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      Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS 26-mediated amplification of bla TEM-1B

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          Abstract

          A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the β-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS 26-flanked pseudo-compound transposon, PTn 6762, which harbours bla TEM-1B. The TU re-inserts into the chromosome adjacent to IS 26 and forms a tandem array of TUs, which increases the copy number of bla TEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in bla TEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of bla TEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.

          Abstract

          An E. coli and K. pneumoniae phenotype resistant to piperacillin/tazobactam has recently emerged. Here, the authors show that hyperproduction of the β-lactamase driving this resistance occurs due to excision and reinsertion of a translocatable unit containing bla TEM-1B, creating a tandem array.

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          Prokka: rapid prokaryotic genome annotation.

          T Seemann (2014)
          The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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            Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

            The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate “hybrid” assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.
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              In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.

              In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S. Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
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                Author and article information

                Contributors
                alasdair.hubbard@lstmed.ac.uk
                thomas.edwards@lstmed.ac.uk
                Journal
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                1 October 2020
                1 October 2020
                2020
                : 11
                : 4915
                Affiliations
                [1 ]GRID grid.48004.38, ISNI 0000 0004 1936 9764, Department of Tropical Disease Biology, , Liverpool School of Tropical Medicine, Pembroke Place, ; Liverpool, L3 5QA UK
                [2 ]GRID grid.10025.36, ISNI 0000 0004 1936 8470, Liverpool University Hospital Foundation Trust, ; Prescot Street, Liverpool, L7 8XP UK
                [3 ]GRID grid.417858.7, ISNI 0000 0004 0421 1374, Alder Hey Children’s NHS Foundation Trust, ; Eaton Road, Liverpool, L12 2AP UK
                [4 ]GRID grid.10025.36, ISNI 0000 0004 1936 8470, Department of Clinical Infection, Microbiology and Immunology, , University of Liverpool, ; Liverpool, L69 7BE UK
                [5 ]GRID grid.48004.38, ISNI 0000 0004 1936 9764, Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, ; Liverpool, L3 5QA UK
                [6 ]GRID grid.444715.7, ISNI 0000 0000 8673 4005, School of Tropical Medicine and Global Health, , University of Nagasaki, ; Nagasaki, Japan
                [7 ]GRID grid.6374.6, ISNI 0000000106935374, Present Address: Faculty of Science and Engineering, , University of Wolverhampton, Wulfruna Building MA, ; Wulfruna Street, Wolverhampton, WV1 1LY UK
                Author information
                http://orcid.org/0000-0001-6668-9179
                http://orcid.org/0000-0002-5609-1138
                http://orcid.org/0000-0002-3732-5912
                http://orcid.org/0000-0002-0760-3088
                http://orcid.org/0000-0003-4058-4461
                Article
                18668
                10.1038/s41467-020-18668-2
                7530762
                33004811
                12ed2496-9e12-4a8c-ae13-9ab24f8de35d
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 March 2020
                : 3 September 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000272, DH | National Institute for Health Research (NIHR);
                Award ID: NIHR200632
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100009187, RCUK | MRC | Medical Research Foundation;
                Award ID: MR/S004793/1
                Award Recipient :
                Funded by: Liverpool School of Tropical Medicine Director’s Catalyst Fund
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                molecular evolution,bacterial genetics,antimicrobial resistance,clinical microbiology

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