Research publications

The publications from the research projects and networks supported under the JPIAMR framework involve insights to the diverse aspects of AMR including transmission, therapeutics, diagnostics, interventions, surveillance, environmental reservoirs of microbes and resistance genes as well as technological platforms and policy papers.

The publications where JPIAMR has been acknowledged to support the researchers via grants are listed below.

In case we have missed any publication, please contact us at secretariat.jpiamr@vr.se with the details.

Click on the arrows next to each heading to sort by call, project or title.

Call YearCall NameProject AcronymPublication
2016AMR Networks/Working GroupsAMR RDTNature Reviews Microbiology, 2018. 
Developmental roadmap for antimicrobial susceptibility testing systems
2016AMR Networks/Working GroupsAMR RDTEuropean Journal of Clinical Microbiology & Infectious Diseases, 2019. 
The successful uptake and sustainability of rapid infectious disease and antimicrobial resistance point-of-care testing requires a complex ‘mix-and-match’ implementation package
2016AMR Networks/Working GroupsAppropriate use of antibiotics: the role of CAM treatment strategiesEvidence-based Complementary and Alternative Medicine, 2019. 
The Contribution of Complementary and Alternative Medicine to Reduce Antibiotic Use: A Narrative Review of Health Concepts, Prevention, and Treatment Strategies
2016AMR Networks/Working GroupsAppropriate use of antibiotics: the role of CAM treatment strategiesBMJ Open, 2018.
Do NHS GP surgeries employing GPs additionally trained in integrative or complementary medicine have lower antibiotic prescribing rates? Retrospective cross-sectional analysis of national primary care prescribing data in England in 2016
2016AMR Networks/Working GroupsBEAM AllianceBEAM Alliance Position Paper, 2017.
Key Guidelines to implement effective measures toward SMEs to revive the antibacterial R&D field
2016AMR Networks/Working GroupsBehavioural Approaches to Antibiotic Stewardship ProgramsClinical Microbiology and Infection, 2018. 
Prioritizing research areas for antibiotic stewardship programmes in hospitals: a behavioural perspective
2016AMR Networks/Working GroupsBehavioural Approaches to Antibiotic Stewardship ProgramsJournal of Antimicrobial Chemotherapy, 2020.
A behavioural approach to specifying interventions: what insights can be gained for the reporting and implementation of interventions to reduce antibiotic use in hospitals?
2017AMR Networks/Working GroupsBehavioural Approaches to Antibiotic Stewardship ProgramsFront. Sociol, 2020.
Barriers and Facilitators to Implementation of Antibiotic Stewardship Programmes in Hospitals in Developed Countries
2016AMR Networks/Working GroupsConsensus group on the design, analysis and reporting of antibiotic stewardship trialsClinical Microbiology and Infection, 2019.
Optimizing design of research to evaluate antibiotic stewardship interventions: consensus recommendations of a multinational working group
2016AMR Networks/Working GroupsFARB - Flies (Diptera: Muscidae) and the spread of antimicrobial resistant bacteriaTravel Medicine and Infectious Disease, 2018. 
The role of ‘filth flies’ in the spread of antimicrobial resistance
2016AMR Networks/Working GroupsPHAGEFORWARDViruses, 2018. 
Expert Opinion on Three Phage Therapy Related Topics: Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains
2016AMR Networks/Working GroupsVetCASThttp://www.eucast.org/ast_of_veterinary_pathogens/
2016AMR Networks/Working GroupsVetCASTFrontiers in Microbiology, 2017.
En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach
2015Antimicrobial Resistance through the JPIAMRABIMMUNEEuropean Journal of Pharmaceutical Sciences, 2019. 
High voriconazole target-site exposure after approved sequence dosing due to nonlinear pharmacokinetics assessed by long-term microdialysis
2015Antimicrobial Resistance through the JPIAMRABIMMUNEFrontiers in Immunology, 2019.
Therapeutic Synergy Between Antibiotics and Pulmonary Toll-Like Receptor 5 Stimulation in Antibiotic-Sensitive or -Resistant Pneumonia
2015Antimicrobial Resistance through the JPIAMRABIMMUNEDrug Metabolism Reviews, 2019.
Novel insights into the complex pharmacokinetics of voriconazole: a review of its metabolism
2015Antimicrobial Resistance through the JPIAMRABIMMUNEJournal of Clinical Medicine, 2020.
