A vanA vancomycin-resistant Enterococcus faecium ST80 outbreak resulting from a single importation event

Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients

(2021) Kelly L. Wyres et al.   BMC INFECTIOUS DISEASES

Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis

(2021) Claire L Gorrie et al.   Lancet Microbe

A three-year whole genome sequencing perspective of Enterococcus faecium sepsis in Australia

(2020) Terence Lee et al.   PLoS One

Clinical and molecular epidemiology of vancomycin-resistant Enterococcus faecium bacteremia from an Indian tertiary hospital

(2020) Chandrabhan Rao et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome

(2019) Mette Pinholt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Defining the Role of the Environment in the Emergence and Persistence of vanA Vancomycin-Resistant Enterococcus (VRE) in an Intensive Care Unit: A Molecular Epidemiological Study

(2018) Andie S. Lee et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Relentless spread and adaptation of non-typeable vanA vancomycin-resistant Enterococcus faecium: a genome-wide investigation

(2018) Sebastiaan J van Hal et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis

(2018) Kelvin W. C. Leong et al.   Scientific Reports

Emergence of vanA Enterococcus faecium in Denmark, 2005–15

(2017) Anette M. Hammerum et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

stringMLST: a fast k-mer based tool for multilocus sequence typing

(2016) Anuj Gupta et al.   BIOINFORMATICS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

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

(2015) Mark de Been et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Molecular Epidemiology of Enterococcal Bacteremia in Australia

(2014) G. W. Coombs et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Molecular epidemiology of vancomycin-resistant enterococcal bacteraemia: results from the Canadian Nosocomial Infection Surveillance Program, 1999-2009

(2013) M. McCracken et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Trends and Significance of VRE Colonization in the ICU: A Meta-Analysis of Published Studies

(2013) Panayiotis D. Ziakas et al.   PLoS One

Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci

(2013) B. P. Howden et al.   mBio

Intestinal colonisation and blood stream infections due to vancomycin-resistant enterococci (VRE) and extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBLE) in patients with haematological and oncological malignancies

(2012) B. J. Liss et al.   INFECTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Emergence of Metallo- -Lactamase NDM-1-Producing Multidrug-Resistant Escherichia coli in Australia

(2010) L. Poirel et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS