Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

Homologous Recombination within Large Chromosomal Regions Facilitates Acquisition of β-Lactam and Vancomycin Resistance in Enterococcus faecium

(2016) Mónica García-Solache et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

plasmidSPAdes: assembling plasmids from whole genome sequencing data

(2016) Dmitry Antipov et al.   BIOINFORMATICS

Chromosome conformation capture technologies and their impact in understanding genome function

(2016) Satish Sati et al.   CHROMOSOMA

Bacterial chromatin: converging views at different scales

(2016) Remus T Dame et al.   CURRENT OPINION IN CELL BIOLOGY

Extensive Mobilome-Driven Genome Diversification in Mouse Gut-AssociatedBacteroides vulgatusmpk

(2016) Anna Lange et al.   Genome Biology and Evolution

The evolutionary dynamics of integrons in changing environments

(2016) Jan Engelstädter et al.   ISME Journal

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater

(2016) William Calero-Cáceres et al.   WATER RESEARCH

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer

(2016) Carla Novais et al.   Frontiers in Microbiology

Carriage of Extended-Spectrum Beta-Lactamase-Plasmids Does Not Reduce Fitness but Enhances Virulence in Some Strains of Pandemic E. coli Lineages

(2016) Katharina Schaufler et al.   Frontiers in Microbiology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Is El Niño a long-distance corridor for waterborne disease?

(2016) Jaime Martinez-Urtaza et al.   Nature Microbiology

Bacterial Chromosome Organization and Segregation

(2015) Anjana Badrinarayanan et al.   Annual Review of Cell and Developmental Biology

blaCTX-M-1/9/1Hybrid Genes May Have Been Generated fromblaCTX-M-15on an IncI2 Plasmid

(2015) Lanping Liu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Abundance of Antibiotic Resistance Genes in Bacteriophage following Soil Fertilization with Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction

(2015) Joseph Ross et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Prevalence and characterization of hybrid blaCTX-M among Escherichia coli isolates from livestock and other animals

(2015) Pak-Leung Ho et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

(2015) Jean-François Flot et al.   FEBS LETTERS

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

(2015) Sarah J Spencer et al.   ISME Journal

Within-host diversity of MRSA antimicrobial resistances

(2015) Kinga I. Stanczak-Mrozek et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

(2015) Mark de Been et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Prioritizing risks of antibiotic resistance genes in all metagenomes

(2015) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Transfer of antibiotic-resistance genes via phage-related mobile elements

(2015) Maryury Brown-Jaque et al.   PLASMID

Limited dissemination of the wastewater treatment plant core resistome

(2015) Christian Munck et al.   Nature Communications

Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants

(2015) An-Dong Li et al.   Frontiers in Microbiology

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells

(2015) Manu V. Tamminen et al.   Frontiers in Microbiology

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

(2015) Holly B Bratcher et al.   BMC GENOMICS

Rapid High Resolution Genotyping of Francisella tularensis by Whole Genome Sequence Comparison of Annotated Genes (“MLST+”)

(2015) Markus H. Antwerpen et al.   PLoS One

Metabolic Compensation of Fitness Costs Associated with Overexpression of the Multidrug Efflux Pump MexEF-OprN in Pseudomonas aeruginosa

(2014) Jorge Olivares et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013

(2014) D. Schmid et al.   CLINICAL MICROBIOLOGY AND INFECTION

Sludge As a Potential Important Source of Antibiotic Resistance Genes in Both the Bacterial and Bacteriophage Fractions

(2014) William Calero-Cáceres et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

(2014) Romain Guérillot et al.   Genome Biology and Evolution

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

(2014) Molly K Gibson et al.   ISME Journal

CTX-M-137, a hybrid of CTX-M-14-like and CTX-M-15-like β-lactamases identified in an Escherichia coli clinical isolate

(2014) Guo-Bao Tian et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes

(2014) S. R. Leopold et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

(2014) T. A. Kohl et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

An Improved Method for Including Upper Size Range Plasmids in Metamobilomes

(2014) Anders Norman et al.   PLoS One

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

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

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

(2014) Mark de Been et al.   PLoS Genetics

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Proliferation and significance of clinically relevant β-lactamases

(2013) Karen Bush   Annals of the New York Academy of Sciences

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples

(2013) Pablo Quirós et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparative Population Analysis of Klebsiella pneumoniae Strains with Extended-Spectrum β-Lactamases Colonizing Patients in Rehabilitation Centers in Four Countries

(2013) A. Baraniak et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Novel CTX-M-116 β-Lactamase Gene Discovered in Proteus mirabilis Is Composed of Parts of the CTX-M-22 and CTX-M-23 Genes