Linezolid Concentrations in Plasma and Subcutaneous Tissue are Reduced in Obese Patients, Resulting in a Higher Risk of Underdosing in Critically Ill Patients: A Controlled Clinical Pharmacokinetic Study
2015Antimicrobial Resistance through the JPIAMRABIMMUNETalanta, 2019.
A rapid, simple and sensitive liquid chromatography tandem mass spectrometry assay to determine amoxicillin concentrations in biological matrix of little volume
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2018. 
Automated time-lapse microscopy a novel method for screening of antibiotic combination effects against multidrug-resistant Gram-negative bacteria
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2018. 
Semi-mechanistic pharmacokinetic–pharmacodynamic modelling of antibiotic drug combinations
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2018. 
PK/PD characterization of combined antimicrobial agents: a real challenge and an urgent need
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONInternational Journal of Antimicrobial Agents, 2019. 
An alternative strategy for combination therapy: Interactions between polymyxin B and non-antibiotics
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONJournal of Antimicrobial Chemotherapy, 2019.
Population pharmacokinetics of piperacillin in febrile children receiving cancer chemotherapy: the impact of body weight and target on an optimal dosing regimen
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONAntimicrobial Agents and Chemotherapy, 2020.
Extension of Pharmacokinetic/Pharmacodynamic Time-Kill Studies To Include Lipopolysaccharide/Endotoxin Release from Escherichia coli Exposed to Cefuroxime
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONMolecular Pharmaceutics, 2020.
Model-Informed Drug Development in Pulmonary Delivery: Semimechanistic Pharmacokinetic–Pharmacodynamic Modeling for Evaluation of Treatments against Chronic Pseudomonas aeruginosa Lung Infections
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONAntimicrobial Agents and Chemotherapy, 2020.
Efficacy of Antibiotic Combinations against MultidrugResistant Pseudomonas aeruginosa in Automated Time-Lapse
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2020.
Evaluation of polymyxin B in combination with 13 other antibiotics against carbapenemase-producing Klebsiella pneumoniae in time-lapse microscopy and time-kill experiments
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONInternational Journal of Antimicrobial Agents, 2020.
Combination of polymyxin B and minocycline against multidrug-resistant Klebsiella pneumoniae: interaction quantified by pharmacokinetic/pharmacodynamic modelling from in vitro data
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2020.
Semi-mechanistic PK/PD modelling of combined polymyxin B and minocycline against a polymyxin-resistant strain of Acinetobacter baumannii
2015Antimicrobial Resistance through the JPIAMRCO-ACTIONClinical Microbiology and Infection, 2020.
Population pharmacokinetics of colistin and the relation to survival in critically ill patients infected with colistin susceptible and carbapenem-resistant bacteria
2016Antimicrobial Resistance through the JPIAMRCO-ACTIONInternational Journal of Antimicrobial Agents, 2020.
Pharmacodynamics of immune response biomarkers of interest for evSaluation of treatment effects in bacterial infections
2015Antimicrobial Resistance through the JPIAMRCombinatorialsMolecular Microbiology, 2017. 
Silver potentiates aminoglycoside toxicity by enhancing their uptake
2015Antimicrobial Resistance through the JPIAMRCombinatorialsNature, 2018. 
Species-specific activity of antibacterial drug combinations
2015Antimicrobial Resistance through the JPIAMRCombinatorialsNucleic Acid Research, 2018. 
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39
2015Antimicrobial Resistance through the JPIAMRCombinatorialsbioRxiv, 2018. 
RocS drives chromosome segregation and nucleoid occlusion in Streptococcus pneumoniae
2015Antimicrobial Resistance through the JPIAMRCombinatorialsNucleic Acids Research, 2018. 
High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions
2015Antimicrobial Resistance through the JPIAMRCombinatorialsCell Reports, 2018. 
Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling
2015Antimicrobial Resistance through the JPIAMRCombinatorialsGenes, 2019. 
Three new integration vectors and fluorescent proteins for use in the opportunistic human pathogen Streptococcus pneumoniae
2015Antimicrobial Resistance through the JPIAMRCombinatorialsCPT:Pharmacometrics & Systemics Pharmacology, 2017.
