Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany

Falgenhauer, Linda; Imirzalioglu, Can; Ghosh, Hiren; Gwozdzinski, Konrad; Schmiedel, Judith; Gentil, Katrin; Bauerfeind, Rolf; Kämpfer, Peter; Seifert, Harald; Michael, Geovana Brenner; Schwarz, Štefan; Pfeifer, Yvonne; Werner, Guido; Pietsch, Michael; Roesler, Uwe; Guerra, Beatriz; Fischer, Jennie; Sharp, Hannah; Käsbohrer, Annemarie; Goesmann, Alexander; Hille, Katja; Kreienbrock, Lothar; Chakraborty, Trinad

doi:10.1016/j.ijantimicag.2016.03.019

Cited by 93 publications

(93 citation statements)

References 37 publications

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“…First, our results extend data on the mobility of IS Apl 1- mcr-1 to a chromosomal location and reveal a new dimension in the transmissible nature of mcr-1 in colistin-resistant Enterobacteriaceae isolates and their ecology. Second, clonal isolates of ST410 have been isolated from diverse environments, livestock, companion animals, and humans and, as we demonstrate here, in turkey hen meat ( 7 , 8 ). Thus, the simultaneous spread of the mcr-1 and bla CTX-M-15 genes mediated by a single bacterial clone is real and suggests that mcr-1 is already present in the diverse reservoirs inhabited by these isolates.…”

mentioning

confidence: 54%

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

Falgenhauer¹,

Waezsada²,

Gwozdzinski³

et al. 2016

Emerg. Infect. Dis.

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confidence: 54%

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

Falgenhauer¹,

Waezsada²,

Gwozdzinski³

et al. 2016

Emerg. Infect. Dis.

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“…Notably, recent publications from Germany and Italy described the clonal expansion of fluoroquinolone (FQ)-resistant CTX-M-15-producing E. coli ST410 in both human and animal populations. 8, 9 Our previous and current studies also identified E. coli ST410 clinical isolates co-harboring multiple resistance determinants, including bla NDM ( bla NDM-1/4 ), ESBL S ( bla CTX-M-15, bla SHV-12 / bla TEM-1 ) and ampC genes ( bla CMY-30 / bla CMY-61 ). 5 In addition, NDM-5 producing E. coli ST410 was recently detected in Egypt.…”

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confidence: 54%

First identification of NDM-4-producing Escherichia coli ST410 in China

Qin

Zhou

Zhang

et al. 2016

Emerging Microbes & Infections

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“…Conversely, if the same gene integrates in the chromosome of an already highly virulent strain, it can lead to the emergence of a well-adapted and dangerous clone. To highlight this, we chose a genome dataset of E. coli wherein many strains exhibited a chromosomal integration of CTX-M-15 coding gene, one of the main enzymes responsible for resistance to wide spectrum antibiotics such as cephalosporins in E. coli (14). Using PlaScope we accurately identify 20/21 of these chromosomal insertions.…”

Section: Resultsmentioning

confidence: 99%

“…In a second step, we evaluated our method on Extended-Spectrum Beta-lactamase (ESBL) carrying E. coli strains sequenced by Falgenhauer et al (14). This dataset is particularly challenging because of an unusual high rate of chromosomal integration of CTX-M-15 coding genes.…”

Section: Application To Resistance Virulence Gene and Operon Locationsmentioning

confidence: 99%

PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains

Royer

Decousser

Branger

et al. 2018

Preprint

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Plasmid prediction may be of great interest when studying bacteria such as Enterobacteriaceae. Indeed many resistance and virulence genes are located on such replicons and can have major impact in terms of pathogenicity and spreading capacities.Beyond strains outbreak, plasmids outbreaks have been reported especially for some extended-spectrum beta-lactamase or carbapenemase producing Enterobacteriaceae.Several tools are now available to explore the "plasmidome" from whole-genome sequence data, with many interesting and various approaches. However recent benchmarks have highlighted that none of them succeed to combine high sensitivity and specificity. With this in mind we developed PlaScope, a targeted approach to recover plasmidic sequences in Escherichia coli. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, it performs a classification of contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, Plasflow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes containing plasmids. Finally we tested our method on a dataset of E. coli strains exhibiting an elevated rate of extended-spectrum beta-lactamase coding gene chromosomal integration, and we were able to identify 20/21 of these events. Moreover virulence genes and operons predicted locations were also in agreement with the literature. Similar approaches could also be developed for other well-characterized bacteria such as Klebsiella pneumoniae. Data summary1. All the genomes were downloaded from the National Center for Biotechnology Information Sequence Read Archive and Genome database (Supplementary table 1 and 2). The source code of PlaScope is available on Github(https://github.com/GuilhemRoyer/PlaScope). ImportancePlasmid exploration could be of great interest since these replicons are pivotal in the adaptation of bacteria to their environment. They are involved in the exchange of many genes within and between species, with a significant impact on antibiotic resistance and virulence in particular. However, plasmid characterization has been a laborious task for many years, requiring complex conjugation or electroporation manipulations for example.With the advent of whole genome sequencing techniques, access to these sequences is now potentially easier provided that appropriate tools are available. Many softwares have been developed to explore the plasmidome of a large variety of bacteria, but they rarely managed to combine sensitivity and specificity. Here, we focus on a single species, E. coli, and we use the many data available to overcome this problem. With our tool called PlaScope, we achieve high performance compared with two other classifiers, Plasflow and cBar, and we demonstrate the utility of such an approach to determine the location of virulence or resistance genes. We think that PlaScope could be very useful in the ana...

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Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany

Cited by 93 publications

References 37 publications

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

First identification of NDM-4-producing Escherichia coli ST410 in China

PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains

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Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany

Cited by 93 publications

References 37 publications

Chromosomal Locations ofmcr-1andblaCTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

Chromosomal Locations ofmcr-1andblaCTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

First identification of NDM-4-producing Escherichia coli ST410 in China

PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains

Contact Info

Product

Resources

About

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410

Chromosomal Locations ofmcr-1andbla_CTX-M-15in Fluoroquinolone-ResistantEscherichia coliST410