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      Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

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          Abstract

          Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. e nterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S. enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase ( gyrA) and DNA topoisomerase IV ( parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. e nterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS 26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. e nterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.

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          Toward almost closed genomes with GapFiller

          De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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            Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

            Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery 1,2 , spreading efficiently via low-dose fecal-oral transmission 3,4 . Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality 4-6 . Classical approaches have shown S. sonnei is genetically conserved and clonal 7 . We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage.
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              CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

              Background Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. Results We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. Conclusion The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.
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                Author and article information

                Journal
                Microb Genom
                Microb Genom
                mgen
                mgen
                Microbial Genomics
                Microbiology Society
                2057-5858
                July 2019
                20 May 2019
                20 May 2019
                : 5
                : 7
                Affiliations
                [1 ] departmentDepartment of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , Parkville, Victoria 3010, Australia
                [2 ] departmentDepartment of Infectious Diseases, Central Clinical School , Monash University , Melbourne, Victoria 3004, Australia
                [3 ] departmentUnité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur , 75015 Paris, France
                [4 ] ISP, Institut National de la Recherche Agronomique, Université François Rabelais de Tours , UMR 1282, Nouzilly, France
                [5 ] Laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST , 94701 Maisons-Alfort, France
                [6 ] Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES) , 35306 Fougères, France
                [7 ] departmentResearch Group for Genomic Epidemiology , National Food Institute, Technical University of Denmark , Kongens Lyngby, Denmark
                [8 ] departmentDepartment of Microbiome Research and Applied Bioinformatics , University of Hohenheim , Stuttgart, Germany
                [9 ] departmentInstitute for Genome Sciences , University of Maryland School of Medicine , Baltimore, MD, USA
                [10 ] departmentBacterial Diseases Unit , Sciensano , Brussels, Belgium
                [11 ] departmentAsia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Science , University of Melbourne , Parkville, Victoria 3010, Australia
                [12 ] London School of Hygiene and Tropical Medicine , London WC1E 7HT, UK
                Author notes
                [†]

                These authors contributed equally to this work.

                *Correspondence: Jane Hawkey, jane.hawkey@ 123456monash.edu
                *Correspondence: François-Xavier Weill, francois-xavier.weill@ 123456pasteur.fr
                Article
                000269
                10.1099/mgen.0.000269
                6700661
                31107206
                © 2019 The Authors

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Categories
                Research Article
                Microbial evolution and epidemiology: Population Genomics
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                st198, sgi, kentucky, mdr, phylogenomics, salmonella

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