Translational Pharmacometric Evaluation of Typical Antibiotic Broad‐Spectrum Combination Therapies Against Staphylococcus Aureus Exploiting In Vitro Information
2015Antimicrobial Resistance through the JPIAMRCombinatorialsbioRxiv, 2020.
Dissecting the collateral damage of antibiotics on gut microbes
2015Antimicrobial Resistance through the JPIAMRCombinatorialsCell Host & Microbe, 2020.
Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer
2015Antimicrobial Resistance through the JPIAMRCombinatorialsNature Microbiology, 2019.
RocS drives chromosome segregation and nucleoid protection in Streptococcus pneumoniae
2015Antimicrobial Resistance through the JPIAMRABIMMUNEPharmaceutical Research, 2021. Which Analysis Approach Is Adequate to Leverage Clinical Microdialysis Data? A Quantitative Comparison to Investigate Exposure and Reponse Exemplified by Levofloxacin.
2015Antimicrobial Resistance through the JPIAMRABIMMUNERespiratory Research, 2021. Post-treatment with the PPAR-γ agonist pioglitazone inhibits inflammation and bacterial growth during Klebsiella pneumonia
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ARMISBiointerface Research in Applied Chemistry, 2019.
Prevalence of vancomycin resistance phenotypes among Enterococcus species isolated from
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ImpresUJAMDA, 2020.
Antibiotic Stewardship in European Nursing Homes: Experiences From the Netherlands, Norway, Poland, and Sweden
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
INARTACCESS MICROBIOLOGY, 2019.
Occurrence of extended-spectrum β-lactamase (ESBL)/AmpC producing bacteria in wastewater treatment plant effluent
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
INARTAntibiotics and Antimicrobial Resistance Genes, 2020.
Treatment Technologies for Removal of Antibiotics, Antibiotic Resistance Bacteria and Antibiotic-Resistant Genes
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
AB-AssistantBMJ Open 2020.
Study protocol for an international, multicentre stepped-wedge cluster randomised trial to evaluate the impact of a digital antimicrobial stewardship smartphone application
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
RESILIENCEThe Lancet Infectious Diseases, 2020.
Evidence for action: a One Health learning platform on interventions to tackle antimicrobial resistance
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ASBJ Antibiotics, 2020.
Industry incentives and antibiotic resistance: an introduction to the antibiotic susceptibility bonus
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
INARTFrontiers in Microbiology, 2021. Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture.
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ASBFrontiers in Medicine, 2021. Surveillance of Resistance to New Antibiotics in an Era of Limited Treatment Options.
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
REDUCEAMUFrontiers in Microbiology, 2021. Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
REDUCEAMUFront. Vet. Sci., 2021. Geographic Drivers of Antimicrobial Use and Resistance in Pigs in Khon Kaen Province, Thailand
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ExcludeMRSAIrish Veterinary Journal, 2021. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
ExcludeMRSAmSystems, 2021. Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
AMResilienceBMC Infectious Diseases, 2021. Characterizing social-ecological context and success factors of antimicrobial resistance interventions across the One Health spectrum: analysis of 42 interventions targeting E. coli
2014InnovaResistanceDesInMBLJournal of Enzyme Inhibition and Medicinal Chemistry, 2017. 
Beta-lactamase database (BLDB) – structure and function
2014InnovaResistanceDesInMBLInternational Journal of Antimicrobial Agents, 2017. 
Performance of the Xpert® Carba-R v2 in the daily workflow of a hygiene unit in a country with a low prevalence of carbapenemase-producing Enterobacteriaceae
2014InnovaResistanceDesInMBLProteins: Structure, Function, and Bioinformatics, 2016. 
Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2018. 
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2018. 
SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2016. 
Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2019. 
Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
2014InnovaResistanceDesInMBLThe Journal of Molecular Diagnotics, 2020.
Evaluation of the BD MAX Check-Points CPO Assay for the Detection of Carbapenemase Producers Directly from Rectal Swabs
2014InnovaResistanceDesInMBLJournal of Antimicrobial Chemotherapy, 2019.
Evaluation of the RESIST-4 K-SeT assay, a multiplex immunochromatographic assay for the rapid detection of OXA-48-like, KPC, VIM and NDM carbapenemases
2014InnovaResistanceDesInMBLACS Infectious Diseases, 2019.
Genetic, Biochemical, and Structural Characterization of CMY-136 β-Lactamase, a Peculiar CMY-2 Variant
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2019.
False-Positive Carbapenem-Hydrolyzing Confirmatory Tests Due to ACT-28, a Chromosomally Encoded AmpC with Weak Carbapenemase Activity from Enterobacter kobei
2014InnovaResistanceDesInMBLJournal of Antimicrobial Chemotherapy, 2019.
SME-4-producing Serratia marcescens from Argentina belonging to clade 2 of the S. marcescens phylogeny
2014InnovaResistanceDesInMBLJournal of Antimicrobial Chemotherapy, 2019.
Unravelling ceftazidime/avibactam resistance of KPC-28, a KPC-2 variant lacking carbapenemase activity
2014InnovaResistanceDesInMBLJournal of Clinical Microbiology, 2019.
Evaluation of the Amplidiag CarbaR+MCR Kit for Accurate Detection of Carbapenemase-Producing and Colistin-Resistant Bacteria
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2018.
Genetic and Biochemical Characterization of OXA-535, a Distantly Related OXA-48-Like β-Lactamase
2014InnovaResistanceDesInMBLDrug Resistance Updates, 2018.
A close look onto structural models and primary ligands of metallo-β-lactamases
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2017.
Molecular Characterization of OXA-198 Carbapenemase-Producing Pseudomonas aeruginosa Clinical Isolates
2014InnovaResistanceDesInMBLJournal of Antimicrobial Chemotherapy, 2018.
A multiplex lateral flow immunoassay for the rapid identification of NDM-, KPC-, IMP- and VIM-type and OXA-48-like carbapenemase-producing Enterobacteriaceae
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2018.
Genetic and Biochemical Characterization of OXA-519, a Novel OXA-48-Like β-Lactamase
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2018.
Diversity of Carbapenemase-Producing Escherichia coli Isolates
2014InnovaResistanceDesInMBLJournal of Clinical Microbiology, 2019.
Evaluation of the Amplidiag CarbaR+MCR Kit for Accurate Detection of Carbapenemase-Producing and Colistin-Resistant Bacteria
2014InnovaResistanceDesInMBLJournal of Clinical Microbiology, 2018.
Evaluation of the Amplidiag CarbaR+VRE Kit for Accurate Detection of Carbapenemase-Producing Bacteria
2014InnovaResistanceDesInMBLFrontiers in Microbiology, 2018.
Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2018.
Proposing Kluyvera georgiana as the Origin of the Plasmid-Mediated Resistance Gene fosA4
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2018.
Complete Sequence of the IncA/C1 Plasmid pCf587 Carrying blaPER-2 from Citrobacter freundii
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2017.
Comparison of Two Phenotypic Algorithms To Detect Carbapenemase-Producing Enterobacteriaceae
2014InnovaResistanceDesInMBLJournal of Antimicrobial Chemotherapy, 2017.
Prospective evaluation of the OKN K-SeT assay, a new multiplex immunochromatographic test for the rapid detection of OXA-48-like, KPC and NDM carbapenemases
2014InnovaResistanceDesInMBLAntimicrobial Agents and Chemotherapy, 2016.
First Occurrence of OXA-72-Producing Acinetobacter baumannii in Serbia
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2020.
Prediction of octanol-water partition coefficients for the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields
2014InnovaResistanceDesInMBLFrontiers in Microbiology, 2020.
Genetics of Acquired Antibiotic Resistance Genes in Proteus spp.
2014InnovaResistanceDesInMBLCurrent Drug Targets, 2016.
Structural and Functional Aspects of Class A Carbapenemases
2014InnovaResistanceDesInMBLScientific Reports, 2020.
A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales
2014InnovaResistanceDesInMBLInternational Journal of Biological Macromolecules.
2020. Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates
2014InnovaResistanceEVOBIOTICNucleic Acids Research, 2015. 
Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)
2014InnovaResistanceEVOBIOTICNature Communications, 2015. 
An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products
2014InnovaResistanceNAPCLICurrent Opinion in Microbiology, 2017. 
The divisome at 25: the road ahead
2014InnovaResistanceNAPCLImBio, 2018. 
Structural analysis of the interaction between the bacterial cell division proteins FtsQ and FtsB
2014InnovaResistanceNAPCLIMolecular Microbiology, 2018.
Induced conformational changes activate the peptidoglycan synthase PBP1B
2014InnovaResistanceNAPCLIThe Cell Surface, 2018.
