Exploring the Genome and Phenotype of Multi-Drug Resistant Klebsiella pneumoniae of Clinical Origin

Evolution of antibiotic multiresistance in Escherichia coli and Klebsiella pneumoniae isolates from urinary tract infections: A 12-year analysis (2003–2014)

(2017) David M. Arana et al.   ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA

Import and spread of extended-spectrum β-lactamase-producing Enterobacteriaceae by international travellers (COMBAT study): a prospective, multicentre cohort study

(2017) Maris S Arcilla et al.   LANCET INFECTIOUS DISEASES

Characterisation of the first KPC-2-producing Klebsiella pneumoniae ST340 from Peru

(2017) Gertrudis Horna et al.   Journal of Global Antimicrobial Resistance

Detection of Colistin Resistance Genemcr-1in Hypervirulent Klebsiella pneumoniae and Escherichia coli Isolates from an Infant with Diarrhea in China

(2016) Dan-xia Gu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

First Report of the Globally Disseminated IncX4 Plasmid Carrying themcr-1Gene in a Colistin-Resistant Escherichia coli Sequence Type 101 Isolate from a Human Infection in Brazil

(2016) Miriam R. Fernandes et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Klebsiella pneumoniae bloodstream infection, antimicrobial resistance and consumption trends in Ireland: 2008 to 2013

(2016) M. Brady et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids inSalmonellaTyphimurium

(2016) Tereza Kubasova et al.   Genome Biology and Evolution

Simultaneous colonisation by ST340 Klebsiella pneumoniae producing NDM-5 and ST399 Escherichia coli producing NDM-7

(2016) Mar Olga Pérez-Moreno et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245Klebsiella pneumoniaeclones circulating in Spain

(2016) María Pérez-Vázquez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Klebsiella pneumoniae: Going on the Offense with a Strong Defense

(2016) Michelle K. Paczosa et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Isolation and Characterization of Aquatic-Borne Klebsiella pneumoniae from Tropical Estuaries in Malaysia

(2016) Anis Barati et al.   International Journal of Environmental Research and Public Health

KPC-3-Producing Klebsiella pneumoniae in Portugal Linked to Previously Circulating Non-CG258 Lineages and Uncommon Genetic Platforms (Tn4401d-IncFIA and Tn4401d-IncN)

(2016) Carla Rodrigues et al.   Frontiers in Microbiology

Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods

(2016) Chang-Ro Lee et al.   Frontiers in Microbiology

First report of nosocomial infection caused by Klebsiella pneumoniae ST147 producing OXA-48 and VEB-8 β-lactamases in Tunisia

(2016) Rym Ouertani et al.   Journal of Global Antimicrobial Resistance

Draft genome sequence of a CTX-M-15-producing Klebsiella pneumoniae sequence type 340 (clonal complex 258) isolate from a food-producing animal

(2016) Louise Cerdeira et al.   Journal of Global Antimicrobial Resistance

Diffusion and transmission of carbapenem-resistant Klebsiella pneumoniae in the medical and surgical wards of a university hospital in Milan, Italy

(2016) Anna L. Ridolfo et al.   Journal of Infection and Public Health

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

IntermingledKlebsiella pneumoniaePopulations Between Retail Meats and Human Urinary Tract Infections

(2015) Gregg S. Davis et al.   CLINICAL INFECTIOUS DISEASES

Coproduction of KPC-2 and QnrB19 in Klebsiella pneumoniae ST340 isolate in Brazil

(2015) Willames M.B.S. Martins et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Dissemination of multidrug-resistant blaCTX-M-15/IncFIIk plasmids in Klebsiella pneumoniae isolates from hospital- and community-acquired human infections in Tunisia

(2015) Wejdene Mansour et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Deep transcriptome profiling of clinicalKlebsiella pneumoniaeisolates reveals strain and sequence type-specific adaptation

(2015) Sebastian Bruchmann et al.   ENVIRONMENTAL MICROBIOLOGY

The complex epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae

(2015) Ruthy Tal Jasper et al.   Future Microbiology

Lateral dissemination and inter-patient transmission ofblaKPC-3: role of a conjugative plasmid in spreading carbapenem resistance

(2015) Nathalie Tijet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

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

Determining the resistance of carbapenem-resistantKlebsiella pneumoniaeto common disinfectants and elucidating the underlying resistance mechanisms

(2015) Wei Guo et al.   Pathogens and Global Health

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

Emergence of carbapenemase-producing Gram-negative bacteria in Saint Petersburg, Russia

(2014) Vladimir A. Ageevets et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: A successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFII K )

(2014) Carla Rodrigues et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Highly conjugative IncX4 plasmids carrying bla CTX-M in Escherichia coli from humans and food animals

(2014) Wai-U Lo et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Carbapenemase-producing Klebsiella pneumoniae: molecular and genetic decoding

(2014) Liang Chen et al.   TRENDS IN MICROBIOLOGY

Replicon typing of plasmids carrying blaCTX-M-1 in Enterobacteriaceae of animal, environmental and human origin

(2014) Katrin Zurfluh et al.   Frontiers in Microbiology

Comparative Population Analysis of Klebsiella pneumoniae Strains with Extended-Spectrum β-Lactamases Colonizing Patients in Rehabilitation Centers in Four Countries

