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      The Ferric Citrate Uptake System Encoded in a Novel bla CTX–M–3- and bla TEM–1-Harboring Conjugative Plasmid Contributes to the Virulence of Escherichia coli

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          Abstract

          Escherichia coli is one major cause of bacterial infections and can horizontally acquire antimicrobial resistance and virulence genes through conjugation. Because conjugative plasmids can rapidly spread among bacteria of different species, the plasmids carrying both antimicrobial resistance and virulence genes may pose a significant threat to public health. Therefore, the identification and characterization of these plasmids may facilitate a better understanding of E. coli pathogenesis and the development of new strategies against E. coli infections. Because iron uptake ability is a potential virulence trait of bacteria, we screened for E. coli conjugative plasmids able to confer both iron uptake ability and ampicillin resistance. The plasmid pEC41, which was derived from the bacteremia clinical isolate EC41, was identified. EC41, which carried the fimH27 allele, belonged to sequence type (ST) 405 and phylogroup D. According to the sequencing analyses, pEC41 was 86 kb in size, and its backbone structure was almost identical to that of another highly conjugative plasmid, pCTX-M3, in which the extended-spectrum β-lactamase gene bla CTX–M–3 was originally identified. pEC41 carried bla CTX–M–3 and bla TEM–1. The ferric citrate uptake ( fec) system was identified in pEC41 and was responsible for conferring iron uptake ability. The fec system contributes to the pathogenesis of EC41 in systemic infections but not in urinary tract infections (UTIs). However, this system promoted competitive fitness of a cystitis-associated clinical isolate to colonize urinary tracts. Additionally, the distribution of the fec system was related to E. coli isolates associated with human bacteremia and UTIs. In summary, the present study identified a novel conjugative plasmid, pEC41, which conferred both antimicrobial resistance and an extra iron uptake ability to E. coli. The iron uptake ability was encoded in the fec system and contributed to E. coli pathogenesis. This study is the first to show that the fec system is a virulence factor in E. coli.

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          Most cited references51

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          One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

          We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.
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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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              Easyfig: a genome comparison visualizer

              Summary: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures. Availability: Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site: http://easyfig.sourceforge.net/. Contact: s.beatson@uq.edu.au
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                26 May 2021
                2021
                : 12
                : 667782
                Affiliations
                [1] 1Institute of Molecular Medicine, College of Medicine, National Cheng Kung University , Tainan, Taiwan
                [2] 2Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University , Tainan, Taiwan
                [3] 3Center of Infectious Disease and Signaling Research, National Cheng Kung University , Tainan, Taiwan
                [4] 4Department of Biotechnology, National Kaohsiung Normal University , Kaohsiung, Taiwan
                [5] 5Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University , Taipei, Taiwan
                [6] 6Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University , Tainan, Taiwan
                [7] 7Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University , Tainan, Taiwan
                [8] 8Department of Statistics, Institute of Data Science, Center for Innovative FinTech Business Models, National Cheng Kung University , Tainan, Taiwan
                [9] 9Department of Internal Medicine, National Cheng Kung University Hospital , Tainan, Taiwan
                [10] 10Department of Medicine, College of Medicine, National Cheng Kung University , Tainan, Taiwan
                [11] 11Center of Allergy and Clinical Immunology Research (ACIR), National Cheng Kung University , Tainan, Taiwan
                Author notes

                Edited by: Michal Letek, Universidad de León, Spain

                Reviewed by: João Pedro Rueda Furlan, University of São Paulo, Brazil; Hongxia Jiang, South China Agricultural University, China; Alvaro Mourenza Flórez, Universidad de León, Spain

                *Correspondence: Ching-Hao Teng, chteng@ 123456mail.ncku.edu.tw

                These authors have contributed equally to this work

                This article was submitted to Infectious Diseases, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2021.667782
                8187952
                34122381
                b7f274f4-c08e-4d9e-ac08-8241b7b289cf
                Copyright © 2021 Huang, Wong, Wang, Hashimoto, Lin, Lee, Wu, Wang, Lin, Jeng, Wang, Chen and Teng.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 14 February 2021
                : 23 April 2021
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 51, Pages: 15, Words: 0
                Funding
                Funded by: Ministry of Science and Technology, Taiwan 10.13039/501100004663
                Award ID: MOST 106-2320-B-006-032
                Award ID: MOST 108-2320-B-017-002-MY3
                Award ID: MOST 108-2320-B-006-034-MY3
                Award ID: MOST 109-2320-B-006-060)
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                iron uptake system,blactx–m–3,esbl,bacteremia,urinary tract infections,ferric citrate,e. coli,conjugative plasmid

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