Joint Programming Initiative on Antimicrobial Resistance

Publications from JPIAMR Supported Projects

The efforts of JPIAMR to combat AMR by supporting excellent scientific research and researchers are now being realised by the publications from JPIAMR funded research.

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.

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
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
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
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
2018Network Call on SurveillanceCoEval-AMRClinical Microbiology and Infection, 2020.
Evaluating integrated surveillance of antimicrobial resistance: experiences from use of three evaluation tools
2018Network Call on SurveillanceICALMIntensive Care Medicine, 2019.
The association of cardiovascular failure with treatment for ventilator-associated lower respiratory tract infection
2018Network Call on SurveillanceICALMIntensive Care Medicine, 2020.
Antibiotic prophylaxis in the ICU: to be or not to be administered for patients undergoing procedures?
2018Network Call on SurveillanceWAWESBook Chapter Antibiotics and Antimicrobial Resistance Genes (Springer International Publishing)’ eBook ISBN 978-3-030-40422-2, Hardcover ISBN 978-3-030-40421-5, 2020.
Chapter 1 –* ‘Entry routes of antibiotics and antimicrobial resistance in the environment' P17, P19 Chapter 6 –‘Antimicrobial/antibiotic resistance genes due to manure and agricultural waste applications’ P19
2018Network Call on SurveillanceWAWESAntimicrobial Agents and Chemotherapy, 2019.
Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic-Resistant Bacteria
2018JPIAMR-VRI Network CallCONNECTHuman Genetics, 2020.
Delineation of phenotypes and genotypes related to cohesin structural protein RAD21
2018JPIAMR-VRI Network CallTRANSLOCATION-transferMicroorganisms, 2020.
When Combined with Colistin, an Otherwise Ineffective Rifampicin–Linezolid Combination Becomes Active in Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii
2016Transmission DynamicsAWAREEnvironment International, 2018. 
Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms
2016Transmission DynamicsAWAREJournal of Environmental Protection, 2017.
Physico-Chemical and Microbiological Assessment of Organic Pollution in Plain Salty Lakes from Protected Regions
2016Transmission DynamicsAWAREPlosOne, 2020.
Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania
2016Transmission DynamicsAWAREMEDICHUB MEDIA, 2018.
Review on methods for analyzing the antibiotic resistance in wastewater samples
2016Transmission DynamicsBEAT-AMRbioRxiv, 2020.
An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1
2016Transmission DynamicsCollateral DamagePNAS, 2018.
Cellular hysteresis as a principle to maximize the efficacy of antibiotic therapy
2016Transmission DynamicsCollateral DamageNature Communications, 2018.
Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli
2016Transmission DynamicsCollateral DamageScandinavian Journal of Primary Health Care, 2020.
Retrospective study of men with E. coli UTI treated with an oral antibiotic, and risk for a new prescription or hospital admission due to UTI
2016Transmission DynamicsCollateral DamagePloS Biology, 2020.
Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin
2016Transmission DynamicsGene-gasJournal of Visualized Experiments: JoVE, 2018. 
Ultrasensitive Detection of Biomarkers by Using a Molecular Imprinting Based Capacitive Biosensor
2016Transmission DynamicsGene-gasFrontiers in Microbiology, 2020.
Biotechnological Potential of Bdellovibrio and Like Organisms and Their Secreted Enzymes
2016Transmission DynamicsGene-gasSensors and Actuators B: Chemical, 2018.
Bacteriophages as biorecognition elements in capacitive biosensors: Phage and host bacteria detection
2016Transmission DynamicsJumpARCell, 2018. 
Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance
2016Transmission DynamicsJumpARCurrent Opinion in Structural Biology, 2019.
Jump ahead with a twist: DNA acrobatics drive transposition forward
2016Transmission DynamicsMODERNAntimicrobial Resistance & Infection Control, 2018.
Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence
2016Transmission DynamicsMODERNThe Journal of Hospital Infection, 2019.
Vagino-rectal colonization and maternal–neonatal transmission of Enterobacteriaceae producing extended-spectrum β-lactamases or carbapenemases: a cross-sectional study
2016Transmission DynamicsMODERNInternational Journal of Antimicrobial Agents, 2018.
Incidence and Risk Factors for Acquisition of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Newborns in Seville, Spain: A Prospective Cohort Study
2016Transmission DynamicsMODERNAntimicrobial Resistance & Infection Control, 2018.
Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence
2016Transmission DynamicsPET-RiskVeterinary Microbiology, 2019. 
Clonal relatedness of Proteus mirabilis strains causing urinary tract infections in companion animals and humans
2016Transmission DynamicsPET-RiskJournal of Antimicrobial Chemotherapy, 2019.
Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes
2016Transmission DynamicsPET-RiskMicrobial Drug Resistance, 2020.
Sharing of Clinically Important Antimicrobial Resistance Genes by Companion Animals and Their Human Household Members
2016Transmission DynamicsPET-RiskJournal of Antimicrobial Chemotherapy, 2019.
Emergence of Escherichia coli ST131 H30/H30-Rx subclones in companion animals
2016Transmission DynamicsPNEUMOSPREADJournal of Allergy and Clinical Immunology, 2020.
Regulating T cell differentiation through the polyamine spermidine
2016Transmission DynamicsPNEUMOSPREADNature Microbiology, 2019.
Pneumolysin binds to the mannose receptor C type 1 (MRC-1) leading to anti-inflammatory responses and enhanced pneumococcal survival
2016Transmission DynamicsPREPAREHeredity, 2018. 
The fitness landscape of the codon space across environments
2016Transmission DynamicsPREPAREEvolution, 2019.
How phenotypic convergence arises in experimental evolution
2016Transmission DynamicsPREPAREEvolution, 2019.
Environment changes epistasis to alter trade‐offs along alternative evolutionary paths
2016Transmission DynamicsPREPARENature Ecology & Evolution, 2020.
Dysbiosis personalizes fitness effect of antibiotic resistance in the mammalian gut
2016Transmission DynamicsPREPAREPLOS Biology, 2020.
Low mutational load and high mutation rate variation in gut commensal bacteria
2016Transmission DynamicsRestrict-Pneumo-AMRInternational Journal of Chronic Obstructive Pulmonary Disease, 2019.
Personalized medicine for patients with COPD: where are we?
2016Transmission DynamicsRestrict-Pneumo-AMRFrontiers in Immunology, 2019.
Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota
2016Transmission DynamicsRestrict-Pneumo-AMRNature Communications, 2020.
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.
2016Transmission DynamicsSpARKFrontiers in Microbiology, 2019.
Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov
2016Transmission DynamicsSpARKbioRxiv, 2020.
Genomic Epidemiology with Mixed Samples
2016Transmission DynamicsSpARKWellcome Open Res, 2020. 
High-resolution sweep metagenomics using ultrafast read mapping and inference
2016Transmission DynamicsST131TSEurosurveillance, 2019.
Emergence of diversity in carbapenemase-producing Escherichia coli ST131, England, January 2014 to June 2016
2016Transmission DynamicsST131TSInfection, Genetics and Evolution, 2020.
The evolutionary puzzle of Escherichia coli ST131
2016Transmission DynamicsST131TSmBio, 2020.
Simulating multi-level dynamics of antimicrobial resistance in a membrane computing model
2016Transmission DynamicsSTARCSEnvironment International, 2018. 
Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids
2016Transmission DynamicsSTARCSMicrobiome, 2018. 
In-depth resistome analysis by targeted metagenomics
2016Transmission DynamicsSTARCSScience of The Total Environment, 2018. 
Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal
2016Transmission DynamicsSTARCSbioRxiv, 2019. 
Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome
2016Transmission DynamicsSTARCSMicrobial Genomics, 2018.
mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
2016Transmission DynamicsSTARCSEnvironmental Microbiology Reports, 2018.
Long‐term carriage and rapid transmission of extended spectrum beta‐lactamase‐producing E. coli within a flock of Mallards in the absence of antibiotic selection
2016Transmission DynamicsSTARCSFrontiers in Microbiology, 2017.
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment
2016Transmission DynamicsSTARCSAnnals of the New York Academy of Sciences, 2016.
Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
2016Transmission DynamicsSTARCSBioinformatics, 2017.
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks
2016Transmission DynamicsSTARCSNature Microbiology, 2018.
Prediction of the intestinal resistome by a three-dimensional structure-based method
2016Transmission DynamicsSTARCSF1000Research, 2018.
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
2016Transmission DynamicsSTARCSFoodborne Pathogens and Disease, 2018.
Are Food Animals Responsible for Transfer of Antimicrobial-Resistant Escherichia coli or Their Resistance Determinants to Human Populations? A Systematic Review
2016Transmission DynamicsSTARCSEnvironmental Microbiology, 2019.
Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species
2016Transmission DynamicsSTARCSRoyal Society of Open Science, 2017.
Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans
2016Transmission DynamicsSTARCSBioinformatics, 2020.
gplas: a comprehensive tool for plasmid analysis using short-read graphs
2016Transmission DynamicsTransPredbioRxiv, 2018. 
Conjugation factors controlling F-plasmid antibiotic resistance transmission
2016Transmission DynamicsTransPredPlos Computational Biology, 2018.
Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
2016Transmission DynamicsTransPredScientific Reports, 2020.
Complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies
2016Transmission DynamicsTransPredDrug Development Research, 2018.
Inhibiting conjugation as a tool in the fight against antibiotic resistance
2016Transmission DynamicsTransPredbioRxiv, 2020.
Genomic epidemiology and evolution of Escherichia coli in wild animals
2016Transmission DynamicsGene-gasFront. Microbiol, 2017.
Revisiting Antibiotic Resistance Spreading in Wastewater Treatment Plants – Bacteriophages as a Much Neglected Potential Transmission Vehicle
2016Transmission DynamicsGene-gasJournal of Bacteriology, 2020.
Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle
2016Transmission DynamicsST131TSClinical Microbiol and Infection, 2020.
Molecular epidemiology of Escherichia coli causing bloodstream infections in a centralized Canadian region: a population-based surveillance study
2016Transmission DynamicsST131TSAntimicrob Agents Chemother, 2020.
Emerging Antimicrobial Resistant High-Risk clones among Klebsiella pneumoniae: ST307 and ST147
2016Transmission DynamicsST131TSFront Microbiol, 2020.
Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages
2016Transmission DynamicsST131TSJ Antimicrob Chemother, 2019.
Emergence of the C1-M27 cluster in ST131 Escherichia coli from companion animals in France
2016Transmission DynamicsST131TSAppl Environ Microbiol, 2020.
A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains
2016Transmission DynamicsSTARCSFront. Microbiol, 2020.
Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health
2016Transmission DynamicsBEAT-AMRJournal of Hospital Infection, 2020.
Selection of resistance by antimicrobial coatings in the healthcare setting