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.

Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia

“…Genomic DNA was extracted and sequenced as described elsewhere [31,32]. Briefly, genomic DNA was extracted from VRE colonies using the Quick-DNA Fungal/Bacterial kit (Zymo Research, Irvine, CA, USA).…”

Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus

“…et al, 2018 ). Similarly, no phylogenetic studies have been completed for E. faecalis , but a novel ST736 clone associated with daptomycin resistance has been identified for E. faecium ( Wang et al, 2014 ) in some United States hospitals ( Wang et al, 2018 ), as has daptomycin-resistant ST80 E. faecium ( Udaondo et al, 2020 ).…”

Insertion sequences associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia

“…Genomic DNA was extracted and sequenced as described in (23,24). Briefly, genomic DNA was extracted from VRE colonies using the Quick-DNA Fungal/Bacterial kit (Zymo Research, Irvine, CA, USA).…”

“…Fully resolved assemblies for E. faecalis isolates were obtained using Flye v2.8.2 assembler(32) with Oxford Nanopore reads, with 2 rounds of polishing using the Oxford //nanoporetech.github.io/medaka/index.html). For both E. faecium and E. faecalis, final polishing with Illumina data was performed through 2 rounds of Pilon v1 23.…”