Lateral gene transfer, bacterial genome evolution, and the Anthropocene

Architecture and Characteristics of Bacterial Nanotubes

(2016) Gyanendra P. Dubey et al.   DEVELOPMENTAL CELL

Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia

(2016) Xue-Mei Han et al.   ENVIRONMENTAL POLLUTION

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers

(2016) Lorenzo Proia et al.   ENVIRONMENTAL POLLUTION

Antibiotic concentration and antibiotic-resistant bacteria in two shallow urban lakes after stormwater event

(2016) Songhe Zhang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

In 2035, will all bacteria be multiresistant? Yes

(2016) George Dimopoulos et al.   INTENSIVE CARE MEDICINE

The evolutionary dynamics of integrons in changing environments

(2016) Jan Engelstädter et al.   ISME Journal

Antimicrobial resistance in wildlife

(2016) Marion Vittecoq et al.   JOURNAL OF APPLIED ECOLOGY

The SOS Response Master Regulator LexA Regulates the Gene Transfer Agent of Rhodobacter capsulatus and Represses Transcription of the Signal Transduction Protein CckA

(2016) Kevin S. Kuchinski et al.   JOURNAL OF BACTERIOLOGY

Co-selection of antibiotic and heavy metal resistance in freshwater bacteria

(2016) Andrea Di Cesare et al.   JOURNAL OF LIMNOLOGY

Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance

(2016) Felipe C Cabello et al.   LANCET INFECTIOUS DISEASES

Exploring the Role of Coliform Bacteria in Class 1 Integron Carriage and Biofilm Formation During Drinking Water Treatment

(2016) Anca Farkas et al.   MICROBIAL ECOLOGY

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms

(2016) Sara V. Lundström et al.   SCIENCE OF THE TOTAL ENVIRONMENT

An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance

(2016) Jekaterina Jutkina et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

(2016) Timothy A. Johnson et al.   mBio

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments

(2016) Remy Chait et al.   Nature Communications

Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates ofPseudomonas aeruginosa

(2016) Piklu Roy Chowdhury et al.   Open Biology

Antibiotics as a selective driver for conjugation dynamics

(2016) Allison J. Lopatkin et al.   Nature Microbiology

Horizontal Gene Flow in Managed Ecosystems

(2015) Cheryl P. Andam et al.   Annual Review of Ecology Evolution and Systematics

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

Differential Roles of Antimicrobials in the Acquisition of Drug Resistance through Activation of the SOS Response in Acinetobacter baumannii

(2015) Luis M. Jara et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Ancient horizontal gene transfer and the last common ancestors

(2015) Gregory P Fournier et al.   BMC EVOLUTIONARY BIOLOGY

Bacteriophage-mediated spread of bacterial virulence genes

(2015) José R Penadés et al.   CURRENT OPINION IN MICROBIOLOGY

Soil-borne reservoirs of antibiotic-resistant bacteria are established following therapeutic treatment of dairy calves

(2015) Jinxin Liu et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

(2015) Liping Ma et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial DNA records historical delivery of anthropogenic mercury

(2015) Alexandre J Poulain et al.   ISME Journal

Homologues of Genetic Transformation DNA Import Genes Are Required for Rhodobacter capsulatus Gene Transfer Agent Recipient Capability Regulated by the Response Regulator CtrA

(2015) Cedric A. Brimacombe et al.   JOURNAL OF BACTERIOLOGY

Bacterial antimicrobial metal ion resistance

(2015) Jon L. Hobman et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations

(2015) Stefan Helfrich et al.   MOLECULAR MICROBIOLOGY

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Tackling antibiotic resistance: the environmental framework

(2015) Thomas U. Berendonk et al.   NATURE REVIEWS MICROBIOLOGY

Metabolic cross-feeding via intercellular nanotubes among bacteria

(2015) Samay Pande et al.   Nature Communications

Antimicrobial-Induced DNA Damage and Genomic Instability in Microbial Pathogens

(2015) Rebecca S. Shapiro   PLoS Pathogens

Potential impacts of aquatic pollutants: sub-clinical antibiotic concentrations induce genome changes and promote antibiotic resistance

(2015) Louise Chow et al.   Frontiers in Microbiology

Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics

(2015) Michael Gillings et al.   Genes

A Role for Tn6029 in the Evolution of the Complex Antibiotic Resistance Gene Loci in Genomic Island 3 in Enteroaggregative Hemorrhagic Escherichia coli O104:H4

(2015) Piklu Roy Chowdhury et al.   PLoS One

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

(2014) Cristiane C. Thompson et al.   ARCHIVES OF MICROBIOLOGY

Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

(2014) Jelle Slager et al.   CELL

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

(2014) Michael R Gillings et al.   ISME Journal

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

(2014) Arun M. Nanda et al.   JOURNAL OF BACTERIOLOGY

Bacterial Genome Instability

(2014) E. Darmon et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Integrons: Past, Present, and Future

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

Microbiological effects of sublethal levels of antibiotics

(2014) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Pollution from drug manufacturing: review and perspectives

(2014) D. G. J. Larsson   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ancient and modern environmental DNA

(2014) Mikkel Winther Pedersen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacterial Vesicles in Marine Ecosystems

(2014) S. J. Biller et al.   SCIENCE

Selection of a Multidrug Resistance Plasmid by Sublethal Levels of Antibiotics and Heavy Metals

(2014) E. Gullberg et al.   mBio

Management Options for Reducing the Release of Antibiotics and Antibiotic Resistance Genes to the Environment

(2013) Amy Pruden et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Phosphate Concentration and the Putative Sensor Kinase Protein CckA Modulate Cell Lysis and Release of the Rhodobacter capsulatus Gene Transfer Agent

(2013) A. B. Westbye et al.   JOURNAL OF BACTERIOLOGY

The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria

(2013) Elizabeth MH Wellington et al.   LANCET INFECTIOUS DISEASES

Host range diversification within the IncP-1 plasmid group

(2013) H. Yano et al.   MICROBIOLOGY-SGM

Identification and Characterization of Integron-Mediated Antibiotic Resistance in the Phytopathogen Xanthomonas oryzae pv. oryzae

(2013) Ying Xu et al.   PLoS One

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

(2013) Michael R. Gillings   Frontiers in Microbiology

Evolution of variation in presence and absence of genes in bacterial pathways

(2012) Andrew R Francis et al.   BMC EVOLUTIONARY BIOLOGY

Population Genomics: How Bacterial Species Form and Why They Don't Exist

(2012) W. Ford Doolittle   CURRENT BIOLOGY

Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?

(2012) Xavier Charpentier et al.   CURRENT OPINION IN MICROBIOLOGY

The role of bacterial outer membrane vesicles for intra- and interspecies delivery

(2012) James Berleman et al.   ENVIRONMENTAL MICROBIOLOGY

Correlation Between Upstream Human Activities and Riverine Antibiotic Resistance Genes

(2012) Amy Pruden et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The interconnection between biofilm formation and horizontal gene transfer

(2012) Jonas Stenløkke Madsen et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Broad diversity of conjugative plasmids in integron-carrying bacteria from wastewater environments

(2012) Alexandra Moura et al.   FEMS MICROBIOLOGY LETTERS

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

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

Are humans increasing bacterial evolvability?

(2012) Michael R. Gillings et al.   TRENDS IN ECOLOGY & EVOLUTION

Diversity and Evolution of AbaR Genomic Resistance Islands in Acinetobacter baumannii Strains of European Clone I

(2011) Lenka Krizova et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Intercellular Nanotubes Mediate Bacterial Communication

(2011) Gyanendra P. Dubey et al.   CELL

Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae

(2011) Elena S. Antonova et al.   FEMS MICROBIOLOGY LETTERS

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation

(2011) Jeremy E Koenig et al.   ISME Journal

Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment

(2011) William H Gaze et al.   ISME Journal

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

(2011) Chris S. Smillie et al.   NATURE

Biased gene transfer in microbial evolution

(2011) Cheryl P. Andam et al.   NATURE REVIEWS MICROBIOLOGY

Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements

(2011) Erik Kristiansson 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

Aquatic systems: maintaining, mixing and mobilising antimicrobial resistance?

