Omics of antimicrobials and antimicrobial resistance

Antibiotic discovery: combining isolation chip (iChip) technology and co-culture technique

(2018) Adil Farooq Lodhi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation

(2018) Ji Lu et al.   ENVIRONMENT INTERNATIONAL

Comparative subtractive proteomics based ranking for antibiotic targets against the dirtiest superbug: Acinetobacter baumannii

(2018) Sajjad Ahmad et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Systematically integrated metabonomic-proteomic studies of Escherichia coli under ciprofloxacin stress

(2018) Wanxin Li et al.   Journal of Proteomics

Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics

(2018) Christopher J. Schwalen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comparative transcriptomics of multidrug-resistant Acinetobacter baumannii in response to antibiotic treatments

(2018) Hao Qin et al.   Scientific Reports

Outer membrane vesicles from β-lactam-resistant Escherichia coli enable the survival of β-lactam-susceptible E. coli in the presence of β-lactam antibiotics

(2018) Si Won Kim et al.   Scientific Reports

The Genome-Scale Integrated Networks in Microorganisms

(2018) Tong Hao et al.   Frontiers in Microbiology

Antimicrobial drug discovery: lessons of history and future strategies

(2018) Anthony Travis et al.   Expert Opinion on Drug Discovery

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets

(2018) Pablo Ivan Pereira Ramos et al.   Scientific Reports

The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies

(2017) Andrew C. Pawlowski et al.   ISME Journal

Secretable Small RNAs via Outer Membrane Vesicles in Periodontal Pathogens

(2017) J.-W. Choi et al.   JOURNAL OF DENTAL RESEARCH

A robust, single-injection method for targeted, broad-spectrum plasma metabolomics

(2017) Kefeng Li et al.   Metabolomics

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

(2017) Fredrik Boulund et al.   MOLECULAR & CELLULAR PROTEOMICS

Metabolic constraints on the evolution of antibiotic resistance

(2017) Mattia Zampieri et al.   Molecular Systems Biology

Antibiotics and specialized metabolites from the human microbiota

(2017) Walaa K. Mousa et al.   NATURAL PRODUCT REPORTS

In situ cultivation of previously uncultivable microorganisms using the ichip

(2017) Brittany Berdy et al.   Nature Protocols

Transcriptome differences between enrofloxacin-resistant and enrofloxacin-susceptible strains of Aeromonas hydrophila

(2017) Fengjiao Zhu et al.   PLoS One

Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine

(2017) Charles O. Nwuche et al.   PLoS One

Inhibition of the ATP Synthase Eliminates the Intrinsic Resistance of Staphylococcus aureus towards Polymyxins

(2017) Martin Vestergaard et al.   mBio

Importance of Core Genome Functions for an Extreme Antibiotic Resistance Trait

(2017) Larry A. Gallagher et al.   mBio

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii

(2017) Mohd Hafidz Mahamad Maifiah et al.   Scientific Reports

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

(2017) Paul A. Jensen et al.   Cell Reports

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations

(2017) Mattia Zampieri et al.   Cell Reports

Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets

(2017) Petra Dersch et al.   Frontiers in Microbiology

iTRAQ-based proteome analysis of fluoroquinolone-resistant Staphylococcus aureus

(2017) Van Chi Thai et al.   Journal of Global Antimicrobial Resistance

Reactive oxygen: A novel antimicrobial mechanism for targeting biofilm-associated infection

(2017) Matthew S. Dryden et al.   Journal of Global Antimicrobial Resistance

Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution

(2017) Keesha E. Erickson et al.   mSphere

Comparative metabolomics revealing Staphylococcus aureus metabolic response to different antibiotics

(2017) Katie Schelli et al.   Microbial Biotechnology

RNA-Seq differential expression analysis: An extended review and a software tool

(2017) Juliana Costa-Silva et al.   PLoS One

Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry

(2016) Juntuo Zhou et al.   ANALYST

Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes

(2016) Boahemaa Adu-Oppong et al.   Annals of the New York Academy of Sciences

Characterization and prediction of the mechanism of action of antibiotics through NMR metabolomics

(2016) Verena Hoerr et al.   BMC MICROBIOLOGY

Considerations and caveats in anti-virulence drug development

(2016) Damien Maura et al.   CURRENT OPINION IN MICROBIOLOGY

Genomic and proteomic profiles of Acholeplasma laidlawii strains differing in sensitivity to ciprofloxacin

(2016) E. S. Medvedeva et al.   Doklady Biochemistry and Biophysics

Identifying targets for antibiotic development using omics technologies

(2016) Marina R. Pulido et al.   DRUG DISCOVERY TODAY

An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens

(2016) Shishir K. Gupta et al.   GENE

Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters

(2016) Ashley Parker et al.   JOURNAL OF BACTERIOLOGY

Lysine succinylation of Mycobacterium tuberculosis isocitrate lyase (ICL) fine-tunes the microbial resistance to antibiotics

(2016) Mingliang Zhou et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Alternatives to antibiotics—a pipeline portfolio review

