Amy Pruden

Bio: Amy Pruden is an academic researcher from Virginia Tech. The author has contributed to research in topics: Legionella pneumophila & Manure. The author has an hindex of 55, co-authored 236 publications receiving 11997 citations. Previous affiliations of Amy Pruden include University of Cincinnati & Colorado State University.

Antibiotic Resistance Genes as Emerging Contaminants: Studies in Northern Colorado†

Abstract: This study explores antibiotic resistance genes (ARGs) as emerging environmental contaminants. The purpose of this study was to investigate the occurrence of ARGs in various environmental compartments in northern Colorado, including Cache La Poudre (Poudre) River sediments, irrigation ditches, dairy lagoons, and the effluents of wastewater recycling and drinking water treatment plants. Additionally, ARG concentrations in the Poudre River sediments were analyzed at three time points at five sites with varying levels of urban/agricultural impact and compared with two previously published time points. It was expected that ARG concentrations would be significantly higher in environments directly impacted by urban/agricultural activity than in pristine and lesser-impacted environments. Polymerase chain reaction (PCR) detection assays were applied to detect the presence/absence of several tetracycline and sulfonamide ARGs. Quantitative real-time PCR was used to further quantify two tetracycline ARGs (tet(W) and...

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

Abstract: Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.

Management Options for Reducing the Release of Antibiotics and Antibiotic Resistance Genes to the Environment

Abstract: Background: There is growing concern worldwide about the role of polluted soil and water environments in the development and dissemination of antibiotic resistance.Objective: Our aim in this study ...

Correlation Between Upstream Human Activities and Riverine Antibiotic Resistance Genes

Abstract: Antimicrobial resistance remains a serious and growing human health challenge. The water environment may represent a key dissemination pathway of resistance elements to and from humans. However, quantitative relationships between landscape features and antibiotic resistance genes (ARGs) have not previously been identified. The objective of this study was to examine correlations between ARGs and putative upstream anthropogenic sources in the watershed. sul1 (sulfonamide) and tet(W) (tetracycline) were measured using quantitative polymerase chain reaction in bed and suspended sediment within the South Platte River Basin, which originates from a pristine region in the Rocky Mountains and runs through a gradient of human activities. A geospatial database was constructed to delineate surface water pathways from animal feeding operations, wastewater treatment plants, and fish hatchery and rearing units to river monitoring points. General linear regression models were compared. Riverine sul1 correlated with upstream capacities of animal feeding operations (R(2) = 0.35, p < 0.001) and wastewater treatment plants (R(2) = 0.34, p < 0.001). Weighting for the inverse distances from animal feeding operations along transport pathways strengthened the observed correlations (R(2) = 0.60-0.64, p < 0.001), suggesting the importance of these pathways in ARG dissemination. Correlations were upheld across the four sampling events during the year, and averaging sul1 measurements in bed and suspended sediments over all events yielded the strongest correlation (R(2) = 0.92, p < 0.001). Conversely, a significant relationship with landscape features was not evident for tet(W), which, in contrast to sul1, is broadly distributed in the pristine region and also relatively more prevalent in animal feeding operation lagoons. The findings highlight the need to focus attention on quantifying the contribution of water pathways to the antibiotic resistance disease burden in humans and offer insight into potential strategies to control the spread of ARGs.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance.

Abstract: Antibiotics are widely used in humans and animals, but there is a big concern about their negative impacts on ecosystem and human health after use. So far there is a lack of information on emission inventory and environmental fate of antibiotics in China. We studied national consumption, emissions, and multimedia fate of 36 frequently detected antibiotics in China by market survey, data analysis, and level III fugacity modeling tools. Based on our survey, the total usage for the 36 chemicals was 92700 tons in 2013, an estimated 54000 tons of the antibiotics was excreted by human and animals, and eventually 53800 tons of them entered into the receiving environment following various wastewater treatments. The fugacity model successfully predicted environmental concentrations (PECs) in all 58 river basins of China, which are comparable to the reported measured environmental concentrations (MECs) available in some basins. The bacterial resistance rates in the hospitals and aquatic environments were found to b...