Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis

Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals

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Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

(2019) Kelly L. Wyres et al.   PLoS Genetics

Emergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy

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Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

(2019) Sophia David et al.   Nature Microbiology

Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae

(2019) Francesco Comandatore et al.   Genome Biology and Evolution

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(2018) Emmanuel Paradis et al.   BIOINFORMATICS

‘How to do it’—molecular investigation of a hospital outbreak

(2018) A. Nutman et al.   CLINICAL MICROBIOLOGY AND INFECTION

ESBL-Producing Klebsiella pneumoniae in the Broiler Production Chain and the First Description of ST3128

(2018) Katrin Daehre et al.   Frontiers in Microbiology

Isolation of the first New Delhi metallo-ß-lactamase-1 (NDM-1) producing, colistin resistant, Klebsiella pneumoniae sequence type ST15, from a digestive carrier in Albania, May 2018

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Evolving beta-lactamase epidemiology in Enterobacteriaceae from Italian nationwide surveillance, October 2013: KPC-carbapenemase spreading among outpatients

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PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

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Evolution and dissemination of the Klebsiella pneumoniae clonal group 258 throughout Israeli post-acute care hospitals, 2008–13

(2017) Amos Adler et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks

(2017) Scott A. Cunningham et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace

(2017) Latania K. Logan et al.   JOURNAL OF INFECTIOUS DISEASES

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

(2017) Clémentine Henri et al.   Frontiers in Microbiology

Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting

(2016) Alexander Mellmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

(2016) John P. Dekker et al.   JOURNAL OF CLINICAL MICROBIOLOGY

KlebSeq, a Diagnostic Tool for Surveillance, Detection, and Monitoring of Klebsiella pneumoniae

(2016) Jolene R. Bowers et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

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Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance

(2015) Johann D. D. Pitout et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

Infections caused by KPC-producing Klebsiella pneumoniae: differences in therapy and mortality in a multicentre study

(2015) Mario Tumbarello et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

(2015) Erika Scaltriti et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital

(2015) Raffaella Onori et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Evolution of Hypervirulent Klebsiella pneumoniae

(2015) Carsten Struve et al.   mBio

Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic

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Genomic Epidemiology of Klebsiella pneumoniae in Italy and Novel Insights into the Origin and Global Evolution of Its Resistance to Carbapenem Antibiotics

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Population Structure of KPC-Producing Klebsiella pneumoniae Isolates from Midwestern U.S. Hospitals

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

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

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Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding

(2014) Liang Chen et al.   TRENDS IN MICROBIOLOGY

Epidemic Klebsiella pneumoniae ST258 Is a Hybrid Strain

(2014) L. Chen et al.   mBio

QUAST: quality assessment tool for genome assemblies

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Emergence of an extensively drug-resistant ArmA- and KPC-2-producing ST101 Klebsiella pneumoniae clone in Italy

(2013) M. L. Mezzatesta et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

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

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

Treatment Outcome of Bacteremia Due to KPC-Producing Klebsiella pneumoniae: Superiority of Combination Antimicrobial Regimens

(2012) Zubair A. Qureshi et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

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

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Emergence in Italy of Klebsiella pneumoniae Sequence Type 258 Producing KPC-3 Carbapenemase

(2009) T. Giani et al.   JOURNAL OF CLINICAL MICROBIOLOGY