(2016) Lloyd Czaplewski et al.   LANCET INFECTIOUS DISEASES

A feed-forward loop between SroC and MgrR small RNAs modulates the expression of eptB and the susceptibility to polymyxin B in Salmonella Typhimurium

(2016) Lillian G. Acuña et al.   MICROBIOLOGY-SGM

The green tea polyphenol EGCG inhibitsE. colibiofilm formation by impairing amyloid curli fibre assembly and downregulating the biofilm regulator CsgD via the σE-dependent sRNA RybB

(2016) Diego O. Serra et al.   MOLECULAR MICROBIOLOGY

Antibacterial drug discovery in the resistance era

(2016) Eric D. Brown et al.   NATURE

A role for the bacterial GATC methylome in antibiotic stress survival

(2016) Nadia R Cohen et al.   NATURE GENETICS

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

(2016) Hongan Long et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

(2016) Keding Cheng et al.   Proteomics Clinical Applications

Spatiotemporal microbial evolution on antibiotic landscapes

(2016) M. Baym et al.   SCIENCE

Antibiotic Adjuvants: Rescuing Antibiotics from Resistance

(2016) Gerard D. Wright   TRENDS IN MICROBIOLOGY

Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries

(2016) Mithila Rajagopal et al.   mBio

Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells

(2016) Jakob Haaber et al.   Nature Communications

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

(2016) Louie Wurch et al.   Nature Communications

Proteomic response of methicillin-resistant S. aureus to a synergistic antibacterial drug combination: a novel erythromycin derivative and oxacillin

(2016) Xiaofen Liu et al.   Scientific Reports

Proteomics As a Tool for Studying Bacterial Virulence and Antimicrobial Resistance

(2016) Francisco J. Pérez-Llarena et al.   Frontiers in Microbiology

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

(2015) James T. Morton et al.   BMC BIOINFORMATICS

Boosting Bacterial Metabolism to Combat Antibiotic Resistance

(2015) Prerna Bhargava et al.   Cell Metabolism

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

(2015) Daniel R. Garza et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Application of iChip to Grow “Uncultivable” Microorganisms and its Impact on Antibiotic Discovery

(2015) Rinzhin T. Sherpa et al.   JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES

Annotation of the Staphylococcus aureus Metabolome Using Liquid Chromatography Coupled to High-Resolution Mass Spectrometry and Application to the Study of Methicillin Resistance

(2015) Sandrine Aros-Calt et al.   JOURNAL OF PROTEOME RESEARCH

In vitro Characterization of Bacteriocin Produced by Lactic Acid Bacteria Isolated from Nem Chua, a Traditional Vietnamese Fermented Pork

(2015) Komkhae Pilasombut et al.   Korean Journal for Food Science of Animal Resources

Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology

(2015) Marco Fondi et al.   MICROBIOLOGICAL RESEARCH

Protective role of E. coli outer membrane vesicles against antibiotics

(2015) Heramb M. Kulkarni et al.   MICROBIOLOGICAL RESEARCH

Comparative Phosphoproteomics Reveals the Role of AmpC β-lactamase Phosphorylation in the Clinical Imipenem-resistant StrainAcinetobacter baumanniiSK17

(2015) Juo-Hsin Lai et al.   MOLECULAR & CELLULAR PROTEOMICS

A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise

(2015) David Lalaouna et al.   MOLECULAR CELL

Mining the microbial dark matter

(2015) Corie Lok   NATURE

Twenty years of bacterial genome sequencing

(2015) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

Prediction of Leymus arenarius (L.) antimicrobial peptides based on de novo transcriptome assembly

(2015) Anna A. Slavokhotova et al.   PLANT MOLECULAR BIOLOGY

Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage

(2015) Peter Belenky et al.   Cell Reports

Adaptive Resistance in Bacteria Requires Epigenetic Inheritance, Genetic Noise, and Cost of Efflux Pumps

(2015) Santiago Sandoval Motta et al.   PLoS One

Membrane vesicle-mediated release of bacterial RNA

(2015) Annika E. Sjöström et al.   Scientific Reports

Interaction between Mutations and Regulation of Gene Expression during Development ofDe NovoAntibiotic Resistance

(2014) Nadine Händel et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

From microbial gene essentiality to novel antimicrobial drug targets

(2014) Fredrick M Mobegi et al.   BMC GENOMICS

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii

(2014) P. Anitha et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Diversity and dynamics of bacteriocins from human microbiome

(2014) Jinshui Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

Proteomic tools to decipher microbial community structure and functioning

(2014) Florence Arsène-Ploetze et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Therapeutic enhancement of newly derived bacteriocins against Giardia lamblia

(2014) Eglal I. Amer et al.   EXPERIMENTAL PARASITOLOGY

Extracellular membrane vesicles secreted by mycoplasma Acholeplasma laidlawii PG8 are enriched in virulence proteins

(2014) Vladislav M. Chernov et al.   Journal of Proteomics

Thiopeptide Antibiotics: Retrospective and Recent Advances

(2014) Xavier Just-Baringo et al.   Marine Drugs

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

Global Transcriptome and Physiological Responses of Acinetobacter oleivorans DR1 Exposed to Distinct Classes of Antibiotics

