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

Major role of pKpQIL-like plasmids in the early dissemination of KPC-type carbapenemases in the UK

(2017) M. Doumith et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples

(2017) Antonina A. Votintseva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

(2017) Minh Duc Cao et al.   Nature Communications

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

(2017) N. Stoesser et al.   Scientific Reports

Multicentre evaluation of a real-time PCR assay to detect genes encoding clinically relevant carbapenemases in cultured bacteria

(2016) Matthew J. Ellington et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

KPC enzymes in the UK: an analysis of the first 160 cases outside the North-West region

(2016) Jacqueline Findlay et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2016) Sean Conlan et al.   mBio

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

(2016) Nicole Stoesser et al.   mBio

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

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

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

MgrB Inactivation Is a Common Mechanism of Colistin Resistance in KPC-Producing Klebsiella pneumoniae of Clinical Origin

(2014) Antonio Cannatelli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Poretools: a toolkit for analyzing nanopore sequence data

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

How to detect carbapenemase producers? A literature review of phenotypic and molecular methods

(2014) D. Hammoudi et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

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

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

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

The Importance of Long-term Acute Care Hospitals in the Regional Epidemiology of Klebsiella pneumoniae Carbapenemase–Producing Enterobacteriaceae

(2013) Michael Y. Lin et al.   CLINICAL INFECTIOUS DISEASES

Persistence of Klebsiella pneumoniae clones with OXA-48 or NDM carbapenemases causing bacteraemias in a Riyadh hospital

(2013) Mohamed H. Al-Agamy et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

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

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

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

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

A pilot study of rapid benchtop sequencing ofStaphylococcus aureusandClostridium difficilefor outbreak detection and surveillance

(2012) David W Eyre et al.   BMJ Open

Dissemination ofblaKPC-2by the Spread of Klebsiella pneumoniae Clonal Complex 258 Clones (ST258, ST11, ST437) and Plasmids (IncFII, IncN, IncL/M) among Enterobacteriaceae Species in Brazil

(2011) Leonardo Neves Andrade et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Functional Characterization of Tn4401, a Tn3-Based Transposon Involved inblaKPCGene Mobilization

(2011) Gaelle Cuzon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Phylogenetic diversity of Escherichia coli strains producing NDM-type carbapenemases

(2011) S. Mushtaq et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

First outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in Germany

(2010) C. Wendt et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

PCR characterization and typing of Klebsiella pneumoniae using capsular type-specific, variable number tandem repeat and virulence gene targets

(2010) J. F. Turton et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Genetic Structures at the Origin of Acquisition of the  -Lactamase blaKPC Gene

(2008) T. Naas et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY