scholarly journals Vancomycin-resistant Enterococcus faecium high-resolution typing by core genome multilocus sequence typing

2016 ◽  
Vol 10 (10) ◽  
pp. 1159-1161 ◽  
Author(s):  
Antonella Santona ◽  
Elisa Taviani ◽  
Massimo Deligios ◽  
Ahmed A. Al-Qahtani ◽  
Mohammed N. Al-Ahdal ◽  
...  
Keyword(s):  
High Resolution ◽  
Full Text ◽  
Enterococcus Faecium ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Vancomycin Resistant

This item has no abstract. Follow the links below to access the full text.

scholarly journals Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

2015 ◽  
Vol 53 (12) ◽  
pp. 3788-3797 ◽  
Author(s):  
Mark de Been ◽  
Mette Pinholt ◽  
Janetta Top ◽  
Stefan Bletz ◽  
Alexander Mellmann ◽  
...  
Keyword(s):  
High Resolution ◽  
Enterococcus Faecium ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Target Genes ◽  
Multidrug Resistant ◽  
Single Nucleotide ◽  
Content Type ◽  
Genome Wide ◽  
Computationally Intensive

Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology ofE. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme forE. faecium. cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. TheE. faeciumcgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of theE. faeciumcgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing ofE. faeciumoutbreaks.

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

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.

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

2020 ◽  
Vol 7 (6) ◽  
Author(s):  
Zulema Udaondo ◽  
Piroon Jenjaroenpun ◽  
Thidathip Wongsurawat ◽  
Erik Meyers ◽  
Courtney Anderson ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Myeloid Leukemia ◽  
Core Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Single Nucleotide ◽  
Oxford Nanopore ◽  
Speed Up ◽  
Vancomycin Resistant ◽  
Resistant Genotypes ◽  
Selection Of

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.

Sign in / Sign up

Export Citation Format

Share Document