(2014) Aram Heo et al.   PLoS One

Adaptation of Mycoplasmas to Antimicrobial Agents:Acholeplasma laidlawiiExtracellular Vesicles Mediate the Export of Ciprofloxacin and a Mutant Gene Related to the Antibiotic Target

(2014) Elena S. Medvedeva et al.   TheScientificWorldJOURNAL

Genome-Wide Saturation Mutagenesis of Burkholderia pseudomallei K96243 Predicts Essential Genes and Novel Targets for Antimicrobial Development

(2014) M. G. Moule et al.   mBio

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

(2014) Viktória Lázár et al.   Nature Communications

Antimicrobial targets localize to the extracellular vesicle-associated proteome of Pseudomonas aeruginosa grown in a biofilm

(2014) Amber J. Park et al.   Frontiers in Microbiology

The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella

(2014) Bradley L. Bearson et al.   Frontiers in Microbiology

Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistantPseudomonas aeruginosaisolates exposed to waste water and tap water

(2014) Thomas Schwartz et al.   Microbial Biotechnology

Genomic Characterization of Ciprofloxacin Resistance in a Laboratory-Derived Mutant and a Clinical Isolate of Streptococcus pneumoniae

(2013) Andréanne Lupien et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Analysis of the Small RNA Transcriptional Response in Multidrug-Resistant Staphylococcus aureus after Antimicrobial Exposure

(2013) Benjamin P. Howden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Label-Free Quantitative Proteomics Analysis of Antibiotic Response in Staphylococcus aureus to Oxacillin

(2013) Xiaofen Liu et al.   JOURNAL OF PROTEOME RESEARCH

Proteome studies of bacterial antibiotic resistance mechanisms

(2013) Iosif Vranakis et al.   Journal of Proteomics

Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development

(2013) Hsun-Cheng Su et al.   Microbial Drug Resistance

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

Antimicrobial drug resistance affects broad changes in metabolomic phenotype in addition to secondary metabolism

(2013) D. K. Derewacz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approaches to querying bacterial genomes with transposon-insertion sequencing

(2013) Lars Barquist et al.   RNA Biology

β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

(2013) A. Gutierrez et al.   Nature Communications

Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control

(2013) S. T. Rutherford et al.   Cold Spring Harbor Perspectives in Medicine

Anti-infective properties of bacteriocins: an update

(2012) Riadh Hammami et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Microbiology and proteomics, getting the best of both worlds!

(2012) Jean Armengaud   ENVIRONMENTAL MICROBIOLOGY

Analysis of bacterial biofilms using NMR-based metabolomics

(2012) Bo Zhang et al.   Future Medicinal Chemistry

A positive/negative ion–switching, targeted mass spectrometry–based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue

(2012) Min Yuan et al.   Nature Protocols

Two-dimensional gel electrophoresis in bacterial proteomics

(2012) Shirly O. T. Curreem et al.   Protein & Cell

Predicting the in Vivo Mechanism of Action for Drug Leads Using NMR Metabolomics

(2011) Steven Halouska et al.   ACS Chemical Biology

Contribution of bacterial outer membrane vesicles to innate bacterial defense

(2011) Andrew J Manning et al.   BMC MICROBIOLOGY

The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis

(2011) Charles E Massie et al.   EMBO JOURNAL

Exometabolome Analysis Identifies Pyruvate Dehydrogenase as a Target for the Antibiotic Triphenylbismuthdichloride in Multiresistant Bacterial Pathogens

(2011) Timo Birkenstock et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Synergistic effects of baicalein with ciprofloxacin against NorA over-expressed methicillin-resistant Staphylococcus aureus (MRSA) and inhibition of MRSA pyruvate kinase

(2011) Ben C.L. Chan et al.   JOURNAL OF ETHNOPHARMACOLOGY

Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy

(2011) Linda Ejim et al.   Nature Chemical Biology

Proteomic signatures in antibiotic research

(2011) Michaela Wenzel et al.   PROTEOMICS

Horizontal Gene Exchange in Environmental Microbiota

(2011) Rustam I. Aminov   Frontiers in Microbiology

Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae

(2010) Fiona Walsh et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Proteomic analysis of Escherichia coli with experimentally induced resistance to piperacillin/tazobactam

(2010) Kênia Valéria dos Santos et al.   RESEARCH IN MICROBIOLOGY

The role of antibiotics and antibiotic resistance in nature

(2009) Rustam I. Aminov   ENVIRONMENTAL MICROBIOLOGY

Spectrum of activity and mode of action of REP3123, a new antibiotic to treat Clostridium difficile infections

(2009) I. A. Critchley et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides

(2009) Kyung Moon et al.   MOLECULAR MICROBIOLOGY

Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques

(2009) Yingming Zhao et al.   PROTEOMICS

Epigenetic inheritance based evolution of antibiotic resistance in bacteria

(2008) Mike Adam et al.   BMC EVOLUTIONARY BIOLOGY

Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria

(2008) Miranda Batchelor et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS