Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia

Infectious Diseases Society of America 2022 Guidance on the Treatment of Extended-Spectrum β-lactamase Producing Enterobacterales (ESBL-E), Carbapenem-Resistant Enterobacterales (CRE), and Pseudomonas aeruginosa with Difficult-to-Treat Resistance (DTR-P. aeruginosa)

(2022) Pranita D. Tamma et al.   CLINICAL INFECTIOUS DISEASES

Molecular epidemiology, natural history and long-term outcomes of multi-drug resistant Enterobacterales colonization and infections among solid organ transplant recipients

(2021) M Hong Nguyen et al.   CLINICAL INFECTIOUS DISEASES

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

(2021) Margaret M. C. Lam et al.   Nature Communications

Bacterial evolution during human infection: Adapt and live or adapt and die

(2021) Matthew J. Culyba et al.   PLoS Pathogens

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin

(2020) Wei Zhou et al.   CELL

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

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

Evolution of vancomycin-resistantEnterococcus faeciumduring colonization and infection in immunocompromised pediatric patients

(2020) Gayatri Shankar Chilambi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR/Cas9-mediated carbapenemase genes and plasmids curing in carbapenem-resistant Enterobacteriaceae

(2020) Mingju Hao et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients

(2020) M. Hong Nguyen et al.   Microbial Genomics

Definitions and guidelines for research on antibiotic persistence

(2019) Nathalie Q. Balaban et al.   NATURE REVIEWS MICROBIOLOGY

Heteroresistance: A cause of unexplained antibiotic treatment failure?

(2019) Victor I. Band et al.   PLoS Pathogens

Drug Penetration Gradients Associated with Acquired Drug Resistance in Tuberculosis Patients

(2018) Keertan Dheda et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

A 4.5-Year Within-Patient Evolution of a Colistin-Resistant Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae Sequence Type 258

(2018) Agnès B Jousset et al.   CLINICAL INFECTIOUS DISEASES

Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis

(2018) Evelina Tacconelli et al.   LANCET INFECTIOUS DISEASES

Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae

(2018) Rebekah M. Martin et al.   Frontiers in Cellular and Infection Microbiology

Precise and efficient genome editing in Klebsiella pneumoniae using CRISPR-Cas9 and CRISPR-assisted cytidine deaminase

(2018) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya

(2018) J Michael Miller et al.   CLINICAL INFECTIOUS DISEASES

The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort

(2018) Matthew J. Dorman et al.   mBio

Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients

(2017) Danesh Moradigaravand et al.   Genome Medicine

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

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

Severe infections emerge from commensal bacteria by adaptive evolution

(2017) Bernadette C Young et al.   eLife

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Multiple Variants of Klebsiella pneumoniae Producing Carbapenemase in One Patient

(2016) Michael R. Mulvey et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of a capsular variant and characterization of capsular acetylation in Klebsiella pneumoniae PLA-associated type K57

(2016) Chun-Ru Hsu et al.   Scientific Reports

Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae

(2016) Rebekah M. Martin et al.   mSphere

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

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

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

(2015) Gavin K. Paterson et al.   Nature Communications

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Progressive genomic convergence of twoHelicobacter pyloristrains during mixed infection of a patient with chronic gastritis

(2014) Qizhi Cao et al.   GUT

Whole-Genome Sequencing of Burkholderia pseudomallei Isolates from an Unusual Melioidosis Case Identifies a Polyclonal Infection with the Same Multilocus Sequence Type

(2014) Erin P. Price et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Carbapenem-Resistant Klebsiella pneumoniae Exhibit Variability in Capsular Polysaccharide and Capsule Associated Virulence Traits

(2014) Elizabeth Diago-Navarro et al.   JOURNAL OF INFECTIOUS DISEASES

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

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

Epidemiology and Molecular Characterization of Bacteremia Due to Carbapenem-ResistantKlebsiella pneumoniaein Transplant Recipients

(2013) C. J. Clancy et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Characterization of Porin Expression in Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae Identifies Isolates Most Susceptible to the Combination of Colistin and Carbapenems

(2013) Jae H. Hong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Mutations of theompK36Porin Gene and Promoter Impact Responses of Sequence Type 258, KPC-2-Producing Klebsiella pneumoniae Strains to Doripenem and Doripenem-Colistin

(2013) Cornelius J. Clancy et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

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

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

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

Genomic Variation among Contemporary Pseudomonas aeruginosa Isolates from Chronically Infected Cystic Fibrosis Patients

(2012) Jade C. S. Chung et al.   JOURNAL OF BACTERIOLOGY

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

(2011) Benjamin P. Howden et al.   PLoS Pathogens

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

Bad Bugs, No Drugs: No ESKAPE! An Update from the Infectious Diseases Society of America

(2008) Helen W. Boucher et al.   CLINICAL INFECTIOUS DISEASES