Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

Surveillance for control of antimicrobial resistance

(2018) Evelina Tacconelli et al.   LANCET INFECTIOUS DISEASES

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism

(2018) Amir Zarrinpar et al.   Nature Communications

Antimicrobial consumption and resistance in adult hospital inpatients in 53 countries: results of an internet-based global point prevalence survey

(2018) Ann Versporten et al.   Lancet Global Health

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects

(2017) Elena Buelow et al.   Microbiome

Colonization with third-generation cephalosporin-resistant Enterobacteriaceae on hospital admission: prevalence and risk factors

(2016) A. Hamprecht et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Resistance Mechanisms, Epidemiology, and Approaches to Screening for Vancomycin-Resistant Enterococcus in the Health Care Setting

(2016) Matthew L. Faron et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Translational metagenomics and the human resistome: confronting the menace of the new millennium

(2016) Matthias Willmann et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Microbial diversity in individuals and their household contacts following typical antibiotic courses

(2016) Shira R. Abeles et al.   Microbiome

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

Mechanisms of drug resistance: quinolone resistance

(2015) David C. Hooper et al.   Annals of the New York Academy of Sciences

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics

(2015) Matthias Willmann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Proton pump inhibitors affect the gut microbiome

(2015) Floris Imhann et al.   GUT

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation

(2014) Y. Taur et al.   BLOOD

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

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

Integrons: Past, Present, and Future

(2014) Michael R. Gillings   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success

(2014) Liam S. Redgrave et al.   TRENDS IN MICROBIOLOGY

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

(2014) M. J. Coyne et al.   mBio

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2011) Chris S. Smillie et al.   NATURE

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Chemotherapy Treatment in Pediatric Patients with Acute Myeloid Leukemia Receiving Antimicrobial Prophylaxis Leads to a Relative Increase of Colonization with Potentially Pathogenic Bacteria in the Gut

(2009) Michel J. van Vliet et al.   CLINICAL INFECTIOUS DISEASES