Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains

A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study

(2018) Danxia Gu et al.   LANCET INFECTIOUS DISEASES

Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis

(2018) Evelina Tacconelli et al.   LANCET INFECTIOUS DISEASES

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

(2018) Rebecca A. Weingarten et al.   mBio

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak

(2018) Jason C. Kwong et al.   PeerJ

Carriage of blaKPC-2 by a virulence plasmid in hypervirulent Klebsiella pneumoniae

(2018) Ning Dong et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic

(2018) Francois Balloux et al.   TRENDS IN MICROBIOLOGY

Comparative analysis of bla KPC-2- and rmtB-carrying IncFII-family pKPC-LK30/pHN7A8 hybrid plasmids from Klebsiella pneumoniae CG258 strains disseminated among multiple Chinese hospitals

(2018) Lining Shi et al.   Infection and Drug Resistance

Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission

(2017) Jessica Martin et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

(2017) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks

(2017) Gustavo C. Cerqueira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic characterization of novel IncFII-type multidrug resistant plasmids p0716-KPC and p12181-KPC from Klebsiella pneumoniae

(2017) Jiao Feng et al.   Scientific Reports

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

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

Outbreak by Hypermucoviscous Klebsiella pneumoniae ST11 Isolates with Carbapenem Resistance in a Tertiary Hospital in China

(2017) Lingling Zhan et al.   Frontiers in Cellular and Infection Microbiology

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli

(2017) N. Stoesser et al.   Scientific Reports

Horizontal Transfer of Carbapenemase-Encoding Plasmids and Comparison with Hospital Epidemiology Data

(2016) C. A. Hardiman et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A prolonged outbreak of KPC-3-producing Enterobacter cloacae and Klebsiella pneumoniae driven by multiple mechanisms of resistance transmission at a large academic burn center

(2016) Hajime Kanamori et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, bla KPC , in Klebsiella Species Is Elusive but Not Rare

(2016) Amy J. Mathers et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance GeneblaKPC

(2016) Anna E. Sheppard et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of the genetic environment of the blaKPC-2 gene among Klebsiella pneumoniae isolates from a Chinese Hospital

(2016) Pinghua Shen et al.   Brazilian Journal of Infectious Diseases

An Outbreak of Infections Caused by a Klebsiella pneumoniae ST11 Clone Coproducing Klebsiella pneumoniae Carbapenemase-2 and RmtB in a Chinese Teaching Hospital

(2016) Ming-Xiang Zou et al.   CHINESE MEDICAL JOURNAL

Spectrum of excess mortality due to carbapenem-resistant Klebsiella pneumoniae infections

(2016) C. Hauck et al.   CLINICAL MICROBIOLOGY AND INFECTION

Inferences from tip-calibrated phylogenies: a review and a practical guide

(2016) Adrien Rieux et al.   MOLECULAR ECOLOGY

Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization

(2016) Sean Conlan et al.   mBio

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

Outbreak by Ventilator-Associated ST11 K. pneumoniae with Co-production of CTX-M-24 and KPC-2 in a SICU of a Tertiary Teaching Hospital in Central China

(2016) Longhua Hu et al.   Frontiers in Microbiology

Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

(2015) Amy J. Mathers et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

WGS accurately predicts antimicrobial resistance inEscherichia coli

(2015) Gregory H. Tyson et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Complete sequences of KPC-2-encoding plasmid p628-KPC and CTX-M-55-encoding p628-CTXM coexisted in Klebsiella pneumoniae

(2015) Li Wang et al.   Frontiers in Microbiology

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

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing

(2014) N. C. Gordon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A nosocomial outbreak of KPC-2-producing Klebsiella pneumoniae in a Chinese hospital: dissemination of ST11 and emergence of ST37, ST392 and ST395

(2013) J. Yang et al.   CLINICAL MICROBIOLOGY AND INFECTION

Impact of carbapenem resistance on the outcome of patients' hospital-acquired bacteraemia caused by Klebsiella pneumoniae

(2013) K. Hussein et al.   JOURNAL OF HOSPITAL INFECTION

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

(2013) L Silvia Munoz-Price et al.   LANCET INFECTIOUS DISEASES

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Molecular Dissection of an Outbreak of Carbapenem-Resistant Enterobacteriaceae Reveals Intergenus KPC Carbapenemase Transmission through a Promiscuous Plasmid

(2011) A. J. Mathers et al.   mBio

ST11, the dominant clone of KPC-producing Klebsiella pneumoniae in China

(2010) Yan Qi et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria

(2009) Patrice Nordmann et al.   LANCET INFECTIOUS DISEASES

Detection of the Klebsiella pneumoniae Carbapenemase Type 2 Carbapenem-Hydrolyzing Enzyme in Clinical Isolates of Citrobacter freundii and K. oxytoca Carrying a Common Plasmid

(2008) J. K. Rasheed et al.   JOURNAL OF CLINICAL MICROBIOLOGY