Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection

Gut Microbiota Dysbiosis and Diarrhea in Kidney Transplant Recipients

(2018) John Richard Lee et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Intestinal microbiome as a risk factor for urinary tract infections in children

(2018) Niko Paalanne et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench

(2018) Wei-Kai Wu et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

The challenge of urinary tract infections in renal transplant recipients

(2018) Ian Hollyer et al.   Transplant Infectious Disease

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

(2018) Philip Burnham et al.   Nature Communications

Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant

(2018) Ying Taur et al.   Science Translational Medicine

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Community profiling of the urinary microbiota: considerations for low-biomass samples

(2018) Lisa Karstens et al.   Nature Reviews Urology

Genetic relatedness of the Escherichia coli fecal population and strains causing urinary tract infection in the same host

(2018) Maryam Bahadori et al.   MicrobiologyOpen

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Association between virulence profile, biofilm formation and phylogenetic groups of Escherichia coli causing urinary tract infection and the commensal gut microbiota: A comparative analysis

(2017) Zahra Hashemizadeh et al.   MICROBIAL PATHOGENESIS

UroPathogenic Escherichia coli (UPEC) Infections: Virulence Factors, Bladder Responses, Antibiotic, and Non-antibiotic Antimicrobial Strategies

(2017) Maria E. Terlizzi et al.   Frontiers in Microbiology

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection

(2016) Emmanuel Montassier et al.   Genome Medicine

Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

(2016) Philip Burnham et al.   Scientific Reports

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Urinary tract infections: epidemiology, mechanisms of infection and treatment options

(2015) Ana L. Flores-Mireles et al.   NATURE REVIEWS MICROBIOLOGY

Evaluation of Infectious Complications in the First Year After Kidney Transplantation

(2015) A. Yalci et al.   TRANSPLANTATION PROCEEDINGS

Loss of Vancomycin-Resistant Enterococcus Fecal Dominance in an Organ Transplant Patient With Clostridium difficile Colitis After Fecal Microbiota Transplant

(2015) Joshua Stripling et al.   Open Forum Infectious Diseases

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Impact of urinary tract infection on allograft function after kidney transplantation

(2014) Ella J. Ariza-Heredia et al.   CLINICAL TRANSPLANTATION

Urinary Tract Infection Syndromes

(2013) Betsy Foxman   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Independent Risk Factors for Urinary Tract Infection and for Subsequent Bacteremia or Acute Cellular Rejection

(2013) John R. Lee et al.   TRANSPLANTATION

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic screening and treatment of asymptomatic bacteriuria in renal transplant recipients

(2010) Silvana Fiorante et al.   KIDNEY INTERNATIONAL