Emergence of a vancomycin-variable Enterococcus faecium ST1421 strain containing a deletion in vanX

Hansen, Thomas Arn; Pedersen, Martin Schou; Nielsen, Lene Nørby; German, Chih Man; Søes, Lillian Marie; Worning, Peder; Østergaard, Christian Richter; Westh, Henrik; Pinholt, Mette; Schønning, Kristian

doi:10.1093/jac/dky308

Cited by 27 publications

(28 citation statements)

References 20 publications

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“…Importantly, if employed in real time on a patient isolate, these methods would have hypothetically shortened median time to effective antimicrobial therapy by 20 and 26 h, respectively. In other less clinically oriented studies, extensive characterization of the genomic context of AMR determinants has been elucidated in Escherichia, Salmonella, Klebsiella, and Enterococcus (56)(57)(58)(59)(60). Complete plasmid sequences, which are difficult to assemble with short-read platforms, have been resolved using ONT on a host of Enterobacteriaceae species (33,59).…”

Section: Nanopore Sequencing In Infectious Disease Researchmentioning

confidence: 99%

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

et al. 2019

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Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.

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Section: Nanopore Sequencing In Infectious Disease Researchmentioning

confidence: 99%

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

et al. 2019

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“…VVE can only be detected by molecular methods and cannot be cultured on selective vancomycin-containing media. Different clones of VVE have caused nosocomial outbreaks and development of vancomycin-resistant revertant mutants in vitro and in vivo has been described [1,3-5]. This makes the detection of VVE highly important in clinical samples in order to assure relevant antibiotic treatment and in screening samples to avoid nosocomial spread.…”

Section: Vancomycin-variable Enterococcimentioning

confidence: 99%

“…In 2015 and 2016, sporadic VVE with different genetic background were detected in the Capital Region of Denmark, in connection with vancomycin-resistant enterococci (VRE) outbreaks (data not shown). In 2016, a VVE clone belonging to ST1421-CT1134, which displays variable vancomycin susceptibility (minimum inhibitory concentration (MIC) 1 to ≥ 256 mg/ml) was detected in screening samples from a hospital in the Capital Region [5]. One strain, Efm-V1511, belonging to this clone was characterised by Hansen et al [5].…”

Section: Vancomycin-variable Enterococcimentioning

confidence: 99%

“…In 2016, a VVE clone belonging to ST1421-CT1134, which displays variable vancomycin susceptibility (minimum inhibitory concentration (MIC) 1 to ≥ 256 mg/ml) was detected in screening samples from a hospital in the Capital Region [5]. One strain, Efm-V1511, belonging to this clone was characterised by Hansen et al [5]. Efm-V1511 had a 49.6 Kp plasmid, which carried the Tn 1546 ( vanA transposon).…”

Section: Vancomycin-variable Enterococcimentioning

confidence: 99%

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Surveillance of vancomycin-resistant enterococci reveals shift in dominating clones and national spread of a vancomycin-variable vanA Enterococcus faecium ST1421-CT1134 clone, Denmark, 2015 to March 2019

et al. 2019

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We describe clonal shifts in vanA Enterococcus faecium isolates from clinical samples obtained from patients in Denmark from 2015 to the first quarter (Q1) of 2019. During Q1 2019, the vancomycin-variable enterococci (VVE) ST1421-CT1134 vanA E. faecium became the most dominant vanA E. faecium clone and has spread to all five regions in Denmark. Among 174 E. faecium isolates with vanA, vanB or vanA/ vanB genes in Q1 2019, 44% belonged to this type.

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“…In the treatment of infections caused by Enterococcus , vancomycin and sometimes with any other aminoglycoside, is used because of its bactericidal efficacy. These antibiotics are usually used to treat infections caused by methicillin-resistant Staphylococcus aureus and other Gram-positive bacteria [ 11 , 12 ]. Vancomycin is used as the last option in the treatment of E nterococcus [ 9 ] as its resistance to antibiotics is as a result of either an inherent or acquired machinery.…”

Section: Introductionmentioning

confidence: 99%

Vancomycin-Resistant Enterococci (VRE) in Nigeria: The First Systematic Review and Meta-Analysis

et al. 2020

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Vancomycin-Resistant Enterococci (VRE) are on the rise worldwide. Here, we report the first prevalence of VRE in Nigeria using systematic review and meta-analysis. International databases MedLib, PubMed, International Scientific Indexing (ISI), Web of Science, Scopus, Google Scholar, and African journals online (AJOL) were searched. Information was extracted by two independent reviewers, and results were reviewed by the third. Two reviewers independently assessed the study quality using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) checklist. OpenMeta analyst was used. The random effect was used, and publication bias was assessed using a funnel plot. Between-study heterogeneity was assessed, and the sources were analysed using the leave-one-out meta-analysis, subgroup analysis, and meta-regression. Nineteen studies met the eligibility criteria and were added to the final meta-analysis, and the study period was from 2009–2018. Of the 2552 isolates tested, 349 were VRE, and E. faecalis was reported the most. The pooled prevalence of VRE in Nigeria was estimated at 25.3% (95% CI; 19.8–30.8%; I2 = 96.26%; p < 0.001). Between-study variability was high (t2 = 0.011; heterogeneity I2 = 96.26% with heterogeneity chi-square (Q) = 480.667, degrees of freedom (df) = 18, and p = 0.001). The funnel plot showed no publication bias, and the leave-one-out forest plot did not affect the pooled prevalence. The South-East region had a moderate heterogeneity though not significant (I2 = 51.15%, p = 0.129). Meta-regression showed that all the variables listed contributed to the heterogeneity except for the animal isolate source (p = 0.188) and studies that were done in 2013 (p = 0.219). Adherence to proper and accurate antimicrobial usage, comprehensive testing, and continuous surveillance of VRE are required.

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Emergence of a vancomycin-variable Enterococcus faecium ST1421 strain containing a deletion in vanX

Abstract: E. faecium carrying pHVH-V1511 is capable of nosocomial transmission and may develop clinical resistance to vancomycin. Strains may not be detected using standard culture methods for VRE.

Cited by 27 publications

References 20 publications

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

Surveillance of vancomycin-resistant enterococci reveals shift in dominating clones and national spread of a vancomycin-variable vanA Enterococcus faecium ST1421-CT1134 clone, Denmark, 2015 to March 2019

Vancomycin-Resistant Enterococci (VRE) in Nigeria: The First Systematic Review and Meta-Analysis

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