Coupling of polymerase and carrier lipid phosphatase prevents product inhibition in peptidoglycan synthesis
2014InnovaResistanceNAPCLIFrontiers in Microbiology, 2019.
Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus
2014InnovaResistanceNAPCLIFrontiers in Microbiology, 2018.
The Fluorescent D-Amino Acid NADA as a Tool to Study the Conditional Activity of Transpeptidases in Escherichia coli
2014InnovaResistanceNAPCLImBio, 2019.
Peptidoglycan Remodeling Enables Escherichia coli To Survive Severe Outer Membrane Assembly Defect
2014InnovaResistanceNAPCLIMolecular Microbiology, 2017.
Peptidoglycan in obligate intracellular bacteria
2014InnovaResistanceNAPCLIBio-protocol, 2018.
Bacterial Cell Wall Precursor Phosphatase Assays Using Thin-layer Chromatography (TLC) and High Pressure Liquid Chromatography (HPLC)
2014InnovaResistanceNAPCLIPNAS, 2018.
Copper inhibits peptidoglycan LD-transpeptidases suppressing β-lactam resistance due to bypass of penicillin-binding proteins
2014InnovaResistanceNAPCLIFrontiers in Cellular and Infection Microbiology, 2017.
AmiD Is a Novel Peptidoglycan Amidase in Wolbachia Endosymbionts of Drosophila melanogaster
2014InnovaResistanceNAPCLIeLife, 2016.
Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli
2014InnovaResistanceNAPCLIChemistry A European Journal, 2018.
Critical Impact of Peptidoglycan Precursor Amidation on the Activity of l,d‐Transpeptidases from Enterococcus faecium and Mycobacterium tuberculosis
2014InnovaResistanceNAPCLIJournal of Biological Chemistry, 2018.
Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus
2014InnovaResistanceNAPCLIStructure, 2020.
Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa
2014InnovaResistanceNAPCLINature Communications, 2019.
Structural Insight Into YcbB-mediated Beta-Lactam Resistance in Escherichia Coli
2014InnovaResistanceNoTBSecJournal of Biological Chemistry, 2016.
iniBAC induction Is Vitamin B12- and MutAB-dependent in Mycobacterium marinum
2014InnovaResistanceNoTBSecPlos Genetics, 2017.
Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose
2014InnovaResistanceNoTBSecPlos Neglected Tropical Diseases, 2019.
Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening
2014InnovaResistanceNoTBSecAntimicrobial Agents and Chemotherapy, 2018.
Rifabutin Acts in Synergy and Is Bactericidal with Frontline Mycobacterium abscessus Antibiotics Clarithromycin and Tigecycline, Suggesting a Potent Treatment Combination
2014InnovaResistanceNoTBSecAntimicrobial Agents and Chemotherapy, 2017.
Antagonism between Front-Line Antibiotics Clarithromycin and Amikacin in the Treatment of Mycobacterium abscessus Infections Is Mediated by the whiB7 Gene
2014InnovaResistanceNoTBSecMolecular Microbiology, 2017.
Regulatory genes coordinating antibiotic‐induced changes in promoter activity and early transcriptional termination of the mycobacterial intrinsic resistance gene whiB7
2014InnovaResistanceNoTBSecScientific Reports 2016.
Repurposing clinically approved cephalosporins for tuberculosis therapy
2014InnovaResistanceNoTBSecPNAS, 2016.
Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria
2014InnovaResistanceNoTBSecCellular Microbiology, 2017.
ESX‐1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis
2014InnovaResistanceNoTBSecNature Microbiology, 2018.
Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis
2014InnovaResistanceNoTBSecPNAS, 2018.
Mycobacterial ESX-1 secretion system mediates host cell lysis through bacterium contact-dependent gross membrane disruptions
2014InnovaResistanceNoTBSecMolecular Microbiology, 2016.
Discovery of the type VII ESX‐1 secretion needle?
2014InnovaResistanceNoTBSecCell Reports, 2018.
Multiplexed Quantitation of Intraphagocyte Mycobacterium tuberculosis secrected proetien effectors
2014InnovaResistanceNoTBSecCell Reports, 2017.
Recombinant BCG Expressing ESX-1 of Mycobacterium marinum Combines Low Virulence with Cytosolic Immune Signaling and Improved TB Protection
2014InnovaResistanceNoTBSecNature REviews Microbiology, 2016.
ESX secretion systems: mycobacterial evolution to counter host immunity
2014InnovaResistanceNoTBSecPlos Pathogens, 2018.
RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection
2014InnovaResistanceNoTBSecPlos One, 2015.
Benzoic Acid-Inducible Gene Expression in Mycobacteria
2014InnovaResistanceNoTBSecInfection and Immunity, 2018.
Genetic Variation/Evolution and Differential Host Responses Resulting from In-Patient Adaptation of Mycobacterium avium
2014InnovaResistanceNPERDMDRPLOS ONE, 2017. 
Effective Control of Molds Using a Combination of Nanoparticles
2014InnovaResistanceNPERDMDRJournal of Nanobiotechnology, 2017. 
Metal nanoparticles: understanding the mechanisms behind antibacterial activity
2014InnovaResistanceNPERDMDRJournal of Materials Chemistry B, 2016. 
A one-step sonochemical synthesis of stable ZnO–PVA nanocolloid as a potential biocidal agent
2014InnovaResistanceNPERDMDRInternational Journal of Nanomedicine, 2016.
Ga@C-dots as an antibacterial agent for the eradication of Pseudomonas aeruginosa
2014InnovaResistanceNPERDMDRChemistry and Physics of Lipids, 2019.
Physical states and thermodynamic properties of model gram-negative bacterial inner membranes
2014InnovaResistanceNPERDMDRCurrent Topics in Medicinal Chemistry, 2017.
Innovative Approaches for Controlling Clinically Relevant Biofilms: Current Trends and Future Prospects
2014InnovaResistanceNPERDMDRJournal of Applied Polymer Science, 2017.
Sonochemical synthesis and stabilization of concentrated antimicrobial silver‐chitosan nanoparticle dispersions
2014InnovaResistanceNPERDMDRACS Appl. Mater. Interfaces, 2017.
Nanotransformation of Vancomycin Overcomes the Intrinsic Resistance of Gram-Negative Bacteria
2014InnovaResistanceNPERDMDRProcess Biochemistry, 2017.
Immobilization of antimicrobial core-shell nanospheres onto silicone for prevention of Escherichia coli biofilm formation
2014InnovaResistanceNPERDMDRNanomedicine: Nanotechnology, Biology and Medicine, 2016.
Escherichia coli and Pseudomonas aeruginosa eradication by nano-penicillin G
2014InnovaResistanceNPERDMDRActa Biomaterialia, 2016.
Bacteria-responsive multilayer coatings comprising polycationic nanospheres for bacteria biofilm prevention on urinary catheters
2014InnovaResistanceNPERDMDRInd. Eng. Chem. Res, 2017.
Hybrid Chitosan–Silver Nanoparticles Enzymatically Embedded on Cork Filter Material for Water Disinfection
2014InnovaResistanceSENBIOTARVirology Journal, 2015. 
Glycoside hydrolase family 32 is present in Bacillus subtilis phages
2014InnovaResistanceSENBIOTARDrug Discovery Today: Technologies, 2018. 
Automated assays for thermodynamic (equilibrium) solubility determination
2014InnovaResistanceSENBIOTARMolecules, 2018.
In Silico and in Vitro-Guided Identification of Inhibitors of Alkylquinolone-Dependent Quorum Sensing in Pseudomonas aeruginosa
2014InnovaResistanceSENBIOTARJournal of Medicinal Chemistry, 2018.
Pseudomonas aeruginosa Quorum Sensing Systems as Drug Discovery Targets: Current Position and Future Perspectives
2014InnovaResistanceSENBIOTARAnnals of the New York Academy of Sciences, 2019. 
Genomics of antibiotic‐resistance prediction in Pseudomonas aeruginosa
2014InnovaResistanceSENBIOTARJournal of Pharmaceutical Sciences, 2019. 
Model-based drug development in pulmonary delivery: Pharmacokinetic analysis of novel drug candidates for treatment of Pseudomonas aeruginosa lung infection
2014InnovaResistanceEVOBIOTICResearch in Microbiology, 2020.
Escherichia coli O-antigen Capsule (Group 4) is Essential for Serum Resistance
2014InnovaResistanceDesInMBLEuropean Journal of Medicinal Chemistry, 2021. Azetidinimines as a novel series of non-covalent broad-spectrum inhibitors of β-lactamases with submicromolar activities against carbapenemases KPC-2 (class A), NDM-1 (class B) and OXA-48 (class D)
2014InnovaResistanceDesInMBLJournal of Computer-Aided Molecular Design, 2021. Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTbioRxiv, 2019.
Spatio-temporal control of DNA replication by the pneumococcal cell cycle regulator CcrZ
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTMolecular Microbiology, 2019.
BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTbioRxiv, 2020.
Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTbioRxiv, 2020.
Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events
2019Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTbioRxiv - June 2020.
Harnessing CRISPR-Cas9 for genome editing in Streptococcus pneumoniae
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTNature Structural & Molecular Biology, 2020.
Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTMicrobiologyOpen, 2020.
Penicillin‐binding protein PBP2a provides variable levels of protection toward different β‐lactams in Staphylococcus aureus RN4220
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsFLAV4AMRInternational Journal of Molecular Sciences, 2020.
Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETPNAS, 2020.
A widespread toxin−antitoxin system exploiting growth control via alarmone signaling
2019Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETNature Reviews Microbiology, 2020.
Target protection as a key antibiotic resistance mechanism
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRESET-MEAngewandte Chemie International Edition, 2021. Large Peptide Permeation Through a Membrane Channel: Understanding Protamine Translocation Through CymA from Klebsiella Oxytoca
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsExploreChemMedChem, 2021. Fragment‐based drug discovery for RNA targets.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETNature Communications, 2021. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTNature Microbiology, 2021. CcrZ is a pneumococcal spatiotemporal cell cycle regulator that interacts with FtsZ and controls DNA replication by modulating the activity of DnaA
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETMolecular Cell, 2021. (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETNature Communications, 2021. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics
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2016Transmission DynamicsPREPAREEPL, 2018 Playing evolution in the laboratory: From the first major evolutionary transition to global warming.
2016Transmission DynamicsPREPAREPeer Community in Evolutionary Biology, 2018. Let’s move beyond costs of resistance!
2016Transmission DynamicsPREPAREHeredity (Edinb). 2018. The fitness landscape of the codon space across environments.
2016Transmission DynamicsPREPAREEvolutionary Applications. 2020. Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection
2016Transmission DynamicsPREPARENat Ecol Evol. 2020. Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut.
2016Transmission DynamicsPREPAREAntimicrob Agents Chemother. 2020. Radial Expansion Facilitates the Maintenance of Double Antibiotic Resistances.
2016Transmission DynamicsPREPARETrends Microbiol. 2018. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance.
2016Transmission DynamicsAWAREFront Microbiol. 2021. Multidrug Resistant Klebsiella pneumoniae ST101 Clone Survival Chain From Inpatients to Hospital Effluent After Chlorine Treatment.
2016Transmission DynamicsAWARESyst Rev. 2019. Do wastewater treatment plants increase antibiotic resistant bacteria or genes in the environment? Protocol for a systematic review.
2016Transmission DynamicsAWAREAntibiotics (Basel). 2021. Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study.
2016Transmission DynamicsAWAREMicrob Genom. 2020. Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes.
2016Transmission DynamicsMACOTRAEpidemics, 2021. Understanding MRSA clonal competition within a UK hospital; the possible importance of density dependence.
2016Transmission DynamicsSpARKWellcome Open Res, 2021. High-resolution sweep metagenomics using ultrafast read mapping and inference
2016Transmission DynamicsPET-RiskJ Antimicrob Chemother, 2021. Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital.
2016Transmission DynamicsPET-RiskAntimicrob Agents Chemother, 2020. OXA-181-Producing Extraintestinal Pathogenic Escherichia coli Sequence Type 410 Isolated from a Dog in Portugal.
2016Transmission DynamicsPET-RiskJournal of Clinical Microbiology, 2019. Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans.
2016Transmission DynamicsPET-RiskJournal of Clinical Microbiology, 2021. Driving Laboratory Standardization of Bacterial Culture and Antimicrobial Susceptibility Testing in Veterinary Clinical Microbiology in Europe and Beyond
2016Transmission DynamicsST131TSEuropean Journal of Clinical Microbiology & Infectious Diseases, 2021. Population-based epidemiology of Escherichia coli ST1193 causing blood stream infections in a centralized Canadian region
2016Transmission DynamicsST131TSPhilosophical Transactions of the Royal Society B Biological Sciences, 2021. Translational demand is not a major source of plasmid-associated fitness costs.
2016Transmission DynamicsMODERNEuropean Journal of Clinical Microbiology & Infectious Diseases, 2021. Higher prevalence of CTX-M-27-producing Escherichia coli belonging to ST131 clade C1 among residents of two long-term care facilities in Southern Spain.
2016Transmission DynamicsMODERNEuropean Journal of Clinical Microbiology & Infectious Diseases, 2021. Interplay between IncF plasmids and topoisomerase mutations conferring quinolone resistance in the Escherichia coli ST131 clone: stability and resistance evolution
2016Transmission DynamicsRestrict-Pneumo-AMRClinical & Experimental Immunology, 2022. The PPAR-γ agonist pioglitazone exerts proinflammatory effects in bronchial epithelial cells during acute Pseudomonas aeruginosa pneumonia.
2016Transmission DynamicsSTARCS GigaScience, 2021. A high-throughput multiplexing and selection strategy to complete bacterial genomes
2016Transmission DynamicsBEAT-AMRThe ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2021. Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms
2016Transmission DynamicsSTARCS The Lancet Microbe, 2022. The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis
2016Transmission DynamicsMACOTRAInternational Journal of Antimicrobial Agents, 2022. MRSA Surveillance Programmes Worldwide: Moving towards a harmonised international approach
2016Transmission DynamicsHECTORbioRxiv, 2022. Genome-wide association reveals host-specific genomic traits in Escherichia coli
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTMicrobiology Spectrum, 2021. Ubericin K, a New Pore-Forming Bacteriocin Targeting mannose-PTS.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTBiophysical Journal, 2021. Switching off: the phenotypic transition to the uninduced state of the lactose uptake pathway
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsDISRUPTNature Protocols, 2022. CRISPRi-seq for genome-wide fitness quantification in bacteria.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsEMBARKNature, 2021. Unravelling the collateral damage of antibiotics on gut bacteria.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsMTI4MDR-TBOrganic & Biomolecular Chemistry, 2021. K2S2O8-mediated coupling of 6-amino-7-aminomethyl-thiazolino-pyridones with aldehydes to construct amyloid affecting pyrimidine-fused thiazolino-2-pyridones.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsMTI4MDR-TBThe Journal of Organic Chemistry, 2021. Tandem Ring Opening/Intramolecular [2 + 2] Cycloaddition Reaction for the Synthesis of Cyclobutane Fused Thiazolino-2-Pyridones.
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsRIBOTARGETPNAS, 2022. A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains
2018Innovations against antibiotic-resistant bacteria: New targets, compounds and toolsAnti-Persistence Research Square, 2022. The structure of SpoT reveals evolutionary tuning of enzymatic output through constraint of the conformational landscape
2018JPIAMR-VRI Network CallNEAR-AMRThe Lancet Microbe, 2021. NIMble innovation - a networked model for public antibiotic trials.
2018Network Call on SurveillanceWAWESCurrent Opinion in Microbiology, 2021. The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment.
2018Network Call on SurveillancePRAISEJournal of Hospital Infection, 2022. Automated surveillance systems for healthcare-associated infections: results from a European survey and experiences from real-life utilization.
2015Antimicrobial Resistance through the JPIAMRCombinatorialsJ Bacteriol. 2016. Antibodies Damage the Resilience of Fimbriae, Causing Them To Be Stiff and Tangled.
2015Antimicrobial Resistance through the JPIAMRCombinatorialsCurr Opin Syst Biol, 2017. Chemical genetics in drug discovery.
2015Antimicrobial Resistance through the JPIAMRCombinatorialsNature. 2018. Species-specific activity of antibacterial drug combinations.
2015Antimicrobial Resistance through the JPIAMRCombinatorialsFront Microbiol. 2018. Enhanced Biofilm Formation and Membrane Vesicle Release by Escherichia coli Expressing a Commonly Occurring Plasmid Gene, kil.
2015Antimicrobial Resistance through the JPIAMRCombinatorialsDiagnostics (Basel). 2020. Guideline for Urine Culture and Biochemical Identification of Bacterial Urinary Pathogens in Low-Resource Settings.
2017Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies,
including One Health approaches
INARTJournal of Environmental Management, 2022. Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting