Genomics and the evolution of antibiotic resistance (Q38808071)

6 September 2017

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title

Genomics and the evolution of antibiotic resistance (English)

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6 September 2017

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antibiotic resistance

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Sasha G Tetu

3

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Michael R. Gillings

object named as

Michael R Gillings

series ordinal

1

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Ian T. Paulsen

object named as

Ian T Paulsen

series ordinal

2

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language of work or name

English

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publication date

21 October 2016

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Annals of the New York Academy of Sciences

6 September 2017

published in

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6 September 2017

volume

1388

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6 September 2017

issue

1

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6 September 2017

page(s)

92-107

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Origins and evolution of antibiotic resistance

6 September 2017

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Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil

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Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants

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Lateral gene transfer and the nature of bacterial innovation

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

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Scaling laws predict global microbial diversity

21 January 2018

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An Estimate of the Total DNA in the Biosphere

21 January 2018

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The evolution of class 1 integrons and the rise of antibiotic resistance

21 January 2018

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Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.

21 January 2018

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Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA.

21 January 2018

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A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons

21 January 2018

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Gene cassettes and cassette arrays in mobile resistance integrons.

21 January 2018

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Recovery of diverse genes for class 1 integron-integrases from environmental DNA samples.

21 January 2018

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Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

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The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs.

21 January 2018

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A class 1 integron present in a human commensal has a hybrid transposition module compared to Tn402: evidence of interaction with mobile DNA from natural environments.

21 January 2018

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Class 1 integrons potentially predating the association with tn402-like transposition genes are present in a sediment microbial community

21 January 2018

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Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases

21 January 2018

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Characterization of the class 3 integron and the site-specific recombination system it determines

21 January 2018

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Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements

21 January 2018

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Potential impact of increased use of biocides in consumer products on prevalence of antibiotic resistance

21 January 2018

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Introduction of biocides into clinical practice and the impact on antibiotic-resistant bacteria

21 January 2018

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Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities

21 January 2018

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Bacterial resistance evolution by recruitment of super-integron gene cassettes

21 January 2018

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Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron

21 January 2018

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Sulfonamide resistance: mechanisms and trends.

21 January 2018

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The integrons In0, In2, and In5 are defective transposon derivatives

21 January 2018

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Integrons found in different locations have identical 5' ends but variable 3' ends

21 January 2018

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Transposons Tn1696 and Tn21 and their integrons In4 and In2 have independent origins

21 January 2018

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Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species.

21 January 2018

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Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Occurrence and characteristics of class 1, 2 and 3 integrons in Escherichia coli, Salmonella and Campylobacter spp. in the Netherlands

21 January 2018

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Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The current ICE age: biology and evolution of SXT-related integrating conjugative elements.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

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The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation

21 January 2018

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Shaping bacterial genomes with integrative and conjugative elements

21 January 2018

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Prokaryote genome fluidity: toward a system approach of the mobilome.

21 January 2018

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Comparison of Tn5397 from Clostridium difficile, Tn916 from Enterococcus faecalis and the CW459tet(M) element from Clostridium perfringens shows that they have similar conjugation regions but different insertion and excision modules

21 January 2018

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ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

21 January 2018

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R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements

21 January 2018

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The role of Bacteroides conjugative transposons in the dissemination of antibiotic resistance genes

21 January 2018

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A new type of conjugative transposon encodes resistance to sulfamethoxazole, trimethoprim, and streptomycin in Vibrio cholerae O139.

21 January 2018

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Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.

21 January 2018

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Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs

21 January 2018

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Site-specific integration of the conjugal Vibrio cholerae SXT element into prfC.

21 January 2018

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Integrating conjugative elements of the SXT/R391 family from fish-isolated Vibrios encode restriction-modification systems that confer resistance to bacteriophages

21 January 2018

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Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner.

21 January 2018

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Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

21 January 2018

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Integrating conjugative elements as vectors of antibiotic, mercury, and quaternary ammonium compound resistance in marine aquaculture environments

21 January 2018

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The extended regulatory networks of SXT/R391 integrative and conjugative elements and IncA/C conjugative plasmids

21 January 2018

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Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow.

21 January 2018

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Evidence for several waves of global transmission in the seventh cholera pandemic

21 January 2018

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Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage.

21 January 2018

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Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.

21 January 2018

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Presence of SXT integrating conjugative element in marine bacteria isolated from the mucus of the coral Fungia echinata from Andaman Sea.

21 January 2018

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Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.

21 January 2018

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Beyond antibiotic resistance: integrating conjugative elements of the SXT/R391 family that encode novel diguanylate cyclases participate to c-di-GMP signalling in Vibrio cholerae.

21 January 2018

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Mobile antibiotic resistance encoding elements promote their own diversity

21 January 2018

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ISCR elements: novel gene-capturing systems of the 21st century?

21 January 2018

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Mobile elements as a combination of functional modules.

21 January 2018

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Are humans increasing bacterial evolvability?

21 January 2018

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The dualistic nature of integrative and conjugative elements

21 January 2018

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Biology of Three ICE Families: SXT/R391, ICEBs1, and ICESt1/ICESt3.

21 January 2018

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Combinatorial events of insertion sequences and ICE in Gram-negative bacteria

21 January 2018

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Conjugative and mobilizable genomic islands in bacteria: evolution and diversity.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

A modular master on the move: the Tn916 family of mobile genetic elements.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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.

21 January 2018

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii

21 January 2018

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Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Genomic diversity and evolution within the species Streptococcus agalactiae

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The human microbiome harbors a diverse reservoir of antibiotic resistance genes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The shared antibiotic resistome of soil bacteria and human pathogens

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Tackling antibiotic resistance: the environmental framework

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Rapid bacterial genome sequencing: methods and applications in clinical microbiology

21 January 2018

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Bioinformatics of antimicrobial resistance in the age of molecular epidemiology

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Identification of virulence factors and antibiotic resistance markers using bacterial genomics

21 January 2018

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Consolidating and Exploring Antibiotic Resistance Gene Data Resources

21 January 2018

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Understanding the mechanisms and drivers of antimicrobial resistance.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

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A function of SmeDEF, the major quinolone resistance determinant of Stenotrophomonas maltophilia, is the colonization of plant roots

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Multidrug-resistance efflux pumps - not just for resistance

21 January 2018

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Functional characterization of the antibiotic resistance reservoir in the human microflora

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The Genomic Enzymology of Antibiotic Resistance

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Molecular mechanisms of antibiotic resistance.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Distinguishing between resistance, tolerance and persistence to antibiotic treatment.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The importance of lag time extension in determining bacterial resistance to antibiotics.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Antibiotic discovery: combatting bacterial resistance in cells and in biofilm communities.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The Prehistory of Antibiotic Resistance.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Transforming clinical microbiology with bacterial genome sequencing.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Predicting the evolution of antibiotic resistance genes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

A family of insertion sequences that impacts integrons by specific targeting of gene cassette recombination sites, the IS1111-attC Group

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Everyman's Guide to Bacterial Insertion Sequences

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Bacterial insertion sequences: their genomic impact and diversity

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

IS26-Mediated Formation of Transposons Carrying Antibiotic Resistance Genes.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Whole genome sequencing in clinical and public health microbiology

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus

21 January 2018

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Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae.

21 January 2018

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The colistin resistance mcr-1 gene is going wild.

21 January 2018

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Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

21 January 2018

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Escherichia coli Harboring mcr-1 and bla CTX-M on a Novel IncF Plasmid: First Report of mcr-1 in the United States

21 January 2018

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Interconnected microbiomes and resistomes in low-income human habitats

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Large-scale metagenomic-based study of antibiotic resistance in the environment

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

The application of ecological theory toward an understanding of the human microbiome

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.13268

Antibiotics and the gut microbiota

21 January 2018

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Antimicrobial Resistance in Agriculture

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Microbiological effects of sublethal levels of antibiotics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Selection of resistance at lethal and non-lethal antibiotic concentrations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Antibiotic treatment enhances the genome-wide mutation rate of target cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

In 2035, will all bacteria be multiresistant? Yes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Tackling antimicrobial resistance at global and local scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

ARDB--Antibiotic Resistance Genes Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

The comprehensive antibiotic resistance database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

RAC: Repository of Antibiotic resistance Cassettes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Identification of acquired antimicrobial resistance genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

PATRIC, the bacterial bioinformatics database and analysis resource

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

BacMet: antibacterial biocide and metal resistance genes database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

Identification and analysis of integrons and cassette arrays in bacterial genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

ACLAME: a CLAssification of Mobile genetic Elements, update 2010

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

The cost of living in the Anthropocene

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.13268

21 January 2018

Identifiers

DOI

10.1111/NYAS.13268

1 reference

6 September 2017

1 reference