Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genomics for molecular epidemiology and detecting transmission of carbapenemase-producing Enterobacterales in Victoria, Australia, 2012-2016

(2019) Norelle L. Sherry et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterization of Extensively Drug-Resistant or Pandrug-Resistant Sequence Type 147 and 101 OXA-48-Producing Klebsiella pneumoniae Causing Bloodstream Infections in Patients in an Intensive Care Unit

(2018) Kalliope Avgoulea et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Novel class 1 integron (In 1390 ) harboring bla GES-5 in a Morganella morganii strain recovered from a remote community

(2018) Quézia Moura et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

(2018) Francesc Coll et al.   NATURE GENETICS

Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

(2018) Laura Becker et al.   Frontiers in Microbiology

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

Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective

(2018) Insha Sultan et al.   Frontiers in Microbiology

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

(2018) Kelly L Wyres et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Risk factors for KPC-producing Enterobacteriaceae acquisition and infection in a healthcare setting with possible local transmission: a case–control study

(2017) K.M. Cronin et al.   JOURNAL OF HOSPITAL INFECTION

VIM-1, VIM-2, and GES-5 Carbapenemases Among Pseudomonas aeruginosa Isolates at a Tertiary Hospital in Istanbul, Turkey

(2017) Gülşah Malkoçoğlu et al.   Microbial Drug Resistance

First Detection of GES-5 Carbapenemase-Producing Acinetobacter baumannii Isolate

(2017) Mohamed H. Al-Agamy et al.   Microbial Drug Resistance

PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

(2016) Marta Nascimento et al.   BIOINFORMATICS

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

Outbreak of colonization by carbapenemase-producing Klebsiella pneumoniae in a neonatal intensive care unit: Investigation, control measures and assessment

(2015) Jiong Zhou et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Characterization of pKP-M1144, a Novel ColE1-Like Plasmid Encoding IMP-8, GES-5, and BEL-1 β-Lactamases, from a Klebsiella pneumoniae Sequence Type 252 Isolate

(2015) Costas C. Papagiannitsis et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Predominance of KPC-3 in a Survey for Carbapenemase-Producing Enterobacteriaceae in Portugal

(2015) Vera Manageiro et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-Genome Sequencing in Outbreak Analysis

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

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

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

GES-5 among theβ-lactamases detected in ubiquitous bacteria isolated from aquatic environment samples

(2013) Vera Manageiro et al.   FEMS MICROBIOLOGY LETTERS

Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria

(2012) Wei-Hua Zhao et al.   CRITICAL REVIEWS IN MICROBIOLOGY

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

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

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

(2010) Annemieke Smet et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Changes in aac(6')-Ib-cr Prevalence and Fluoroquinolone Resistance in Nosocomial Isolates of Escherichia coli Collected from 1991 through 2005

(2008) G. Warburg et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

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

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Genetic support of extended-spectrum β-lactamases

(2008) L. Poirel et al.   CLINICAL MICROBIOLOGY AND INFECTION

Evaluation of Boronic Acid Disk Tests for Differentiating KPC-Possessing Klebsiella pneumoniae Isolates in the Clinical Laboratory

(2008) A. Tsakris et al.   JOURNAL OF CLINICAL MICROBIOLOGY