits collaboration and crosstalk between domains. We suggest the following for authors publishing AMR-related research within the One Health context: (1) increase title/abstract searchability by including both antimicrobial and antibiotic resistance related search terms; (2) include “One Health” in the title/abstract; and (3) prioritize open-access publication.
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    Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale
    Wind, Lauren L.; Keenum, Ishi M.; Gupta, Suraj; Ray, Partha P.; Knowlton, Katharine F.; Ponder, Monica A.; Hession, W. Cully; Pruden, Amy; Krometis, Leigh-Anne H. (Frontiers, 2021-07-09)
    An integrated understanding of factors influencing the occurrence, distribution, and fate of antibiotic resistance genes (ARGs) in vegetable production systems is needed to inform the design and development of strategies for mitigating the potential for antibiotic resistance propagation in the food chain. The goal of the present study was to holistically track antibiotic resistance and associated microbiomes at three distinct pre-harvest control points in an agroecosystem in order to identify the potential impacts of key agricultural management strategies. Samples were collected over the course of a single growing season (67 days) from field-scale plots amended with various organic and inorganic amendments at agronomic rates. Dairy-derived manure and compost amendment samples (n = 14), soil samples (n = 27), and lettuce samples (n = 12) were analyzed via shotgun metagenomics to assess multiple pre-harvest factors as hypothetical control points that shape lettuce resistomes. Pre-harvest factors of interest included manure collection during/post antibiotic use, manure composting, and soil amended with organic (stockpiled manure/compost) versus chemical fertilizer. Microbial community resistome and taxonomic compositions were unique from amendment to soil to lettuce surface according to dissimilarity analysis. The highest resistome alpha diversity (i.e., unique ARGs, n = 642) was detected in amendment samples prior to soil application, while the composted manure had the lowest total ARG relative abundance (i.e., 16S rRNA gene-normalized). Regardless of amendment type, soils acted as an apparent ecological buffer, i.e., soil resistome and taxonomic profiles returned to background conditions 67 d-post amendment application. Effects of amendment conditions surprisingly re-emerged in lettuce phyllosphere resistomes, with the highest total ARG relative abundances recovered on the surface of lettuce plants grown in organically-fertilized soils (i.e., compost- and manure-amended soils). Co-occurrence analysis identified 55 unique ARGs found both in the soil amendments and on lettuce surfaces. Among these, arnA and pmrF were the most abundant ARGs co-occurring with mobile genetic elements (MGE). Other prominent ARG-MGE co-occurrences throughout this pre-harvest lettuce production chain included: TetM to transposon (Clostridiodies difficile) in the manure amendment and TriC to plasmid (Ralstonia solanacearum) on the lettuce surfaces. This suggests that, even with imposing manure management and post-amendment wait periods in agricultural systems, ARGs originating from manure can still be found on crop surfaces. This study demonstrates a comprehensive approach to identifying key control points for the propagation of ARGs in vegetable production systems, identifying potential ARG-MGE combinations that could inform future surveillance. The findings suggest that additional pre-harvest and potentially post-harvest interventions may be warranted to minimize risk of propagating antibiotic resistance in the food chain.
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    Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis
    Keenum, Ishi M.; Wind, Lauren L.; Ray, Partha P.; Guron, Giselle K. P.; Chen, Chaoqi; Knowlton, Katharine F.; Ponder, Monica A.; Pruden, Amy (Wiley, 2022-05-18)
    Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.
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    Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived From Antibiotic-Treated Cows
    Fogler, Kendall; Guron, Giselle K.P.; Wind, Lauren L.; Keenum, Ishi M.; Hession, W. Cully; Krometis, Leigh-Anne H.; Strawn, Laura K.; Pruden, Amy; Ponder, Monica A. (Frontiers, 2019-04-10)
    Cattle are commonly administered antibiotics, resulting in excretion of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs). The aim of this study was to determine if the use of dairy manure collected during antibiotic administration influences the bacterial microbiota of lettuce and radishes, including carriage of ARB and ARGs, when applied as a soil amendment and if composting mitigates the effects. Lettuce and radishes were grown in field-plots amended with raw manure from antibiotic-treated (cephapirin, pirlimycin) cows, composted manure from antibiotic-treated cows, composted manure from antibiotic-free cows, or an inorganic chemical fertilizer (control; 12 plots, n = 3). Surficial vegetable bacteria and antibiotic resistomes (i.e., total ARGs) were characterized using heterotrophic plate counts (HPCs) on antibiotic-containing media, 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and shot-gun metagenomics. The different manure and compost amendments did not result in significant changes to the surficial vegetable bacteria at the phylum level; however, some minor changes at the class and family level were observed. Beta-diversities of the ARGs detected by shotgun metagenomic sequencing were distinctly different between vegetable type (R = 0.30, p = 0.04), with small separations between the resistomes associated with amendment type in unrarefied analysis (R = 0.27, p = 0.02), but not rarefied analysis, of the data. Network analysis highlighted that multi-drug ARG classes commonly co-occurred with plasmid-associated genes and could be a driver of co-and cross-selection of ARGs in the different conditions. Carriage of sul1 and tet(W) ARGs on vegetables quantified by qPCR were strong indicators of manure-based amendment relative to chemical fertilizer, with some reduction incurred via composting (p < 0.05). Also, increased HPCs resistant/tolerant to clindamycin, a class of antibiotics administered to cattle, were on lettuce grown in biological soil amendments relative to chemical fertilizer (p < 0.05). This study demonstrates that amending soil with rawmanure collected fromdairy cows during antibiotic administration may affect the composition of microbiota and resistomes associated with vegetable surfaces. Composting may be an important strategy to reduce some ARGs on fresh produce, but differences in the resistomes of lettuce and radishes suggest the extent of soil contact should be considered.
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    Salt dilution and flushing dynamics of an impaired agricultural−urban stream
    Lakoba, Vasiliy T.; Wind, Lauren L.; DeVilbiss, Stephen; Lofton, Mary E.; Bretz, Kristen; Weinheimer, Alaina R.; Moore, Chloe; Baciocco, Colin; Hotchkiss, Erin R.; Hession, W. Cully (2020-11-09)
    Anthropogenic freshwater salinization is increasing with global change. Rising freshwater salinity threatens ecosystem biodiversity, health, and services via toxicity to organisms and mobilization of nutrients and metals. Brining roads is one major source of freshwater salinization that continues to grow with rising urbanization. While the detrimental effects of salinization in streams are well-documented, high-frequency, temporal patterns in salt transport, particularly during winter road de-icing in mixed land use landscapes, are less understood. To address this knowledge gap, we analyzed high-frequency specific conductance as a proxy for salinity across 114 high-flow events from 2013 to 2018 in an impaired stream draining mixed agriculture−urban land use. The specific conductance was highest in winter (median = 947 μS cm−1) and decreased with first-order kinetics up to 90 days after brining (β1 = −0.003), suggesting lasting impacts of road de-icing on water quality. Although hysteresis patterns suggested a transition from distal to proximal salt sources, they showed no clear correlation of flushing versus dilution to brining events. While seasonal brining increased salinity in receiving streams, unpredictable transport dynamics reduced the efficacy of hysteresis in characterizing salt transport dynamics. Thus, the complexity of mixed land use watersheds requires more spatially and temporally explicit monitoring to characterize stream salinization dynamics.