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  • Articles
    • Latest Articles
    • COVID-19 Research and News from ASM Journals
    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
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Applied and Environmental Science

  • Open Access
    Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System
    Observation | Applied and Environmental Science
    Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System

    Use of the Carba-R assay for detection of carbapenem-resistant Gram-negative organisms (CROs) can provide data for implementation of a rapid infection control response to minimize the spread of CROs in the health care setting.

    K. A. Perry, J. B. Daniels, S. C. Reddy, A. J. Kallen, A. L. Halpin, J. K. Rasheed, J. A. Noble-Wang
  • Open Access
    Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community
    Research Article | Applied and Environmental Science
    Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

    Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge...

    Adit Chaudhary, Imrose Kauser, Anirban Ray, Rachel Poretsky
  • Open Access
    A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
    Research Article | Applied and Environmental Science
    A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

    To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral...

    Norman Goodacre, Aisha Aljanahi, Subhiksha Nandakumar, Mike Mikailov, Arifa S. Khan
  • Open Access
    Inhibition of Cyanobacterial Growth on a Municipal Wastewater Sidestream Is Impacted by Temperature
    Research Article | Applied and Environmental Science
    Inhibition of Cyanobacterial Growth on a Municipal Wastewater Sidestream Is Impacted by Temperature

    Cyanobacteria are viewed as promising platforms to produce fuels and/or high-value chemicals as part of so-called “biorefineries.” Their integration into wastewater treatment systems is particularly interesting because removal of the nitrogen and phosphorus in many wastewater streams is an expensive but necessary part of wastewater treatment. In this study, we evaluated strategies for cultivating Synechococcus sp. strain PCC...

    Travis C. Korosh, Andrew Dutcher, Brian F. Pfleger, Katherine D. McMahon
  • Open Access
    A Novel <em>aadA</em> Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens
    Observation | Applied and Environmental Science
    A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens

    Aminoglycosides are important antimicrobials used worldwide for prophylaxis and/or therapy in multiple production animal species. The emergence of new resistance genes jeopardizes current pathogen detection and treatment methods. The risk of resistance gene transfer to other animal and human pathogens is elevated when resistance genes are carried by mobile genetic elements. This study identified a new variant of a spectinomycin/...

    Andrew Cameron, Cassidy L. Klima, Reuben Ha, Robert J. Gruninger, Rahat Zaheer, Tim A. McAllister
  • Open Access
    Air-Dried Brown Seaweed, <em>Ascophyllum nodosum</em>, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens
    Research Article | Applied and Environmental Science
    Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens

    Maintaining product safety and reducing the carbon footprint of production are two sustainability goals of the livestock industry. The objective of this study was to study the impact of Tasco, a product derived from the brown macroalga Ascophyllum nodosum, on the rumen microbiome and its function. The inclusion of Tasco altered both rumen and fecal microbiota levels without affecting rumen fermentation. Tasco reduced fecal...

    Mi Zhou, Martin Hünerberg, Yanhong Chen, Tim Reuter, Tim A. McAllister, Franklin Evans, Alan T. Critchley, Le Luo Guan
  • Open Access
    A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions
    Research Article | Applied and Environmental Science
    A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions

    By incorporating prior information on disease prevalence, Bayes classifiers have the potential to estimate disease probability better than other common machine-learning methods. Thus, it is important to develop Bayes classifiers specifically tailored for microbiome data. Our method shows higher classification accuracy than the only existing Bayesian classifier and the popular random forest method, and thus provides an alternative option...

    Xiang Gao, Huaiying Lin, Qunfeng Dong
  • Open Access
    Heat Resistance Mediated by pLM58 Plasmid-Borne ClpL in <span class="named-content genus-species" id="named-content-1">Listeria monocytogenes</span>
    Research Article | Applied and Environmental Science
    Heat Resistance Mediated by pLM58 Plasmid-Borne ClpL in Listeria monocytogenes

    Listeria monocytogenes is a dangerous food pathogen causing the severe illness listeriosis that has a high mortality rate in immunocompromised individuals. Although destroyed by pasteurization, L. monocytogenes is among the most heat-resistant non-spore-forming bacteria. This poses a risk to food...

    Anna Pöntinen, Mariella Aalto-Araneda, Miia Lindström, Hannu Korkeala
  • Open Access
    Plasticity of the <em>MFS1</em> Promoter Leads to Multidrug Resistance in the Wheat Pathogen <em>Zymoseptoria tritici</em>
    Research Article | Applied and Environmental Science
    Plasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria tritici

    Disease control through fungicides remains an important means to protect crops from fungal diseases and to secure the harvest. Plant-pathogenic fungi, especially Zymoseptoria tritici, have developed resistance against most currently used active ingredients, reducing or abolishing their efficacy. While target site modification is the most common resistance mechanism against single modes of action, active efflux of multiple drugs...

    Selim Omrane, Colette Audéon, Amandine Ignace, Clémentine Duplaix, Lamia Aouini, Gert Kema, Anne-Sophie Walker, Sabine Fillinger
  • Open Access
    Collection of Viable Aerosolized Influenza Virus and Other Respiratory Viruses in a Student Health Care Center through Water-Based Condensation Growth
    Research Article | Applied and Environmental Science
    Collection of Viable Aerosolized Influenza Virus and Other Respiratory Viruses in a Student Health Care Center through Water-Based Condensation Growth

    The significance of virus aerosols in the natural transmission of respiratory diseases has been a contentious issue, primarily because it is difficult to collect or sample virus aerosols using currently available air sampling devices. We tested a new air sampler based on water vapor condensation for efficient sampling of viable airborne respiratory viruses in a student health care center as a model of a real world environment. The new...

    Maohua Pan, Tania S. Bonny, Julia Loeb, Xiao Jiang, John A. Lednicky, Arantzazu Eiguren-Fernandez, Susanne Hering, Z. Hugh Fan, Chang-Yu Wu

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