Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study

(2017) Hajo Grundmann et al.   LANCET INFECTIOUS DISEASES

High Carbapenem Resistance in Clinical Gram-Negative Pathogens Isolated in Egypt

(2017) Hazim O. Khalifa et al.   Microbial Drug Resistance

Anti-Restriction Protein, KlcAHS, Promotes Dissemination of Carbapenem Resistance

(2017) Wei Liang et al.   Frontiers in Cellular and Infection Microbiology

Isolation and Characterization of NDM-Positive Escherichia coli from Municipal Wastewater in Jeddah, Saudi Arabia

(2016) David Mantilla-Calderon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Active surveillance scheme in three Romanian hospitals reveals a high prevalence and variety of carbapenamase-producing Gram-negative bacteria: a pilot study, December 2014 to May 2015

(2016) Dorina Timofte et al.   Eurosurveillance

Efficient transmission of IncFII Y and IncL plasmids and Klebsiella pneumoniae ST101 clone producing OXA-48, NDM-1 or OXA-181 in Bucharest hospitals

(2016) Ilda Czobor et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

(2016) Nicole Stoesser et al.   mBio

Characterization of an Enterobacter cloacae Strain Producing both KPC and NDM Carbapenemases by Whole-Genome Sequencing

(2015) Wenjing Wu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of Multiple NDM-1-Producing Enterobacteriaceae Isolates from the Same Patient

(2015) Nathalie Tijet et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Dissemination of Carbapenemase-Producing Enterobacteriaceae and Pseudomonas aeruginosa in Romania

(2015) Laurent Dortet et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genomic Characteristics of NDM-Producing Enterobacteriaceae Isolates in Australia and TheirblaNDMGenetic Contexts

(2015) Alexander M. Wailan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

(2015) Chandan Pal et al.   BMC GENOMICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Carbapenemase-Producing Klebsiella pneumoniae in Romania: A Six-Month Survey

(2015) Brandusa Elena Lixandru et al.   PLoS One

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

NDM carbapenemases in the United Kingdom: an analysis of the first 250 cases

(2014) A. Jain et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Serratia marcescens: an outbreak experience

(2014) Petra Gastmeier   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Complete Sequences of Two Plasmids in ablaNDM-1-Positive Klebsiella oxytoca Isolate from Taiwan

(2013) Tzu-Wen Huang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Plasmids and the spread of resistance

(2013) Alessandra Carattoli   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

First description of blaNDM-1, blaOXA-48, blaOXA-181 producing Enterobacteriaceae strains in Romania

(2013) Edit Székely et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data

(2013) N. Stoesser et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Detection of NDM-1-producing Enterobacteriaceae in Romania: report of the SENTRY Antimicrobial Surveillance Program

(2013) L. M. Deshpande et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance

(2013) Alan P. Johnson et al.   JOURNAL OF MEDICAL MICROBIOLOGY

KpsC and KpsS are retaining 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) transferases involved in synthesis of bacterial capsules

(2013) L. M. Willis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Development of a set of multiplex PCR assays for the detection of genes encoding important β-lactamases in Enterobacteriaceae

(2010) Caroline Dallenne et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

How To Detect NDM-1 Producers

(2010) P. Nordmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

In Vivo Acquisition of a Plasmid-Mediated blaKPC-2 Gene among Clonal Isolates of Serratia marcescens

(2010) A. Tsakris et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study

(2010) Karthikeyan K Kumarasamy et al.   LANCET INFECTIOUS DISEASES

Outbreaks of Serratia marcescens in neonatal and pediatric intensive care units: Clinical aspects, risk factors and management

(2009) Alexander Voelz et al.   INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH

Emergence of Serratia marcescens, Klebsiella pneumoniae, and Escherichia coli Isolates Possessing the Plasmid-Mediated Carbapenem-Hydrolyzing  -Lactamase KPC-2 in Intensive Care Units of a Chinese Hospital

(2008) J. C. Cai et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY