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

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

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

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

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

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

(2016) Hollie-Ann Hatherell et al.   BMC Medicine

Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium

(2016) Glen P. Carter et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2016) Sean Conlan et al.   mBio

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

Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

(2015) Y. Jiang et al.   CLINICAL MICROBIOLOGY AND INFECTION

Whole-Genome Sequencing in Outbreak Analysis

(2015) Carol A. Gilchrist et al.   CLINICAL MICROBIOLOGY REVIEWS

An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in the Netherlands (July to December 2013), with inter-institutional spread

(2015) V. Weterings et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Managing a nosocomial outbreak of carbapenem-resistantKlebsiella pneumoniae: an early Australian hospital experience

(2015) L. W. K. Chang et al.   INTERNAL MEDICINE JOURNAL

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

(2015) Jason C. Kwong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Local acquisition and nosocomial transmission of Klebsiella pneumoniae harbouring the blaNDM-1 gene in Australia

(2015) Alex Y C Tai et al.   MEDICAL JOURNAL OF AUSTRALIA

Whole genome sequencing in clinical and public health microbiology

(2015) J.C. Kwong et al.   PATHOLOGY

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae

(2015) Jane W. Marsh 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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

New Delhi metallo-beta-lactamase-producing enterobacteriaceae in an Australian child who had not travelled overseas

(2014) Christopher C Blyth et al.   MEDICAL JOURNAL OF AUSTRALIA

The growing burden of multidrug-resistant infections among returned Australian travellers

(2014) Kyra Y L Chua et al.   MEDICAL JOURNAL OF AUSTRALIA

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

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

Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258Klebsiella pneumoniae

(2014) Frank R. DeLeo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

(2014) Colin J. Worby et al.   PLoS Computational Biology

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Duration of carriage of carbapenem-resistant Enterobacteriaceae following hospital discharge

(2013) Frederic S. Zimmerman et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Antibiotic Treatment of Infections Due to Carbapenem-Resistant Enterobacteriaceae: Systematic Evaluation of the Available Evidence

(2013) Matthew E. Falagas et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

An Ongoing National Intervention to Contain the Spread of Carbapenem-Resistant Enterobacteriaceae

(2013) M. J. Schwaber et al.   CLINICAL INFECTIOUS DISEASES

Managing Transmission of Carbapenem-Resistant Enterobacteriaceae in Healthcare Settings: A View From the Trenches

(2013) T. N. Palmore et al.   CLINICAL INFECTIOUS DISEASES

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Emergence of blaOXA-181-carrying ColE plasmid in Klebsiella pneumoniae in Australia

(2013) Hanna E. Sidjabat et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Detection of Colonization by Carbapenemase-Producing Gram-Negative Bacilli in Patients by Use of the Xpert MDRO Assay

(2013) Fred C. Tenover et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

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

“Down the drain”: carbapenem-resistant bacteria in intensive care unit patients and handwashing sinks

(2013) Despina Kotsanas et al.   MEDICAL JOURNAL OF AUSTRALIA

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole Genome Sequence Analysis of the First Australian OXA-48-Producing Outbreak-Associated Klebsiella pneumoniae Isolates: The Resistome and In Vivo Evolution

(2013) Björn A. Espedido et al.   PLoS One

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

(2013) Tanya Golubchik et al.   PLoS One

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

(2013) David W. Eyre et al.   PLoS Computational Biology

Role of ISKpn7and Deletions inblaKPCGene Expression

(2012) Thierry Naas et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Carbapenemases in Klebsiella pneumoniae and Other Enterobacteriaceae: an Evolving Crisis of Global Dimensions

(2012) L. S. Tzouvelekis et al.   CLINICAL MICROBIOLOGY REVIEWS

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

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

Genomic polish for shoe-leather epidemiology

(2012) Steven Y. C. Tong   NATURE REVIEWS MICROBIOLOGY

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine

Partial Excision ofblaKPCfrom Tn4401in Carbapenem-Resistant Klebsiella pneumoniae

(2011) Liang Chen et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Carbapenem Resistance in Klebsiella pneumoniae Due to the New Delhi Metallo- -lactamase

(2011) H. Sidjabat et al.   CLINICAL INFECTIOUS DISEASES

A case of carbapenemase-producing Klebsiella pneumoniae in Australia

(2011) Nicholas R. Coatsworth et al.   PATHOLOGY

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

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Molecular Epidemiology of KPC-Producing Klebsiella pneumoniae Isolates in the United States: Clonal Expansion of Multilocus Sequence Type 258

(2009) B. Kitchel et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

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