Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing

Abstract In this work, we report 2 cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin resistance in 2 patients with acute myeloid leukemia and myelodysplastic syndrome. Mutations related to daptomycin-nonsusceptible phenotype in liaSR genes were found in all strains of the study, including those with a minimum inhibitory concentration <1 µg/mL collected before daptomycin therapy. Epidemiological investigation using core genome single nucleotide polymorphism and core genome multilocus sequence typing revealed clonality of all the isolates. In this study, we conclude that real-time genome sequencing of clinical isolates can provide rapid access to timely information on daptomycin-resistant genotypes that would help clinicians speed up and optimize the selection of the antibiotic for treatment.

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Epidemiological typing of ST80 vancomycin-resistant Enterococcus faecium: core-genome multi-locus sequence typing versus single nucleotide polymorphism-based typing

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2021.03.005 ◽

2021 ◽

Author(s):

Fredrik Dyrkell ◽

Christian G. Giske ◽

Hong Fang

Keyword(s):

Single Nucleotide Polymorphism ◽

Enterococcus Faecium ◽

Core Genome ◽

Multi Locus Sequence Typing ◽

Vancomycin Resistant Enterococcus ◽

Nucleotide Polymorphism ◽

Epidemiological Typing ◽

Single Nucleotide ◽

Vancomycin Resistant

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Genotypic and Phenotypic Evaluation of the Evolution of High-Level Daptomycin Nonsusceptibility in Vancomycin-Resistant Enterococcus faecium

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01318-12 ◽

2012 ◽

Vol 56 (11) ◽

pp. 6051-6053 ◽

Cited By ~ 43

Author(s):

Romney M. Humphries ◽

Theodoros Kelesidis ◽

Ryan Tewhey ◽

Warren E. Rose ◽

Nicholas Schork ◽

...

Keyword(s):

Enterococcus Faecium ◽

Open Reading Frames ◽

Vancomycin Resistant Enterococcus ◽

Single Nucleotide Variants ◽

Phosphotransferase System ◽

Single Nucleotide ◽

Content Type ◽

Vancomycin Resistant ◽

High Level ◽

Reading Frames

ABSTRACTWhole-genome sequencing and cell membrane studies of three clonalEnterococcus faeciumstrains with daptomycin MICs of 4, 32, and 192 μg/ml were performed, revealing nonsynonymous single nucleotide variants in eight open reading frames, including those predicted to encode a phosphoenolpyruvate-dependent, mannose-specific phosphotransferase system, cardiolipin synthetase, and EzrA. Membrane studies revealed a higher net surface charge among the daptomycin-nonsusceptible isolates and increased septum formation in the isolate with a daptomycin MIC of 192 μg/ml.

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Using core genome MLST typing for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2021.02.007 ◽

2021 ◽

Author(s):

Sanne Kjær Hansen ◽

Lise Andersen ◽

Mette Detlefsen ◽

Anette Holm ◽

Louise Roer ◽

...

Keyword(s):

Infection Control ◽

Enterococcus Faecium ◽

Core Genome ◽

Vancomycin Resistant Enterococcus ◽

Vancomycin Resistant

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Association between vancomycin-resistant Enterococcus faecium colonization and subsequent infection: a retrospective WGS study

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa074 ◽

2020 ◽

Vol 75 (7) ◽

pp. 1712-1715

Author(s):

Ingrid Maria Cecilia Rubin ◽

Martin Schou Pedersen ◽

Sarah Mollerup ◽

Hülya Kaya ◽

Andreas Munk Petersen ◽

...

Keyword(s):

Enterococcus Faecium ◽

Core Genome ◽

Clinical Sample ◽

Median Number ◽

Laboratory Information System ◽

Vancomycin Resistant Enterococcus ◽

Clinical Infection ◽

Subsequent Infection ◽

Invasive Isolate ◽

Vancomycin Resistant

Abstract Background Since 2012, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased dramatically in Copenhagen and vanA E. faecium has become endemic and polyclonal. Objectives To examine whether a patient with a positive VRE clinical sample had the same VREfm in a preceding screening sample (within 60 days). Methods We performed a 30 month retrospective study. From our laboratory information system (LIS), we identified all patients with an invasive VREfm isolate and a VREfm rectal screening isolate within 60 days before infection. VREfm pairs (screening isolate and invasive isolate) were whole-genome sequenced. All isolates were analysed using SeqSphere and core-genome MLST (cgMLST) types were determined. We examined all isolates for the presence of the three most dominant vanA plasmids in the Capital Region of Denmark. Two novel vanA plasmids were closed by Nanopore/Illumina sequencing. Results We found a total of 19 VREfm pairs. Of these, 13 patients had pairs with matching cgMLST types and vanA plasmids and a median number of 6 days from identification of carriage to clinical infection. One patient had a pair with non-matching cgMLST types but matching vanA plasmids and 24 days between identification of carriage to clinical infection. Five patients had pairs with non-matching cgMLST types and non-matching vanA plasmids and a median number of 18 days from identification of carriage to clinical infection. Conclusions Of our 19 pairs, 13 were a match regarding cgMLST types (68%) and 1 more (5%) had matching vanA plasmids. Infection was thus preceded by colonization with the same isolates in 13 out of 19 patients. The five mismatches (26%) could be explained by the longer interval between colonization and infection.

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