Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae

A Global Perspective on the Convergence of Hypervirulence and Carbapenem-Resistance in Klebsiella pneumoniae

(2021) Peng Lan et al.   Journal of Global Antimicrobial Resistance

Cell envelope defects of different capsule‐null mutants in K1 hypervirulent Klebsiella pneumoniae can affect bacterial pathogenesis

(2020) Yi Han Tan et al.   MOLECULAR MICROBIOLOGY

Population genomics of Klebsiella pneumoniae

(2020) Kelly L. Wyres et al.   NATURE REVIEWS MICROBIOLOGY

Phage Resistance in Multidrug-Resistant Klebsiella pneumoniae ST258 Evolves via Diverse Mutations That Culminate in Impaired Adsorption

(2020) Shayla Hesse et al.   mBio

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

(2020) Kathryn E. Holt et al.   ISME Journal

Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae

(2020) Christoph M. Ernst et al.   NATURE MEDICINE

A Frameshift Mutation in wcaJ Associated with Phage Resistance in Klebsiella pneumoniae

(2020) Demeng Tan et al.   Microorganisms

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

(2020) Jorge A. M. de Sousa et al.   ISME Journal

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

(2020) Marie Touchon et al.   PLoS Genetics

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15

(2019) Margaret M C Lam et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

(2019) Sohta A Ishikawa et al.   MOLECULAR BIOLOGY AND EVOLUTION

A conjugative plasmid that augments virulence in Klebsiella pneumoniae

(2019) Xuemei Yang et al.   Nature Microbiology

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

(2019) Li-Gen Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeting the Sugary Armor of Klebsiella Species

(2019) L. Ponoop Prasad Patro et al.   Frontiers in Cellular and Infection Microbiology

K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917

(2019) Manonmani Soundararajan et al.   Frontiers in Microbiology

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

(2018) Rafał J. Mostowy et al.   TRENDS IN MICROBIOLOGY

Diversity and distribution of Klebsiella capsules in Escherichia coli

(2018) Buddhie S. Nanayakkara et al.   Environmental Microbiology Reports

Genetic exchanges are more frequent in bacteria encoding capsules

(2018) Olaya Rendueles et al.   PLoS Genetics

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens

(2017) Olaya Rendueles et al.   PLoS Pathogens

Two T7-like Bacteriophages, K5-2 and K5-4, Each Encodes Two Capsule Depolymerases: Isolation and Functional Characterization

(2017) Pei-Fang Hsieh et al.   Scientific Reports

The Gene Transfer Agent RcGTA Contains Head Spikes Needed for Binding to the Rhodobacter capsulatus Polysaccharide Cell Capsule

(2016) Alexander B. Westbye et al.   JOURNAL OF MOLECULAR BIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258

(2015) Kelly L. Wyres et al.   Genome Biology and Evolution

Mechanisms of genome evolution of Streptococcus

(2015) Cheryl P. Andam et al.   INFECTION GENETICS AND EVOLUTION

Capsule Switching and Antimicrobial Resistance Acquired during Repeated Streptococcus pneumoniae Pneumonia Episodes

(2015) Bin Chang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genetic analysis of capsular polysaccharide synthesis gene clusters in 79 capsular types of Klebsiella spp

(2015) Yi-Jiun Pan et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

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

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nanomechanics measurements of live bacteria reveal a mechanism for bacterial cell protection: the polysaccharide capsule in Klebsiella is a responsive polymer hydrogel that adapts to osmotic stress

(2013) Huabin Wang et al.   Soft Matter

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quorum-sensing regulation of a capsular polysaccharide receptor for theRhodobacter capsulatusgene transfer agent (RcGTA)

(2012) Cedric A. Brimacombe et al.   MOLECULAR MICROBIOLOGY

Gene transfer agents: phage-like elements of genetic exchange

(2012) Andrew S. Lang et al.   NATURE REVIEWS MICROBIOLOGY

On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations

(2011) Xue Zhong et al.   JOURNAL OF THEORETICAL BIOLOGY

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery

(2010) L. Ferrieres et al.   JOURNAL OF BACTERIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Escherichia coli genes affecting recipient ability in plasmid conjugation: Are there any?

(2009) Daniel Pérez-Mendoza et al.   BMC GENOMICS

Restricting ciprofloxacin-induced resistant variant formation in biofilm of Klebsiella pneumoniae B5055 by complementary bacteriophage treatment

(2009) V. Verma et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Federal Funding for the Study of Antimicrobial Resistance in Nosocomial Pathogens: No ESKAPE

(2008) Louis B. Rice   JOURNAL OF INFECTIOUS DISEASES