(2013) N. Fursova et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacteriophages as a reservoir of extended-spectrum β -lactamase and fluoroquinolone resistance genes in the environment

(2013) E. Marti et al.   CLINICAL MICROBIOLOGY AND INFECTION

Potential impact of environmental bacteriophages in spreading antibiotic resistance genes

(2013) Maite Muniesa et al.   Future Microbiology

The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome

(2013) Alan McNally et al.   Genome Biology and Evolution

Staphylococcus aureus genomics and the impact of horizontal gene transfer

(2013) Jodi A. Lindsay   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

(2013) Tanya Golubchik et al.   PLoS One

Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

(2013) F. Lebreton et al.   mBio

Antibiotic resistance shaping multi-level population biology of bacteria

(2013) Fernando Baquero et al.   Frontiers in Microbiology

The intrinsic resistome of bacterial pathogens

(2013) Jorge Olivares et al.   Frontiers in Microbiology

blaNDM-1Is a Chimera Likely Constructed in Acinetobacter baumannii

(2012) M. A. Toleman et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Yersinia–flea interactions and the evolution of the arthropod-borne transmission route of plague

(2012) Iman Chouikha et al.   CURRENT OPINION IN MICROBIOLOGY

Overproduction of the multidrug efflux pump MexEF-OprN does not impair Pseudomonas aeruginosa fitness in competition tests, but produces specific changes in bacterial regulatory networks

(2012) Jorge Olivares et al.   ENVIRONMENTAL MICROBIOLOGY

Hierarchical clustering of genetic diversity associated to different levels of mutation and recombination in Escherichia coli: A study based on Mexican isolates

(2012) Andrea González-González et al.   INFECTION GENETICS AND EVOLUTION

Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus

(2012) A. Zorzet et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A tet(S/M) hybrid from CTn6000 and CTn916 recombination

(2012) C. Novais et al.   MICROBIOLOGY-SGM

Defining the human microbiome

(2012) Luke K Ursell et al.   NUTRITION REVIEWS

A Degenerate Primer MOB Typing (DPMT) Method to Classify Gamma-Proteobacterial Plasmids in Clinical and Environmental Settings

(2012) Andrés Alvarado et al.   PLoS One

Chimeric β-Lactamases: Global Conservation of Parental Function and Fast Time-Scale Dynamics with Increased Slow Motions

(2012) Christopher M. Clouthier et al.   PLoS One

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

(2012) E. Bapteste 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

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

(2012) R. J. L. Willems et al.   mBio

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

(2011) Marta Colomer-Lluch et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Country-to-Country Transfer of Patients and the Risk of Multi-Resistant Bacterial Infection

(2011) B. A. Rogers et al.   CLINICAL INFECTIOUS DISEASES

Beyond serial passages: new methods for predicting the emergence of resistance to novel antibiotics

(2011) José Luis Martínez et al.   CURRENT OPINION IN PHARMACOLOGY

Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA)

(2011) Philip J. Warburton et al.   FEMS MICROBIOLOGY ECOLOGY

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Environmental Samples

(2011) Marta Colomer-Lluch et al.   PLoS One

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge

(2011) Tong Zhang et al.   PLoS One

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

Ecological and Temporal Constraints in the Evolution of Bacterial Genomes

(2011) Luis Boto et al.   Genes

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

(2010) Brian V Jones et al.   BMC GENOMICS

The antibiotic resistome

(2010) Gerard D Wright   Expert Opinion on Drug Discovery

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Compensatory gene amplification restores fitness after inter-species gene replacements

(2010) Peter A. Lind et al.   MOLECULAR MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

(2010) Giovanna Morelli et al.   NATURE GENETICS

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits

(2010) J. M. Manson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic resistance genes in water environment

(2009) Xu-Xiang Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Towards an ecological approach to antibiotics and antibiotic resistance genes

(2009) A. Fajardo et al.   CLINICAL MICROBIOLOGY AND INFECTION

Molecular Darwinian Evolution of Virulence in Yersinia pestis

(2009) D. Zhou et al.   INFECTION AND IMMUNITY

Conjugative plasmids: vessels of the communal gene pool

(2009) A. Norman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ecology and evolution of antibiotic resistance

(2009) F. Baquero et al.   Environmental Microbiology Reports

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

(2009) Jing Tang et al.   PLoS Computational Biology

Role of Intraspecies Recombination in the Spread of Pathogenicity Islands within the Escherichia coli Species

(2009) Sören Schubert et al.   PLoS Pathogens

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

The Neglected Intrinsic Resistome of Bacterial Pathogens

(2008) Alicia Fajardo et al.   PLoS One