(2013) A. Baraniak et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

KpnEF, a New Member of the Klebsiella pneumoniae Cell Envelope Stress Response Regulon, Is an SMR-Type Efflux Pump Involved in Broad-Spectrum Antimicrobial Resistance

(2013) Vijaya Bharathi Srinivasan et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Predominance of IncL/M and IncF plasmid types among CTX-M-ESBL-producingEscherichia coliandKlebsiella pneumoniaein Bulgarian hospitals

(2013) Rumyana Markovska et al.   APMIS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Specific patterns of gyr A mutations determine the resistance difference to ciprofloxacin and levofloxacin in Klebsiella pneumoniae and Escherichia coli

(2013) Yingmei Fu et al.   BMC INFECTIOUS DISEASES

Role of Klebsiella pneumoniae Type 1 and Type 3 Fimbriae in Colonizing Silicone Tubes Implanted into the Bladders of Mice as a Model of Catheter-Associated Urinary Tract Infections

(2013) Caitlin N. Murphy et al.   INFECTION AND IMMUNITY

Phenotypic Characterization of Salmonella Isolated from Food Production Environments Associated with Low–Water Activity Foods

(2013) SARAH FINN et al.   JOURNAL OF FOOD PROTECTION

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Hypervirulent (hypermucoviscous)Klebsiella pneumoniae

(2013) Alyssa S. Shon et al.   Virulence

Molecular characterization of blaESBL–harboring conjugative plasmids identified in multi-drug resistant Escherichia coli isolated from food-producing animals and healthy humans

(2013) Juan Wang et al.   Frontiers in Microbiology

Diverse Sequence Types of Klebsiella pneumoniae Contribute to the Dissemination ofblaNDM-1in India, Sweden, and the United Kingdom

(2012) Christian G. Giske 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

Susceptibility of different phases of biofilm of Klebsiella pneumoniae to three different antibiotics

(2012) Saloni Singla et al.   JOURNAL OF ANTIBIOTICS

Contribution of OqxAB efflux pumps to quinolone resistance in extended-spectrum- -lactamase-producing Klebsiella pneumoniae

(2012) J. M. Rodriguez-Martinez et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

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

Nosocomial Clustering of NDM-1-Producing Klebsiella pneumoniae Sequence Type 340 Strains in Four Patients at a South Korean Tertiary Care Hospital

(2012) M.-N. Kim et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Klebsiella pneumoniae susceptibility to biocides and its association with cepA, qacΔE and qacE efflux pump genes and antibiotic resistance

(2012) A. Abuzaid et al.   JOURNAL OF HOSPITAL INFECTION

Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

(2012) Timothy J. Johnson et al.   PLASMID

Interaction of Lipocalin 2, Transferrin, and Siderophores Determines the Replicative Niche of Klebsiella pneumoniae during Pneumonia

(2012) M. A. Bachman et al.   mBio

Treatment of Klebsiella Pneumoniae Carbapenemase (KPC) infections: a review of published case series and case reports

(2012) Grace C Lee et al.   Annals of Clinical Microbiology and Antimicrobials

Nosocomial Outbreak of VIM-1-Producing Klebsiella pneumoniae Isolates of Multilocus Sequence Type 15: Molecular Basis, Clinical Risk Factors, and Outcome

(2011) Isabel Sánchez-Romero et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

An update of the evolving epidemic of blaKPC-2-carrying Klebsiella pneumoniae in Greece (2009-10)

(2011) P. Giakkoupi et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Characterization of plasmids encoding extended-spectrum  -lactamases and their addiction systems circulating among Escherichia coli clinical isolates in the UK

(2011) M. Doumith et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Emergence of Klebsiella pneumoniae Carbapenemase-Producing Bacteria

(2011) Ryan S. Arnold et al.   SOUTHERN MEDICAL JOURNAL

Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid

(2011) Kathryn E. Holt et al.   PLoS Neglected Tropical Diseases

Resistance Plasmid Families in Enterobacteriaceae

(2009) A. Carattoli   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Identification of a Conserved Chromosomal Region Encoding Klebsiella pneumoniae Type 1 and Type 3 Fimbriae and Assessment of the Role of Fimbriae in Pathogenicity

(2009) C. Struve et al.   INFECTION AND IMMUNITY

Fluorometric determination of ethidium bromide efflux kinetics in Escherichia coli

(2009) Laura Paixão et al.   Journal of Biological Engineering

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

Detection and molecular characterisation of plasmidic AmpC β-lactamases in Klebsiella pneumoniae isolates from a tertiary-care hospital in Dublin, Ireland

(2008) C. Roche et al.   CLINICAL MICROBIOLOGY AND INFECTION

Characterization of Klebsiella pneumoniae Type 1 Fimbriae by Detection of Phase Variation during Colonization and Infection and Impact on Virulence

(2008) C. Struve et al.   INFECTION AND IMMUNITY

Expansion and countrywide dissemination of ST11, ST15 and ST147 ciprofloxacin-resistant CTX-M-15-type  -lactamase-producing Klebsiella pneumoniae epidemic clones in Hungary in 2005--the new 'MRSAs'?

(2008) I. Damjanova et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY