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      Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State

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      Author(s): a , , a , b
      Publication date (Electronic):
      Journal: Genome Announcements
      Publisher: American Society for Microbiology

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          ABSTRACT

          Strains of the ciprofloxacin-resistant (Cip r) Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 (ST198) have rapidly and extensively disseminated globally to become a major food safety and public health concern. Here, we report the complete genome sequence of a Cip r S. Kentucky ST198 strain, PU131, isolated from a human patient in Washington State (USA).

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          Is Open Access

          The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

          Catherine Yoshida, Peter Kruczkiewicz, Chad Laing … (2016)
          For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.
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            International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin.

            Simon Le Hello, Rene Hendriksen, Benoit Doublet … (2011)
            National Salmonella surveillance systems from France, England and Wales, Denmark, and the United States identified the recent emergence of multidrug-resistant isolates of Salmonella enterica serotype Kentucky displaying high-level resistance to ciprofloxacin. A total of 489 human cases were identified during the period from 2002 (3 cases) to 2008 (174 cases). These isolates belonged to a single clone defined by the multilocus sequence type ST198, the XbaI-pulsed-field gel electrophoresis cluster X1, and the presence of the Salmonella genomic island 1 variant SGI1-K. This clone was probably selected in 3 steps in Egypt during the 1990s and the early 2000s and has now spread to several countries in Africa and, more recently, in the Middle East. Poultry has been identified as a potential major vehicle for infection by this clone. Continued surveillance and appropriate control measures should be implemented by national and international authorities to limit the spread of this strain.
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              Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects.

              Fabien Darfeuille, Francis Repoila (2009)
              Regulatory ncRNAs (non-coding RNAs) adjust bacterial physiology in response to environmental cues. ncRNAs can base-pair to mRNAs and change their translation efficiency and/or their stability, or they can bind to proteins and modulate their activity. ncRNAs have been discovered in several species throughout the bacterial kingdom. This review illustrates the diversity of physiological processes and molecular mechanisms where ncRNAs are key regulators.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 1 March 2018
                Publication date Collection: March 2018
                Volume: 6
                Issue: 9
                Electronic Location Identifier: e00125-18
                Affiliations
                [a ]Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
                [b ]U.S. National Poultry Research Center, United States Department of Agriculture, Athens, Georgia, USA
                Author notes
                Address correspondence to Devendra H. Shah, dshah@ 123456wsu.edu .
                Article
                Publisher ID: genomeA00125-18
                DOI: 10.1128/genomeA.00125-18
                PMC ID: 5834327
                PubMed ID: 29496839
                SO-VID: 8e308abe-fd07-4d22-8b56-e018d113b994
                License:

                This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

                History
                Date received : 31 January 2018
                Date accepted : 8 February 2018
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 21, Pages: 3, Words: 1521
                Funding
                Funded by: Safe Food Initiative and Agricultural Animal Health Program at Washington State University;
                Award Recipient : Award Recipient :
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date March 2018

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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