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      Draft Genome Sequences of Pseudomonas spp. Isolated from Berry Surfaces in Commercial Cranberry Bogs in Massachusetts, USA

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      Microbiology Resource Announcements

      American Society for Microbiology

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          ABSTRACT

          The surfaces of plants are colonized by a rich diversity of microbes but are largely unexplored. Here, we present the draft genome sequences of five Pseudomonas spp. isolated from cultivated cranberry fruit surfaces. Although the isolates represent four different species, their genomes all contain conserved iron sequestration and uptake genes.

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          Most cited references 23

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          RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

          The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.
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            Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

            The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
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              The epidemiology, pathogenesis and treatment of Pseudomonas aeruginosa infections.

              Pseudomonas aeruginosa is an important bacterial pathogen, particularly as a cause of infections in hospitalised patients, immunocompromised hosts and patients with cystic fibrosis. Surveillance of nosocomial P. aeruginosa infections has revealed trends of increasing antimicrobial resistance, including carbapenem resistance and multidrug resistance. Mechanisms of antimicrobial resistance include multidrug efflux pumps, ss-lactamases and downregulation of outer membrane porins. Mechanisms of virulence include secreted toxins and the ability to form biofilms. The effective treatment of infections caused by P. aeruginosa includes prevention when possible, source control measures as necessary and prompt administration of appropriate antibacterial agents. Antibacterial de-escalation should be pursued in patients with an appropriate clinical response, especially when antibacterial susceptibilities are known. Multidrug-resistant P. aeruginosa may require treatment with less commonly used antibacterials (e.g. colistin), but newer anti-pseudomonal antibacterials are expected to be available in the near future.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Resour Announc
                Microbiol Resour Announc
                mra
                Microbiology Resource Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2576-098X
                8 July 2021
                July 2021
                : 10
                : 27
                Affiliations
                [a ]Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, Arizona, USA
                [b ]College of Veterinary Medicine, Midwestern University, Glendale, Arizona, USA
                University of Arizona
                Author notes

                Marit H. Koszewski and Sheyda Motevalli contributed equally to this work. Author order was determined alphabetically.

                Citation Koszewski MH, Motevalli S, Soby SD. 2021. Draft genome sequences of Pseudomonas spp. isolated from berry surfaces in commercial cranberry bogs in Massachusetts, USA. Microbiol Resour Announc 10:e00204-21. https://doi.org/10.1128/MRA.00204-21.

                Article
                MRA00204-21
                10.1128/MRA.00204-21
                8265235
                34236228
                Copyright © 2021 Koszewski et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 23, Pages: 4, Words: 1887
                Product
                Funding
                Funded by: Midwestern University (MWU), FundRef https://doi.org/10.13039/100012807;
                Award Recipient :
                Categories
                Genome Sequences
                Custom metadata
                July 2021

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