Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement

Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis

(2022) Christopher JL Murray et al.   LANCET

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients

(2021) Diwakar Davar et al.   SCIENCE

Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

(2021) Blake G. Lindner et al.   WATER RESEARCH

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

(2021) Varun Aggarwala et al.   Nature Microbiology

Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota

(2020) Hiroko Nagao-Kitamoto et al.   NATURE MEDICINE

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation

(2020) Jonathan U. Peled et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reference Standardization for Quantification and Harmonization of Large-Scale Metabolomics

(2020) Ken H. Liu et al.   ANALYTICAL CHEMISTRY

Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective

(2020) Haggai Bar-Yoseph et al.   CLINICAL INFECTIOUS DISEASES

Shiga toxin-producing E. coli transmission via fecal microbiota transplant

(2020) Caroline Zellmer et al.   CLINICAL INFECTIOUS DISEASES

Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease

(2020) Lingjia Kong et al.   GASTROENTEROLOGY

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

(2020) Suryang Kwak et al.   Microbiome

National Estimates of Healthcare Costs Associated With Multidrug-Resistant Bacterial Infections Among Hospitalized Patients in the United States

(2020) Richard E Nelson et al.   CLINICAL INFECTIOUS DISEASES

The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli

(2019) Enrique Joffre et al.   Scientific Reports

Chlorhexidine versus routine bathing to prevent multidrug-resistant organisms and all-cause bloodstream infections in general medical and surgical units (ABATE Infection trial): a cluster-randomised trial

(2019) Susan S Huang et al.   LANCET

Intestinal Bile Acids Induce a Morphotype Switch in Vancomycin-Resistant Enterococcus that Facilitates Intestinal Colonization

(2019) Peter T. McKenney et al.   Cell Host & Microbe

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

The Role of Fecal Microbiota Transplantation in Reducing Intestinal Colonization With Antibiotic-Resistant Organisms: The Current Landscape and Future Directions

(2019) Michael H Woodworth et al.   Open Forum Infectious Diseases

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Incidence of Bloodstream Infections, Length of Hospital Stay, and Survival in Patients With Recurrent Clostridioides difficile Infection Treated With Fecal Microbiota Transplantation or Antibiotics

(2019) Gianluca Ianiro et al.   ANNALS OF INTERNAL MEDICINE

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2019) Matthew Magruder et al.   Nature Communications

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases

(2019) Manli Zou et al.   FEBS Open Bio

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

Temporal dynamics and risk factors for bloodstream infection with extended-spectrum β-lactamase-producing bacteria in previously colonized individuals: National population-based cohort study

(2018) Joakim Isendahl et al.   CLINICAL INFECTIOUS DISEASES

Costs and benefits of provocation in bacterial warfare

(2018) Diego Gonzalez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Fecal microbiota transplantation for the treatment of recurrent and severe Clostridium difficile infection in solid organ transplant recipients: A multicenter experience

(2018) Yao-Wen Cheng et al.   AMERICAN JOURNAL OF TRANSPLANTATION

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

(2018) Ying Taur et al.   Science Translational Medicine

Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification

(2018) Matthew T. Sorbara et al.   JOURNAL OF EXPERIMENTAL MEDICINE

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

imGLAD: accurate detection and quantification of target organisms in metagenomes

(2018) Juan C. Castro et al.   PeerJ

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection

(2017) Dina Kao et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

Notes from the Field: Pan-Resistant New Delhi Metallo-Beta-Lactamase-Producing Klebsiella pneumoniae — Washoe County, Nevada, 2016

(2017) Lei Chen et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Impact of Gut Colonization by Antibiotic-Resistant Bacteria on the Outcomes of Allogeneic Hematopoietic Stem Cell Transplantation: A Retrospective, Single-Center Study

(2016) Jaroslaw Bilinski et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With RecurrentClostridium difficileInfection

(2016) Braden Millan et al.   CLINICAL INFECTIOUS DISEASES

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With RecurrentClostridium difficileInfection

(2016) Christine H. Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

High-Resolution Metabolomics Assessment of Military Personnel

(2016) Ken H. Liu et al.   JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL MEDICINE

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Fecal Microbiota Transplantation for RefractoryClostridium difficileColitis in Solid Organ Transplant Recipients

(2014) R. J. Friedman-Moraco et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach

(2014) Tianwei Yu et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Prevention of Colonization and Infection by Klebsiella pneumoniae Carbapenemase-Producing Enterobacteriaceae in Long-term Acute-Care Hospitals

(2014) M. K. Hayden et al.   CLINICAL INFECTIOUS DISEASES

Effects of selective digestive decontamination (SDD) on the gut resistome

(2014) Elena Buelow et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Emergence of Colistin Resistance in Enterobacteriaceae after the Introduction of Selective Digestive Tract Decontamination in an Intensive Care Unit

(2013) Teysir Halaby et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data

(2013) Karan Uppal et al.   BMC BIOINFORMATICS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

apLCMS—adaptive processing of high-resolution LC/MS data

(2009) Tianwei Yu et al.   BIOINFORMATICS