Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

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

(2022) Christopher JL Murray et al.   LANCET

Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections

(2022) Mathew Stracy et al.   SCIENCE

Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

(2021) Beneditta Suwono et al.   PLoS One

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals

(2021) Sergio Arredondo-Alonso et al.   Genome Medicine

A framework for identifying the recent origins of mobile antibiotic resistance genes

(2021) Stefan Ebmeyer et al.   Communications Biology

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

(2021) Amy Langdon et al.   Genome Medicine

Characterization of the human skin resistome and identification of two microbiota cutotypes

(2021) Zhiming Li et al.   Microbiome

Elevated rates of horizontal gene transfer in the industrialized human microbiome

(2021) Mathieu Groussin et al.   CELL

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

(2021) Xuanji Li et al.   Cell Host & Microbe

Functional and structural characterization of a two-MAb cocktail for delayed treatment of enterovirus D68 infections

(2021) Chao Zhang et al.   Nature Communications

Forecasting the dissemination of antibiotic resistance genes across bacterial genomes

(2021) Mostafa M. H. Ellabaan et al.   Nature Communications

Safety assessment of Lactiplantibacillus (formerly Lactobacillus) plantarum Q180

(2021) Yoo Jin Kwon et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

(2021) Alaric W. D’Souza et al.   Genome Medicine

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner

(2021) Emmanuel Montassier et al.   Nature Microbiology

Functions predict horizontal gene transfer and the emergence of antibiotic resistance

(2021) Hao Zhou et al.   Science Advances

Abundance and diversity of resistomes differ between healthy human oral cavities and gut

(2020) Victoria R. Carr et al.   Nature Communications

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

Potential Elimination of Human Gut Resistome by Exploiting the Benefits of Functional Foods

(2020) Christina Tsigalou et al.   Frontiers in Microbiology

Revealing antibiotic resistance in therapeutic and dietary probiotic supplements

(2020) Joseph Selvin et al.   Journal of Global Antimicrobial Resistance

Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage

(2020) Jiachao Zhang et al.   Gut Microbes

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study

(2020) Ronan M. Doyle et al.   Microbial Genomics

Safety assessment of the candidate oral probiotic Lactobacillus crispatus YIT 12319: Analysis of antibiotic resistance and virulence-associated genes

(2020) Tomohiko Terai et al.   FOOD AND CHEMICAL TOXICOLOGY

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1

(2020) Kazeem Adekunle Alayande et al.   PLoS One

Genomic and Proteomic Characterization of the Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain

(2020) Daniel Jaén-Luchoro et al.   Microorganisms

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

The structural basis of promiscuity in small multidrug resistance transporters

(2020) Ali A. Kermani et al.   Nature Communications

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

(2019) Katariina M. M. Pärnänen et al.   Science Advances

Poultry as a vector for emerging multidrug resistant Enterococcus spp.: First report of vancomycin (van) and the chloramphenicol–florfenicol (cat-fex-cfr) resistance genes from pigeon and duck faeces

(2019) Kamelia M. Osman et al.   MICROBIAL PATHOGENESIS

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

(2019) G. A. Arango-Argoty et al.   Microbiome

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

(2019) Matthias Willmann et al.   BMC BIOLOGY

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut

(2019) Erik Bakkeren et al.   NATURE

Probiotic treatment induced change of inflammation related metabolites in IBS-D patients/double-blind, randomized, placebo-controlled trial

(2019) Jinjoo Kim et al.   FOOD SCIENCE AND BIOTECHNOLOGY

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation

(2018) Melise Chaves Silveira et al.   Evolutionary Bioinformatics

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

(2018) Katariina Pärnänen et al.   Nature Communications

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults

(2018) Chad W. MacPherson et al.   Scientific Reports

Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants

(2018) Eirin Esaiassen et al.   Frontiers in Pediatrics

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study

(2016) Elisa Salvetti et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

(2016) María X. Maldonado-Gómez et al.   Cell Host & Microbe

Reduction of Antibiotic Resistance Genes in Intestinal Microbiota of Patients With RecurrentClostridium difficileInfection After Fecal Microbiota Transplantation

(2016) Hanne Jouhten et al.   CLINICAL INFECTIOUS DISEASES

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

(2016) Braden Millan et al.   CLINICAL INFECTIOUS DISEASES

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children

(2016) Guojun Wu et al.   Scientific Reports

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

In Vivo Horizontal Gene Transfer of the Carbapenemase OXA-48 During a Nosocomial Outbreak

(2015) S. Gottig et al.   CLINICAL INFECTIOUS DISEASES

Antibiotic resistance genes in the environment: prioritizing risks

(2015) Johan Bengtsson-Palme et al.   NATURE REVIEWS MICROBIOLOGY

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library

(2014) Fiona Fouhy et al.   PLoS One

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

(2014) M. J. Coyne et al.   mBio

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters

(2014) George Diallinas   Frontiers in Pharmacology

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution

(2013) Bärbel Stecher et al.   NATURE REVIEWS MICROBIOLOGY

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

(2013) Aimée M. Moore et al.   PLoS One

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion

(2012) Gong Cheng et al.   FEMS MICROBIOLOGY LETTERS

Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora

(2012) L. Cremet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

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

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

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

(2011) Chris S. Smillie et al.   NATURE

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Both Oral Metronidazole and Oral Vancomycin Promote Persistent Overgrowth of Vancomycin-Resistant Enterococci during Treatment of Clostridium difficile-Associated Disease

(2008) W. N. Al-Nassir et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine

(2008) M. Trobos et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY