Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

A Real-Time PCR-Based Semi-Quantitative Breakpoint to Aid in Molecular Identification of Urinary Tract Infections

(2014) Wendy L. J. Hansen et al.   PLoS One

Frequency and antimicrobial resistance patterns of bacteria implicated in community urinary tract infections: a ten-year surveillance study (2000–2009)

(2013) Inês Linhares et al.   BMC INFECTIOUS DISEASES

Abrupt Emergence of a Single Dominant Multidrug-Resistant Strain of Escherichia coli

(2013) James R. Johnson et al.   JOURNAL OF INFECTIOUS DISEASES

Human Gut Microbiota Changes Reveal the Progression of Glucose Intolerance

(2013) Xiuying Zhang et al.   PLoS One

Positively selected FimH residues enhance virulence during urinary tract infection by altering FimH conformation

(2013) D. J. Schwartz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response

(2013) Nicolas Dreux et al.   PLoS Pathogens

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults

(2013) Debbie A. Lewis et al.   Frontiers in Cellular and Infection Microbiology

High-Resolution Two-Locus Clonal Typing of Extraintestinal Pathogenic Escherichia coli

(2012) Scott J. Weissman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing

(2012) Daniel D Rhoads et al.   BMC INFECTIOUS DISEASES

Alterations of microbiota in urine from women with interstitial cystitis

(2012) Huma Siddiqui et al.   BMC MICROBIOLOGY

Role of Homologous Recombination in Adaptive Diversification of Extraintestinal Escherichia coli

(2012) Sandip Paul et al.   JOURNAL OF BACTERIOLOGY

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

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

Culture-Dependent and -Independent Investigations of Microbial Diversity on Urinary Catheters

(2012) Y. Xu et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evidence of Uncultivated Bacteria in the Adult Female Bladder

(2012) A. J. Wolfe et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury

(2012) Derrick E Fouts et al.   Journal of Translational Medicine

Uncomplicated Urinary Tract Infection

(2012) Thomas M. Hooton   NEW ENGLAND JOURNAL OF MEDICINE

Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples

(2012) Dana Willner et al.   PLoS One

Rapid Discrimination of Gram-Positive and Gram-Negative Bacteria in Liquid Samples by Using NaOH-Sodium Dodecyl Sulfate Solution and Flow Cytometry

(2012) Atsushi Wada et al.   PLoS One

Kinetics of Uropathogenic Escherichia coli Metapopulation Movement during Urinary Tract Infection

(2012) M. S. Walters et al.   mBio

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

(2011) Huma Siddiqui et al.   BMC MICROBIOLOGY

amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

(2011) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Population Dynamics and Niche Distribution of Uropathogenic Escherichia coli during Acute and Chronic Urinary Tract Infection

(2011) Drew J. Schwartz et al.   INFECTION AND IMMUNITY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Core and Panmetabolism in Escherichia coli

(2011) G. Vieira et al.   JOURNAL OF BACTERIOLOGY

Actinobaculum Bacteremia: a Report of 12 Cases

(2011) E. Gomez et al.   JOURNAL OF CLINICAL MICROBIOLOGY

True Microbiota Involved in Chronic Lung Infection of Cystic Fibrosis Patients Found by Culturing and 16S rRNA Gene Analysis

(2011) V. B. Rudkjobing et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens

(2011) Qunfeng Dong et al.   PLoS One

Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog

(2011) Nardy Kip et al.   Environmental Microbiology Reports

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Structural Basis for Mechanical Force Regulation of the Adhesin FimH via Finger Trap-like β Sheet Twisting

(2010) Isolde Le Trong et al.   CELL

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection

(2010) David E. Nelson et al.   PLoS One

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Variable antibiotic susceptibility in populations of Pseudomonas aeruginosa infecting patients with bronchiectasis

(2009) M. I. Gillham et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Use of fimH Single-Nucleotide Polymorphisms for Strain Typing of Clinical Isolates of Escherichia coli for Epidemiologic Investigation

(2009) R. C. S. Dias et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Positive selection identifies an in vivo role for FimH during urinary tract infection in addition to mannose binding

(2009) Swaine L. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Hidden pathogens uncovered: metagenomic analysis of urinary tract infections

(2008) C. Imirzalioglu et al.   ANDROLOGIA

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

FimH Forms Catch Bonds That Are Enhanced by Mechanical Force Due to Allosteric Regulation

(2008) Olga Yakovenko et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Adaptive mutations in the signal peptide of the type 1 fimbrial adhesin of uropathogenic Escherichia coli

(2008) L. S. Ronald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA