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      Escherichia coli ST471 Producing VIM-4 Metallo-β-Lactamase in Colombia

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          Abstract

          An Escherichia coli isolate sequence-type 471 (ST471) producing Verona integron-encoded metallo-β-lactamases (VIM)-4 was recovered from a rectal swab in a patient without travel records with osteomyelitis in Colombia. The isolate carried a class 1 integron-borne bla VIM-4 gene with a 170-bp duplication in the 3′ end of the gene, preceded by an aac(6′)-Ib gene. The genetic environment of bla VIM-4, bla CMY-2, and sul2 genes showed similarities to the backbone of pKKp4, an IncA/C-type plasmid from a Klebsiella pneumoniae strain carrying bla VIM-4 recovered in Kuwait. This is the first report of bla VIM-4 in Enterobacterales in South America. Our results suggest that bla VIM-4 gene was found on an IncA/C-type plasmid that could play a role in the spread of VIM-4 carbapenemase in Colombia.

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          In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing.

          Alessandra Carattoli, Ea Zankari, Aurora García-Fernández … (2014)
          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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            Identification of acquired antimicrobial resistance genes

            Ea Zankari, Henrik Hasman, Salvatore Cosentino … (2012)
            Objectives Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data. Methods We developed a web-based method, ResFinder that uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de- novo-sequenced isolates. Results When testing the 1862 GenBank files, the method identified the resistance genes with an ID = 100% (100% identity) to the genes in ResFinder. Agreement between in silico predictions and phenotypic testing was found when the method was further tested on 23 isolates of five different bacterial species, with available phenotypes. Furthermore, ResFinder was evaluated on WGS chromosomes and plasmids of 30 isolates. Seven of these isolates were annotated to have antimicrobial resistance, and in all cases, annotations were compatible with the ResFinder results. Conclusions A web server providing a convenient way of identifying acquired antimicrobial resistance genes in completely sequenced isolates was created. ResFinder can be accessed at www.genomicepidemiology.org. ResFinder will continuously be updated as new resistance genes are identified.
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              Multilocus sequence typing of total-genome-sequenced bacteria.

              M. V. Larsen, S Cosentino, S. Rasmussen … (2012)
              Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Microb Drug Resist
                Journal ID (iso-abbrev): Microb Drug Resist
                Journal ID (publisher-id): mdr
                Title: Microbial Drug Resistance
                Publisher: Mary Ann Liebert, Inc., publishers (140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA )
                ISSN (Print): 1076-6294
                ISSN (Electronic): 1931-8448
                Publication date (Print): March 2022
                Publication date (Electronic): 04 March 2022
                Publication date PMC-release: 04 March 2022
                Volume: 28
                Issue: 3
                Pages: 288-292
                Affiliations
                [ 1 ]Department of Microbiology, Bacteria and Cáncer Group, University of Antioquia, Medellín, Colombia.
                [ 2 ]Facultad de Ciencias de la Salud, Biociencias Group, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia.
                [ 3 ]Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali, Colombia.
                [ 4 ]Clínica Imbanaco, Cali, Colombia.
                [ 5 ]Fundación Clínica del Norte, Bello, Colombia.
                Author notes
                [*]Address correspondence to: Ana Mercedes Rada, PhD, Department of Microbiology, Bacteria and Cáncer Group, University of Antioquia, Medellín 050010, Colombia ana.rada@ 123456colmayor.edu.co

                iORCID ID ( https://orcid.org/0000-0002-9624-4776).

                Author information
                https://orcid.org/0000-0002-9624-4776
                Article
                Publisher ID: 10.1089/mdr.2021.0031
                DOI: 10.1089/mdr.2021.0031
                PMC ID: 8968847
                PubMed ID: 34990286
                SO-VID: 831a15d6-865e-4fdd-8637-551e8e7b247e
                Copyright © © Ana Mercedes Rada et al. 2022; Published by Mary Ann Liebert, Inc.
                License:

                This Open Access article is distributed under the terms of the Creative Commons License [CC-BY] ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 3, References: 32, Pages: 5
                Categories
                Subject: Mechanisms

                Keywords: escherichia coli,metallo-β-lactamase, bla vim-4 ,colonization
                Data availability:
                Keywords: escherichia coli, metallo-β-lactamase, bla vim-4 , colonization

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