(2011) Nick G.H. Taylor et al.   TRENDS IN ECOLOGY & EVOLUTION

Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations

(2011) Y. Boucher et al.   mBio

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

(2011) Julien Guglielmini et al.   PLoS Genetics

Pseudomonas aeruginosa Genomic Structure and Diversity

(2011) Jens Klockgether et al.   Frontiers in Microbiology

Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

(2011) Guillaume Cambray et al.   Mobile DNA

Integron Prevalence and Diversity in Manured Soil

(2010) K. G. Byrne-Bailey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Antibiotic Resistance Gene Abundances Associated with Waste Discharges to the Almendares River near Havana, Cuba

(2010) David W. Graham et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The antibiotic resistome

(2010) Gerard D Wright   Expert Opinion on Drug Discovery

What traits are carried on mobile genetic elements and why?

(2010) D J Rankin et al.   HEREDITY

Influence of ciprofloxacin and vancomycin on mutation rate and transposition of IS256 in Staphylococcus aureus

(2010) Michael Nagel et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Complete Nucleotide Sequence of TOL Plasmid pDK1 Provides Evidence for Evolutionary History of IncP-7 Catabolic Plasmids

(2010) H. Yano et al.   JOURNAL OF BACTERIOLOGY

Source, occurrence and fate of antibiotics in the Italian aquatic environment

(2010) Ettore Zuccato et al.   JOURNAL OF HAZARDOUS MATERIALS

Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?

(2010) D. Skurnik et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Does the Wide Use of Quaternary Ammonium Compounds Enhance the Selection and Spread of Antimicrobial Resistance and Thus Threaten Our Health?

(2010) Kristin Hegstad et al.   Microbial Drug Resistance

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Mobility of Plasmids

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

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Fate of antibiotics during municipal water recycling treatment processes

(2010) N. Le-Minh et al.   WATER RESEARCH

Generation of Genic Diversity among Streptococcus pneumoniae Strains via Horizontal Gene Transfer during a Chronic Polyclonal Pediatric Infection

(2010) N. Luisa Hiller et al.   PLoS Pathogens

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Environmental pollution by antibiotics and by antibiotic resistance determinants

(2009) Jose Luis Martinez   ENVIRONMENTAL POLLUTION

Class 1 integrons in benthic bacterial communities: abundance, association with Tn402-like transposition modules and evidence for coselection with heavy-metal resistance

(2009) Carly P. Rosewarne et al.   FEMS MICROBIOLOGY ECOLOGY

Evidence for dynamic exchange ofqac gene cassettes between class 1 integrons and other integrons in freshwater biofilms

(2009) Michael R. Gillings et al.   FEMS MICROBIOLOGY LETTERS

Have we underestimated the importance of humans in the biogeography of free-living terrestrial microorganisms?

(2009) David M. Wilkinson   JOURNAL OF BIOGEOGRAPHY

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Conjugative plasmids: vessels of the communal gene pool

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

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure

(2009) Chu T.T. Binh et al.   RESEARCH IN MICROBIOLOGY

Wastewater bacterial communities bring together broad-host range plasmids, integrons and a wide diversity of uncharacterized gene cassettes

(2009) Alexandra Moura et al.   RESEARCH IN MICROBIOLOGY

The SOS Response Controls Integron Recombination

(2009) E. Guerin et al.   SCIENCE

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

(2009) Rachel A. F. Wozniak et al.   PLoS Genetics

Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity

(2009) Geneviève Garriss et al.   PLoS Genetics

Antibiotics and antibiotic resistance in water environments

(2008) Fernando Baquero et al.   CURRENT OPINION IN BIOTECHNOLOGY

Progress towards understanding the fate of plasmids in bacterial communities

(2008) Frances R. Slater et al.   FEMS MICROBIOLOGY ECOLOGY

Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities

(2008) Meredith S Wright et al.   ISME Journal

Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons?

(2008) Michael R Gillings et al.   ISME Journal

A Family of Insertion Sequences That Impacts Integrons by Specific Targeting of Gene Cassette Recombination Sites, the IS1111-attC Group

(2008) S. G. Tetu et al.   JOURNAL OF BACTERIOLOGY

The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance

(2008) M. Gillings et al.   JOURNAL OF BACTERIOLOGY

Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant

(2008) Andreas Schlüter et al.   JOURNAL OF BIOTECHNOLOGY

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH

Antibiotics and Antibiotic Resistance Genes in Natural Environments

(2008) J. L. Martinez   SCIENCE

Lateral gene transfer challenges principles of microbial systematics

(2008) Eric Bapteste et al.   TRENDS IN MICROBIOLOGY

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION