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 Year	Call Name	Project Acronym	Publication
2016	AMR Networks/Working Groups	AMR RDT	Nature Reviews Microbiology, 2018.  Developmental roadmap for antimicrobial susceptibility testing systems
2016	AMR Networks/Working Groups	AMR RDT	European 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
2016	AMR Networks/Working Groups	Appropriate use of antibiotics: the role of CAM treatment strategies	Evidence-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
2016	AMR Networks/Working Groups	Appropriate use of antibiotics: the role of CAM treatment strategies	BMJ 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
2016	AMR Networks/Working Groups	BEAM Alliance	BEAM Alliance Position Paper, 2017. Key Guidelines to implement effective measures toward SMEs to revive the antibacterial R&D field
2016	AMR Networks/Working Groups	Behavioural Approaches to Antibiotic Stewardship Programs	Clinical Microbiology and Infection, 2018.  Prioritizing research areas for antibiotic stewardship programmes in hospitals: a behavioural perspective
2016	AMR Networks/Working Groups	Behavioural Approaches to Antibiotic Stewardship Programs	Journal 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?
2017	AMR Networks/Working Groups	Behavioural Approaches to Antibiotic Stewardship Programs	Front. Sociol, 2020. Barriers and Facilitators to Implementation of Antibiotic Stewardship Programmes in Hospitals in Developed Countries
2016	AMR Networks/Working Groups	Consensus group on the design, analysis and reporting of antibiotic stewardship trials	Clinical Microbiology and Infection, 2019. Optimizing design of research to evaluate antibiotic stewardship interventions: consensus recommendations of a multinational working group
2016	AMR Networks/Working Groups	FARB - Flies (Diptera: Muscidae) and the spread of antimicrobial resistant bacteria	Travel Medicine and Infectious Disease, 2018.  The role of ‘filth flies’ in the spread of antimicrobial resistance
2016	AMR Networks/Working Groups	PHAGEFORWARD	Viruses, 2018.  Expert Opinion on Three Phage Therapy Related Topics: Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains
2016	AMR Networks/Working Groups	VetCAST	http://www.eucast.org/ast_of_veterinary_pathogens/
2016	AMR Networks/Working Groups	VetCAST	Frontiers in Microbiology, 2017. En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	European Journal of Pharmaceutical Sciences, 2019.  High voriconazole target-site exposure after approved sequence dosing due to nonlinear pharmacokinetics assessed by long-term microdialysis
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Frontiers in Immunology, 2019. Therapeutic Synergy Between Antibiotics and Pulmonary Toll-Like Receptor 5 Stimulation in Antibiotic-Sensitive or -Resistant Pneumonia
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Drug Metabolism Reviews, 2019. Novel insights into the complex pharmacokinetics of voriconazole: a review of its metabolism
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Journal 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
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Talanta, 2019. A rapid, simple and sensitive liquid chromatography tandem mass spectrometry assay to determine amoxicillin concentrations in biological matrix of little volume
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical Microbiology and Infection, 2018.  Automated time-lapse microscopy a novel method for screening of antibiotic combination effects against multidrug-resistant Gram-negative bacteria
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical Microbiology and Infection, 2018.  Semi-mechanistic pharmacokinetic–pharmacodynamic modelling of antibiotic drug combinations
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical Microbiology and Infection, 2018.  PK/PD characterization of combined antimicrobial agents: a real challenge and an urgent need
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	International Journal of Antimicrobial Agents, 2019.  An alternative strategy for combination therapy: Interactions between polymyxin B and non-antibiotics
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Journal 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
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Antimicrobial Agents and Chemotherapy, 2020. Extension of Pharmacokinetic/Pharmacodynamic Time-Kill Studies To Include Lipopolysaccharide/Endotoxin Release from Escherichia coli Exposed to Cefuroxime
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Molecular Pharmaceutics, 2020. Model-Informed Drug Development in Pulmonary Delivery: Semimechanistic Pharmacokinetic–Pharmacodynamic Modeling for Evaluation of Treatments against Chronic Pseudomonas aeruginosa Lung Infections
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Antimicrobial Agents and Chemotherapy, 2020. Efficacy of Antibiotic Combinations against MultidrugResistant Pseudomonas aeruginosa in Automated Time-Lapse
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical 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
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	International 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
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical Microbiology and Infection, 2020. Semi-mechanistic PK/PD modelling of combined polymyxin B and minocycline against a polymyxin-resistant strain of Acinetobacter baumannii
2015	Antimicrobial Resistance through the JPIAMR	CO-ACTION	Clinical 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
2016	Antimicrobial Resistance through the JPIAMR	CO-ACTION	International Journal of Antimicrobial Agents, 2020. Pharmacodynamics of immune response biomarkers of interest for evSaluation of treatment effects in bacterial infections
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Molecular Microbiology, 2017.  Silver potentiates aminoglycoside toxicity by enhancing their uptake
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Nature, 2018.  Species-specific activity of antibacterial drug combinations
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Nucleic Acid Research, 2018.  Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	bioRxiv, 2018.  RocS drives chromosome segregation and nucleoid occlusion in Streptococcus pneumoniae
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Nucleic Acids Research, 2018.  High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Cell Reports, 2018.  Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Genes, 2019.  Three new integration vectors and fluorescent proteins for use in the opportunistic human pathogen Streptococcus pneumoniae
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	CPT:Pharmacometrics & Systemics Pharmacology, 2017. Translational Pharmacometric Evaluation of Typical Antibiotic Broad‐Spectrum Combination Therapies Against Staphylococcus Aureus Exploiting In Vitro Information
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	bioRxiv, 2020. Dissecting the collateral damage of antibiotics on gut microbes
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Cell Host & Microbe, 2020. Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Nature Microbiology, 2019. RocS drives chromosome segregation and nucleoid protection in Streptococcus pneumoniae
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Pharmaceutical Research, 2021. Which Analysis Approach Is Adequate to Leverage Clinical Microdialysis Data? A Quantitative Comparison to Investigate Exposure and Reponse Exemplified by Levofloxacin.
2015	Antimicrobial Resistance through the JPIAMR	ABIMMUNE	Respiratory Research, 2021. Post-treatment with the PPAR-γ agonist pioglitazone inhibits inflammation and bacterial growth during Klebsiella pneumonia
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ARMIS	Biointerface Research in Applied Chemistry, 2019. Prevalence of vancomycin resistance phenotypes among Enterococcus species isolated from
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ImpresU	JAMDA, 2020. Antibiotic Stewardship in European Nursing Homes: Experiences From the Netherlands, Norway, Poland, and Sweden
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	INART	ACCESS MICROBIOLOGY, 2019. Occurrence of extended-spectrum β-lactamase (ESBL)/AmpC producing bacteria in wastewater treatment plant effluent
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	INART	Antibiotics and Antimicrobial Resistance Genes, 2020. Treatment Technologies for Removal of Antibiotics, Antibiotic Resistance Bacteria and Antibiotic-Resistant Genes
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	AB-Assistant	BMJ Open 2020. Study protocol for an international, multicentre stepped-wedge cluster randomised trial to evaluate the impact of a digital antimicrobial stewardship smartphone application
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	RESILIENCE	The Lancet Infectious Diseases, 2020. Evidence for action: a One Health learning platform on interventions to tackle antimicrobial resistance
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ASB	J Antibiotics, 2020. Industry incentives and antibiotic resistance: an introduction to the antibiotic susceptibility bonus
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	INART	Frontiers in Microbiology, 2021. Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture.
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ASB	Frontiers in Medicine, 2021. Surveillance of Resistance to New Antibiotics in an Era of Limited Treatment Options.
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	REDUCEAMU	Frontiers in Microbiology, 2021. Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	REDUCEAMU	Front. Vet. Sci., 2021. Geographic Drivers of Antimicrobial Use and Resistance in Pigs in Khon Kaen Province, Thailand
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ExcludeMRSA	Irish 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
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	ExcludeMRSA	mSystems, 2021. Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	AMResilience	BMC 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
2014	InnovaResistance	DesInMBL	Journal of Enzyme Inhibition and Medicinal Chemistry, 2017.  Beta-lactamase database (BLDB) – structure and function
2014	InnovaResistance	DesInMBL	International 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
2014	InnovaResistance	DesInMBL	Proteins: Structure, Function, and Bioinformatics, 2016.  Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites
2014	InnovaResistance	DesInMBL	Journal of Computer-Aided Molecular Design, 2018.  Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
2014	InnovaResistance	DesInMBL	Journal of Computer-Aided Molecular Design, 2018.  SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies
2014	InnovaResistance	DesInMBL	Journal 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
2014	InnovaResistance	DesInMBL	Journal of Computer-Aided Molecular Design, 2019.  Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
2014	InnovaResistance	DesInMBL	The Journal of Molecular Diagnotics, 2020. Evaluation of the BD MAX Check-Points CPO Assay for the Detection of Carbapenemase Producers Directly from Rectal Swabs
2014	InnovaResistance	DesInMBL	Journal 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
2014	InnovaResistance	DesInMBL	ACS Infectious Diseases, 2019. Genetic, Biochemical, and Structural Characterization of CMY-136 β-Lactamase, a Peculiar CMY-2 Variant
2014	InnovaResistance	DesInMBL	Antimicrobial 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
2014	InnovaResistance	DesInMBL	Journal of Antimicrobial Chemotherapy, 2019. SME-4-producing Serratia marcescens from Argentina belonging to clade 2 of the S. marcescens phylogeny
2014	InnovaResistance	DesInMBL	Journal of Antimicrobial Chemotherapy, 2019. Unravelling ceftazidime/avibactam resistance of KPC-28, a KPC-2 variant lacking carbapenemase activity
2014	InnovaResistance	DesInMBL	Journal of Clinical Microbiology, 2019. Evaluation of the Amplidiag CarbaR+MCR Kit for Accurate Detection of Carbapenemase-Producing and Colistin-Resistant Bacteria
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2018. Genetic and Biochemical Characterization of OXA-535, a Distantly Related OXA-48-Like β-Lactamase
2014	InnovaResistance	DesInMBL	Drug Resistance Updates, 2018. A close look onto structural models and primary ligands of metallo-β-lactamases
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2017. Molecular Characterization of OXA-198 Carbapenemase-Producing Pseudomonas aeruginosa Clinical Isolates
2014	InnovaResistance	DesInMBL	Journal 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
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2018. Genetic and Biochemical Characterization of OXA-519, a Novel OXA-48-Like β-Lactamase
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2018. Diversity of Carbapenemase-Producing Escherichia coli Isolates
2014	InnovaResistance	DesInMBL	Journal of Clinical Microbiology, 2019. Evaluation of the Amplidiag CarbaR+MCR Kit for Accurate Detection of Carbapenemase-Producing and Colistin-Resistant Bacteria
2014	InnovaResistance	DesInMBL	Journal of Clinical Microbiology, 2018. Evaluation of the Amplidiag CarbaR+VRE Kit for Accurate Detection of Carbapenemase-Producing Bacteria
2014	InnovaResistance	DesInMBL	Frontiers in Microbiology, 2018. Transcriptional Landscape of a blaKPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2018. Proposing Kluyvera georgiana as the Origin of the Plasmid-Mediated Resistance Gene fosA4
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2018. Complete Sequence of the IncA/C1 Plasmid pCf587 Carrying blaPER-2 from Citrobacter freundii
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2017. Comparison of Two Phenotypic Algorithms To Detect Carbapenemase-Producing Enterobacteriaceae
2014	InnovaResistance	DesInMBL	Journal 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
2014	InnovaResistance	DesInMBL	Antimicrobial Agents and Chemotherapy, 2016. First Occurrence of OXA-72-Producing Acinetobacter baumannii in Serbia
2014	InnovaResistance	DesInMBL	Journal 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
2014	InnovaResistance	DesInMBL	Frontiers in Microbiology, 2020. Genetics of Acquired Antibiotic Resistance Genes in Proteus spp.
2014	InnovaResistance	DesInMBL	Current Drug Targets, 2016. Structural and Functional Aspects of Class A Carbapenemases
2014	InnovaResistance	DesInMBL	Scientific Reports, 2020. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales
2014	InnovaResistance	DesInMBL	International Journal of Biological Macromolecules. 2020. Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates
2014	InnovaResistance	EVOBIOTIC	Nucleic Acids Research, 2015.  Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)
2014	InnovaResistance	EVOBIOTIC	Nature Communications, 2015.  An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products
2014	InnovaResistance	NAPCLI	Current Opinion in Microbiology, 2017.  The divisome at 25: the road ahead
2014	InnovaResistance	NAPCLI	mBio, 2018.  Structural analysis of the interaction between the bacterial cell division proteins FtsQ and FtsB
2014	InnovaResistance	NAPCLI	Molecular Microbiology, 2018. Induced conformational changes activate the peptidoglycan synthase PBP1B
2014	InnovaResistance	NAPCLI	The Cell Surface, 2018. Coupling of polymerase and carrier lipid phosphatase prevents product inhibition in peptidoglycan synthesis
2014	InnovaResistance	NAPCLI	Frontiers in Microbiology, 2019. Recognition of Peptidoglycan Fragments by the Transpeptidase PBP4 From Staphylococcus aureus
2014	InnovaResistance	NAPCLI	Frontiers in Microbiology, 2018. The Fluorescent D-Amino Acid NADA as a Tool to Study the Conditional Activity of Transpeptidases in Escherichia coli
2014	InnovaResistance	NAPCLI	mBio, 2019. Peptidoglycan Remodeling Enables Escherichia coli To Survive Severe Outer Membrane Assembly Defect
2014	InnovaResistance	NAPCLI	Molecular Microbiology, 2017. Peptidoglycan in obligate intracellular bacteria
2014	InnovaResistance	NAPCLI	Bio-protocol, 2018. Bacterial Cell Wall Precursor Phosphatase Assays Using Thin-layer Chromatography (TLC) and High Pressure Liquid Chromatography (HPLC)
2014	InnovaResistance	NAPCLI	PNAS, 2018. Copper inhibits peptidoglycan LD-transpeptidases suppressing β-lactam resistance due to bypass of penicillin-binding proteins
2014	InnovaResistance	NAPCLI	Frontiers in Cellular and Infection Microbiology, 2017. AmiD Is a Novel Peptidoglycan Amidase in Wolbachia Endosymbionts of Drosophila melanogaster
2014	InnovaResistance	NAPCLI	eLife, 2016. Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli
2014	InnovaResistance	NAPCLI	Chemistry A European Journal, 2018. Critical Impact of Peptidoglycan Precursor Amidation on the Activity of l,d‐Transpeptidases from Enterococcus faecium and Mycobacterium tuberculosis
2014	InnovaResistance	NAPCLI	Journal of Biological Chemistry, 2018. Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus
2014	InnovaResistance	NAPCLI	Structure, 2020. Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa
2014	InnovaResistance	NAPCLI	Nature Communications, 2019. Structural Insight Into YcbB-mediated Beta-Lactam Resistance in Escherichia Coli
2014	InnovaResistance	NoTBSec	Journal of Biological Chemistry, 2016. iniBAC induction Is Vitamin B12- and MutAB-dependent in Mycobacterium marinum
2014	InnovaResistance	NoTBSec	Plos Genetics, 2017. Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose
2014	InnovaResistance	NoTBSec	Plos Neglected Tropical Diseases, 2019. Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening
2014	InnovaResistance	NoTBSec	Antimicrobial Agents and Chemotherapy, 2018. Rifabutin Acts in Synergy and Is Bactericidal with Frontline Mycobacterium abscessus Antibiotics Clarithromycin and Tigecycline, Suggesting a Potent Treatment Combination
2014	InnovaResistance	NoTBSec	Antimicrobial 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
2014	InnovaResistance	NoTBSec	Molecular Microbiology, 2017. Regulatory genes coordinating antibiotic‐induced changes in promoter activity and early transcriptional termination of the mycobacterial intrinsic resistance gene whiB7
2014	InnovaResistance	NoTBSec	Scientific Reports 2016. Repurposing clinically approved cephalosporins for tuberculosis therapy
2014	InnovaResistance	NoTBSec	PNAS, 2016. Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria
2014	InnovaResistance	NoTBSec	Cellular Microbiology, 2017. ESX‐1 and phthiocerol dimycocerosates of Mycobacterium tuberculosis act in concert to cause phagosomal rupture and host cell apoptosis
2014	InnovaResistance	NoTBSec	Nature Microbiology, 2018. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis
2014	InnovaResistance	NoTBSec	PNAS, 2018. Mycobacterial ESX-1 secretion system mediates host cell lysis through bacterium contact-dependent gross membrane disruptions
2014	InnovaResistance	NoTBSec	Molecular Microbiology, 2016. Discovery of the type VII ESX‐1 secretion needle?
2014	InnovaResistance	NoTBSec	Cell Reports, 2018. Multiplexed Quantitation of Intraphagocyte Mycobacterium tuberculosis secrected proetien effectors
2014	InnovaResistance	NoTBSec	Cell Reports, 2017. Recombinant BCG Expressing ESX-1 of Mycobacterium marinum Combines Low Virulence with Cytosolic Immune Signaling and Improved TB Protection
2014	InnovaResistance	NoTBSec	Nature REviews Microbiology, 2016. ESX secretion systems: mycobacterial evolution to counter host immunity
2014	InnovaResistance	NoTBSec	Plos 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
2014	InnovaResistance	NoTBSec	Plos One, 2015. Benzoic Acid-Inducible Gene Expression in Mycobacteria
2014	InnovaResistance	NoTBSec	Infection and Immunity, 2018. Genetic Variation/Evolution and Differential Host Responses Resulting from In-Patient Adaptation of Mycobacterium avium
2014	InnovaResistance	NPERDMDR	PLOS ONE, 2017.  Effective Control of Molds Using a Combination of Nanoparticles
2014	InnovaResistance	NPERDMDR	Journal of Nanobiotechnology, 2017.  Metal nanoparticles: understanding the mechanisms behind antibacterial activity
2014	InnovaResistance	NPERDMDR	Journal of Materials Chemistry B, 2016.  A one-step sonochemical synthesis of stable ZnO–PVA nanocolloid as a potential biocidal agent
2014	InnovaResistance	NPERDMDR	International Journal of Nanomedicine, 2016. Ga@C-dots as an antibacterial agent for the eradication of Pseudomonas aeruginosa
2014	InnovaResistance	NPERDMDR	Chemistry and Physics of Lipids, 2019. Physical states and thermodynamic properties of model gram-negative bacterial inner membranes
2014	InnovaResistance	NPERDMDR	Current Topics in Medicinal Chemistry, 2017. Innovative Approaches for Controlling Clinically Relevant Biofilms: Current Trends and Future Prospects
2014	InnovaResistance	NPERDMDR	Journal of Applied Polymer Science, 2017. Sonochemical synthesis and stabilization of concentrated antimicrobial silver‐chitosan nanoparticle dispersions
2014	InnovaResistance	NPERDMDR	ACS Appl. Mater. Interfaces, 2017. Nanotransformation of Vancomycin Overcomes the Intrinsic Resistance of Gram-Negative Bacteria
2014	InnovaResistance	NPERDMDR	Process Biochemistry, 2017. Immobilization of antimicrobial core-shell nanospheres onto silicone for prevention of Escherichia coli biofilm formation
2014	InnovaResistance	NPERDMDR	Nanomedicine: Nanotechnology, Biology and Medicine, 2016. Escherichia coli and Pseudomonas aeruginosa eradication by nano-penicillin G
2014	InnovaResistance	NPERDMDR	Acta Biomaterialia, 2016. Bacteria-responsive multilayer coatings comprising polycationic nanospheres for bacteria biofilm prevention on urinary catheters
2014	InnovaResistance	NPERDMDR	Ind. Eng. Chem. Res, 2017. Hybrid Chitosan–Silver Nanoparticles Enzymatically Embedded on Cork Filter Material for Water Disinfection
2014	InnovaResistance	SENBIOTAR	Virology Journal, 2015.  Glycoside hydrolase family 32 is present in Bacillus subtilis phages
2014	InnovaResistance	SENBIOTAR	Drug Discovery Today: Technologies, 2018.  Automated assays for thermodynamic (equilibrium) solubility determination
2014	InnovaResistance	SENBIOTAR	Molecules, 2018. In Silico and in Vitro-Guided Identification of Inhibitors of Alkylquinolone-Dependent Quorum Sensing in Pseudomonas aeruginosa
2014	InnovaResistance	SENBIOTAR	Journal of Medicinal Chemistry, 2018. Pseudomonas aeruginosa Quorum Sensing Systems as Drug Discovery Targets: Current Position and Future Perspectives
2014	InnovaResistance	SENBIOTAR	Annals of the New York Academy of Sciences, 2019.  Genomics of antibiotic‐resistance prediction in Pseudomonas aeruginosa
2014	InnovaResistance	SENBIOTAR	Journal of Pharmaceutical Sciences, 2019.  Model-based drug development in pulmonary delivery: Pharmacokinetic analysis of novel drug candidates for treatment of Pseudomonas aeruginosa lung infection
2014	InnovaResistance	EVOBIOTIC	Research in Microbiology, 2020. Escherichia coli O-antigen Capsule (Group 4) is Essential for Serum Resistance
2014	InnovaResistance	DesInMBL	European 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)
2014	InnovaResistance	DesInMBL	Journal of Computer-Aided Molecular Design, 2021. Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	bioRxiv, 2019. Spatio-temporal control of DNA replication by the pneumococcal cell cycle regulator CcrZ
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Molecular Microbiology, 2019. BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	bioRxiv, 2020. Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	bioRxiv, 2020. Unbiased homeologous recombination during pneumococcal transformation allows for multiple chromosomal integration events
2019	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	bioRxiv - June 2020. Harnessing CRISPR-Cas9 for genome editing in Streptococcus pneumoniae
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Nature Structural & Molecular Biology, 2020. Structure of a proton-dependent lipid transporter involved in lipoteichoic acids biosynthesis
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	MicrobiologyOpen, 2020. Penicillin‐binding protein PBP2a provides variable levels of protection toward different β‐lactams in Staphylococcus aureus RN4220
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	FLAV4AMR	International Journal of Molecular Sciences, 2020. Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	PNAS, 2020. A widespread toxin−antitoxin system exploiting growth control via alarmone signaling
2019	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	Nature Reviews Microbiology, 2020. Target protection as a key antibiotic resistance mechanism
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RESET-ME	Angewandte Chemie International Edition, 2021. Large Peptide Permeation Through a Membrane Channel: Understanding Protamine Translocation Through CymA from Klebsiella Oxytoca
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	Explore	ChemMedChem, 2021. Fragment‐based drug discovery for RNA targets.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	Nature Communications, 2021. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Nature Microbiology, 2021. CcrZ is a pneumococcal spatiotemporal cell cycle regulator that interacts with FtsZ and controls DNA replication by modulating the activity of DnaA
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	Molecular Cell, 2021. (p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	Nature Communications, 2021. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	Molecular Cell, 2021. RelA-SpoT Homolog toxins pyrophosphorylate the CCA end of tRNA to inhibit protein synthesis
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	bioRxiv, 2021. Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics
2018	JPIAMR-VRI Network Call	CONNECT	Human Genetics, 2020. Delineation of phenotypes and genotypes related to cohesin structural protein RAD21
2018	JPIAMR-VRI Network Call	TRANSLOCATION-transfer	Microorganisms, 2020. When Combined with Colistin, an Otherwise Ineffective Rifampicin–Linezolid Combination Becomes Active in Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii
2018	JPIAMR-VRI Network Call	TRANSLOCATION-transfer	Expert Opinion on Drug Discovery, 2021. Future prospects for Antimicrobial peptide development: peptidomimetics and antimicrobial combinations.
2018	JPIAMR-VRI Network Call	VeRI BEAM	Drug Discovery Today, 2021. Improving the ability of antimicrobial susceptibility tests to predict clinical outcome accurately: adding metabolic evasion to the equation.
2018	JPIAMR-VRI Network Call	IRAADD	Nature Reviews Chemistry, 2021. Towards the sustainable discovery and development of new antibiotics
2018	Network Call on Surveillance	CoEval-AMR	Clinical Microbiology and Infection, 2020. Evaluating integrated surveillance of antimicrobial resistance: experiences from use of three evaluation tools
2018	Network Call on Surveillance	ICALM	Intensive Care Medicine, 2019. The association of cardiovascular failure with treatment for ventilator-associated lower respiratory tract infection
2018	Network Call on Surveillance	ICALM	Intensive Care Medicine, 2020. Antibiotic prophylaxis in the ICU: to be or not to be administered for patients undergoing procedures?
2018	Network Call on Surveillance	WAWES	Book 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
2018	Network Call on Surveillance	WAWES	Antimicrobial Agents and Chemotherapy, 2019. Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic-Resistant Bacteria
2018	Network Call on Surveillance	CoEval-AMR	Frontiers in Veterinary Science, 2021. Evaluating the Integration of One Health in Surveillance Systems for Antimicrobial Use and Resistance: A Conceptual Framework
2018	Network Call on Surveillance	PRAISE	Clinical Microbiology and Infection, 2021. Getting it right: automated surveillance of healthcare-associated infections
2018	Network Call on Surveillance	PRAISE	Clinical Microbiology and Infection, 2021. PRAISE: providing a roadmap for automated infection surveillance in Europe
2018	Network Call on Surveillance	PRAISE	Clinical Microbiology and Infection, 2021. Governance aspects of large-scale implementation of automated surveillance of healthcare-associated infections
2018	Network Call on Surveillance	PRAISE	Clinical Microbiology and Infection, 2021. Information technology aspects of large-scale implementation of automated surveillance of healthcare-associated infections
2018	Network Call on Surveillance	CoEval-AMR	Frontiers in Veterinary Science, 2021. Assessment of Evaluation Tools for Integrated Surveillance of Antimicrobial Use and Resistance Based on Selected Case Studies
2016	Transmission Dynamics	AWARE	Environment International, 2018.  Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms
2016	Transmission Dynamics	AWARE	Journal of Environmental Protection, 2017. Physico-Chemical and Microbiological Assessment of Organic Pollution in Plain Salty Lakes from Protected Regions
2016	Transmission Dynamics	AWARE	PlosOne, 2020. Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania
2016	Transmission Dynamics	AWARE	MEDICHUB MEDIA, 2018. Review on methods for analyzing the antibiotic resistance in wastewater samples
2016	Transmission Dynamics	BEAT-AMR	bioRxiv, 2020. An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1
2016	Transmission Dynamics	Collateral Damage	PNAS, 2018. Cellular hysteresis as a principle to maximize the efficacy of antibiotic therapy
2016	Transmission Dynamics	Collateral Damage	Nature Communications, 2018. Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli
2016	Transmission Dynamics	Collateral Damage	Scandinavian 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
2016	Transmission Dynamics	Collateral Damage	PloS Biology, 2020. Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin
2016	Transmission Dynamics	Gene-gas	Journal of Visualized Experiments: JoVE, 2018.  Ultrasensitive Detection of Biomarkers by Using a Molecular Imprinting Based Capacitive Biosensor
2016	Transmission Dynamics	Gene-gas	Frontiers in Microbiology, 2020. Biotechnological Potential of Bdellovibrio and Like Organisms and Their Secreted Enzymes
2016	Transmission Dynamics	Gene-gas	Sensors and Actuators B: Chemical, 2018. Bacteriophages as biorecognition elements in capacitive biosensors: Phage and host bacteria detection
2016	Transmission Dynamics	JumpAR	Cell, 2018.  Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance
2016	Transmission Dynamics	JumpAR	Current Opinion in Structural Biology, 2019. Jump ahead with a twist: DNA acrobatics drive transposition forward
2016	Transmission Dynamics	MODERN	Antimicrobial Resistance & Infection Control, 2018. Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence
2016	Transmission Dynamics	MODERN	The 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
2016	Transmission Dynamics	MODERN	International 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
2016	Transmission Dynamics	MODERN	Antimicrobial Resistance & Infection Control, 2018. Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence
2016	Transmission Dynamics	PET-Risk	Veterinary Microbiology, 2019.  Clonal relatedness of Proteus mirabilis strains causing urinary tract infections in companion animals and humans
2016	Transmission Dynamics	PET-Risk	Journal of Antimicrobial Chemotherapy, 2019. Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes
2016	Transmission Dynamics	PET-Risk	Microbial Drug Resistance, 2020. Sharing of Clinically Important Antimicrobial Resistance Genes by Companion Animals and Their Human Household Members
2016	Transmission Dynamics	PET-Risk	Journal of Antimicrobial Chemotherapy, 2019. Emergence of Escherichia coli ST131 H30/H30-Rx subclones in companion animals
2016	Transmission Dynamics	PNEUMOSPREAD	Journal of Allergy and Clinical Immunology, 2020. Regulating T cell differentiation through the polyamine spermidine
2016	Transmission Dynamics	PNEUMOSPREAD	Nature Microbiology, 2019. Pneumolysin binds to the mannose receptor C type 1 (MRC-1) leading to anti-inflammatory responses and enhanced pneumococcal survival
2016	Transmission Dynamics	PREPARE	Heredity, 2018.  The fitness landscape of the codon space across environments
2016	Transmission Dynamics	PREPARE	Evolution, 2019. How phenotypic convergence arises in experimental evolution
2016	Transmission Dynamics	PREPARE	Evolution, 2019. Environment changes epistasis to alter trade‐offs along alternative evolutionary paths
2016	Transmission Dynamics	PREPARE	Nature Ecology & Evolution, 2020. Dysbiosis personalizes fitness effect of antibiotic resistance in the mammalian gut
2016	Transmission Dynamics	PREPARE	PLOS Biology, 2020. Low mutational load and high mutation rate variation in gut commensal bacteria
2016	Transmission Dynamics	Restrict-Pneumo-AMR	International Journal of Chronic Obstructive Pulmonary Disease, 2019. Personalized medicine for patients with COPD: where are we?
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Frontiers in Immunology, 2019. Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Nature Communications, 2020. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.
2016	Transmission Dynamics	SpARK	Frontiers in Microbiology, 2019. Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov
2016	Transmission Dynamics	SpARK	bioRxiv, 2020. Genomic Epidemiology with Mixed Samples
2016	Transmission Dynamics	SpARK	Wellcome Open Res, 2020.  High-resolution sweep metagenomics using ultrafast read mapping and inference
2016	Transmission Dynamics	ST131TS	Eurosurveillance, 2019. Emergence of diversity in carbapenemase-producing Escherichia coli ST131, England, January 2014 to June 2016
2016	Transmission Dynamics	ST131TS	Infection, Genetics and Evolution, 2020. The evolutionary puzzle of Escherichia coli ST131
2016	Transmission Dynamics	ST131TS	mBio, 2020. Simulating multi-level dynamics of antimicrobial resistance in a membrane computing model
2016	Transmission Dynamics	STARCS	Environment International, 2018.  Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids
2016	Transmission Dynamics	STARCS	Microbiome, 2018.  In-depth resistome analysis by targeted metagenomics
2016	Transmission Dynamics	STARCS	Science of The Total Environment, 2018.  Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal
2016	Transmission Dynamics	STARCS	bioRxiv, 2019.  Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome
2016	Transmission Dynamics	STARCS	Microbial Genomics, 2018. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
2016	Transmission Dynamics	STARCS	Environmental 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
2016	Transmission Dynamics	STARCS	Frontiers 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
2016	Transmission Dynamics	STARCS	Annals of the New York Academy of Sciences, 2016. Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
2016	Transmission Dynamics	STARCS	Bioinformatics, 2017. AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks
2016	Transmission Dynamics	STARCS	Nature Microbiology, 2018. Prediction of the intestinal resistome by a three-dimensional structure-based method
2016	Transmission Dynamics	STARCS	F1000Research, 2018. The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
2016	Transmission Dynamics	STARCS	Foodborne 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
2016	Transmission Dynamics	STARCS	Environmental Microbiology, 2019. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species
2016	Transmission Dynamics	STARCS	Royal Society of Open Science, 2017. Modelling the impact of curtailing antibiotic usage in food animals on antibiotic resistance in humans
2016	Transmission Dynamics	STARCS	Bioinformatics, 2020. gplas: a comprehensive tool for plasmid analysis using short-read graphs
2016	Transmission Dynamics	TransPred	bioRxiv, 2018.  Conjugation factors controlling F-plasmid antibiotic resistance transmission
2016	Transmission Dynamics	TransPred	Plos Computational Biology, 2018. Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
2016	Transmission Dynamics	TransPred	Scientific 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
2016	Transmission Dynamics	TransPred	Drug Development Research, 2018. Inhibiting conjugation as a tool in the fight against antibiotic resistance
2016	Transmission Dynamics	TransPred	bioRxiv, 2020. Genomic epidemiology and evolution of Escherichia coli in wild animals
2016	Transmission Dynamics	Gene-gas	Front. Microbiol, 2017. Revisiting Antibiotic Resistance Spreading in Wastewater Treatment Plants – Bacteriophages as a Much Neglected Potential Transmission Vehicle
2016	Transmission Dynamics	Gene-gas	Journal of Bacteriology, 2020. Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle
2016	Transmission Dynamics	ST131TS	Clinical Microbiol and Infection, 2020. Molecular epidemiology of Escherichia coli causing bloodstream infections in a centralized Canadian region: a population-based surveillance study
2016	Transmission Dynamics	ST131TS	Antimicrob Agents Chemother, 2020. Emerging Antimicrobial Resistant High-Risk clones among Klebsiella pneumoniae: ST307 and ST147
2016	Transmission Dynamics	ST131TS	Front Microbiol, 2020. Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages
2016	Transmission Dynamics	ST131TS	J Antimicrob Chemother, 2019. Emergence of the C1-M27 cluster in ST131 Escherichia coli from companion animals in France
2016	Transmission Dynamics	ST131TS	Appl Environ Microbiol, 2020. A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains
2016	Transmission Dynamics	STARCS	Front. Microbiol, 2020. Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health
2016	Transmission Dynamics	BEAT-AMR	Journal of Hospital Infection, 2020. Selection of resistance by antimicrobial coatings in the healthcare setting
2016	Transmission Dynamics	PNEUMOSPREAD	J Mol Med, 2021. Clarithromycin impairs tissue-resident memory and Th17 responses to macrolide-resistant Streptococcus pneumoniae infections.
2016	Transmission Dynamics	STARCS	Genome Medicine, 2021. The global dissemination of hospital clones of Enterococcus faecium
2016	Transmission Dynamics	MODERN	Nature Microbiology, 2021. Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients.
2016	Transmission Dynamics	HECTOR	Frontiers in Microbiology, 2021. Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe.
2016	Transmission Dynamics	TransPred	bioRxiv, 2021. Machine learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes
2016	Transmission Dynamics	PREPARE	Molecular Biology and Evolution, 2021. DNA breaks-mediated fitness cost reveals RNase HI as a new target for selectively eliminating antibiotic resistant bacteria.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Scientific Reports, 2021. Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples.
2016	Transmission Dynamics	JumpAR	Molecular Systems Biology, 2021. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Advanced Drug Delivery Reviews, 2021. The clinical role of host and bacterial-derived extracellular vesicles in pneumonia
2016	Transmission Dynamics	Gene-gas	Journal of Oral Microbiology, 2021. Entamoeba gingivalis: epidemiology, genetic diversity and association with oral microbiota signatures in North Eastern Tanzania
2016	Transmission Dynamics	STARCS	bioRxiv, 2021. A high-throughput multiplexing and selection strategy to complete bacterial genomes
2016	Transmission Dynamics	ST131TS	medRxiv, 2021. Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Mediators of Inflammation, 2021. Hypoxia-Inducible Factor-1α in Macrophages, but Not in Neutrophils, Is Important for Host Defense during Klebsiella pneumoniae-Induced Pneumosepsis
2016	Transmission Dynamics	HECTOR	bioRxiv, 2021. Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution
2016	Transmission Dynamics	TransComp-ESC-R	Microorganisms, 2021. Successful Dissemination of Plasmid-Mediated Extended-Spectrum β-Lactamases in Enterobacterales over Humans to Wild Fauna
2016	Transmission Dynamics	STARCS and ST131TS	Clinical Microbiology Reviews, 2021. Evolutionary Pathways and Trajectories in Antibiotic Resistance
2016	Transmission Dynamics	TransPred	mSystems, 2021. Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes
2016	Transmission Dynamics	TransComp-ESC-R	mBio, 2021. Host Colonization as a Major Evolutionary Force Favoring the Diversity and the Emergence of the Worldwide Multidrug-Resistant Escherichia coli ST131
2016	Transmission Dynamics	BEAT-AMR	Front Microbiol, 2021. Prevalent Synergy and Antagonism Among Antibiotics and Biocides in Pseudomonas aeruginosa.
2016	Transmission Dynamics	BEAT-AMR	Curr Opin Biotechnol, 2020. Environmental drivers of metabolic heterogeneity in clonal microbial populations.
2016	Transmission Dynamics	BEAT-AMR	J Colloid Interface Sci, 2019. Substrate viscosity plays an important role in bacterial adhesion under fluid flow.
2016	Transmission Dynamics	Collateral Damage	Cell. Mol. Life Sci. 77, 2020. Multi-scale modeling of drug binding kinetics to predict drug efficacy.
2016	Transmission Dynamics	Collateral Damage	PLoS Comput Biol, 2020. Drug-target binding quantitatively predicts optimal antibiotic dose levels in quinolones.
2016	Transmission Dynamics	Collateral Damage	Nat Commun, 2019. Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase.
2016	Transmission Dynamics	Collateral Damage	FEMS Microbiology Reviews, 2020. Antibiotic resistance: turning evolutionary principles into clinical reality
2016	Transmission Dynamics	Collateral Damage	EClinicalMedicine, 2019. Three versus five days of pivmecillinam for community-acquired uncomplicated lower urinary tract infection: A randomised, double-blind, placebo-controlled superiority trial.
2016	Transmission Dynamics	Collateral Damage	Infect Drug Resist, 2019. Pivmecillinam compared to other antimicrobials for community-acquired urinary tract infections with Escherichia coli, ESBL-producing or not – a retrospective cohort study.
2016	Transmission Dynamics	Collateral Damage	Antimicrobial Chemotherapy, 2019. Treatment duration of pivmecillinam in men, non-pregnant and pregnant women for community-acquired urinary tract infections caused by Escherichia coli: a retrospective Danish cohort study, Journal of Antimicrobial Chemotherapy
2016	Transmission Dynamics	Collateral Damage	Antibiotics, 2019. "Pivmecillinam for Uncomplicated Lower Urinary Tract Infections Caused by Staphylococcus saprophyticus—Cumulative Observational Data from Four Recent Clinical Studies"
2016	Transmission Dynamics	Collateral Damage	mSphere. 2019. OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs.
2016	Transmission Dynamics	Collateral Damage	PLoS Pathog, 2021. Mechanisms and therapeutic potential of collateral sensitivity to antibiotics.
2016	Transmission Dynamics	Collateral Damage	Antimicrob Agents Chemother, 2020. Ciprofloxacin Pharmacokinetics/Pharmacodynamics against Susceptible and Low-Level Resistant Escherichia coli Isolates in an Experimental Ascending Urinary Tract Infection Model in Mice.
2016	Transmission Dynamics	Collateral Damage	J Glob Antimicrob Resist, 2020. Manganese complex [Mn(CO)3(tpa-κ3N)]Br increases antibiotic sensitivity in multidrug resistant Streptococcus pneumoniae.
2016	Transmission Dynamics	DARWIN	Sci Total Environ, 2020. Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review.
2016	Transmission Dynamics	DARWIN	Environ. Sci. Technol. Lett, 2018. Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community
2016	Transmission Dynamics	DARWIN	FEMS Microbiol Ecol, 2018. Water and sanitation: an essential battlefront in the war on antimicrobial resistance.
2016	Transmission Dynamics	DARWIN	Plasmid, 2018. Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives.
2016	Transmission Dynamics	DARWIN	Environ. Sci. Technol. 2021. Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage
2016	Transmission Dynamics	DARWIN	Water Res, 2019. Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters.
2016	Transmission Dynamics	EMerGE-NeT	PLoS Comput Biol, 2021. Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections.
2016	Transmission Dynamics	EMerGE-NeT	PLoS Comput Biol, 2021. Relevance of intra-hospital patient movements for the spread of healthcare-associated infections within hospitals - a mathematical modeling study.
2016	Transmission Dynamics	EMerGE-NeT	PLoS Comput Biol, 2021. Modelling pathogen spread in a healthcare network: Indirect patient movements.
2016	Transmission Dynamics	EMerGE-NeT	Epidemics, 2020. Impact of inter-hospital transfers on the prevalence of resistant pathogens in a hospital–community system.
2016	Transmission Dynamics	EMerGE-NeT	MATHEMATICA APPLICANDA, 2019. Analysis of the AOK Plus data and derived hospital network.
2016	Transmission Dynamics	EMerGE-NeT	J Infect. 2021. Interventions to reduce infections caused by multidrug resistant Enterobacteriaceae (MDR-E): A systematic review and meta-analysis.
2016	Transmission Dynamics	JumpAR	Nucleic Acids Res, 2021. SMART: recent updates, new developments and status in 2020.
2016	Transmission Dynamics	MODERN	Clinical Microbiology and Infection, 2021. Household acquisition and transmission of extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients
2016	Transmission Dynamics	MODERN	Clinical Microbiology and Infection, 2021. Populations of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: a multicentre European study
2016	Transmission Dynamics	PNEUMOSPREAD	EMBO Mol Med. 2020. Mannose receptor-derived peptides neutralize pore-forming toxins and reduce inflammation and development of pneumococcal disease.
2016	Transmission Dynamics	PNEUMOSPREAD	Cell Microbiol. 2019. Emerging concepts in the pathogenesis of the Streptococcus pneumoniae: From nasopharyngeal colonizer to intracellular pathogen.
2016	Transmission Dynamics	PNEUMOSPREAD	Microorganisms. 2020. Lysogeny in Streptococcus pneumoniae.
2016	Transmission Dynamics	PNEUMOSPREAD	Microorganisms. 2020. Lysogeny in Streptococcus pneumoniae.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	FASEB J. 2020. Influenza virus-mediated suppression of bronchial Chitinase-3-like 1 secretion promotes secondary pneumococcal infection.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	PLoS Comput Biol. 2020. Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	J Cyst Fibros. 2021. Defective BACH1/HO-1 regulatory circuits in cystic fibrosis bronchial epithelial cells.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Proc Natl Acad Sci U S A. 2020. Noncoding RNA MaIL1 is an integral component of the TLR4-TRIF pathway.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	mBio. 2020. A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Sci Rep. 2020. Transcriptional analysis identifies potential biomarkers and molecular regulators in pneumonia and COPD exacerbation
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Cell Signal. 2020. NF-κB-mediated inhibition of microRNA-149-5p regulates Chitinase-3-like 1 expression in human airway epithelial cells.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Nat Commun. 2019. IL-17+ CD8+ T cell suppression by dimethyl fumarate associates with clinical response in multiple sclerosis.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Virulence. 2019. Antibacterial activity of a Tribolium castaneum defensin in an in vitro infection model of Streptococcus pneumoniae.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	J Infect Dis. 2020. Surface Proteome of Plasma Extracellular Vesicles as Biomarkers for Pneumonia and Acute Exacerbation of Chronic Obstructive Pulmonary Disease.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	J Virol. 2019. TMPRSS2 Is the Major Activating Protease of Influenza A Virus in Primary Human Airway Cells and Influenza B Virus in Human Type II Pneumocytes.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	J Clin Invest. 2019. Intestinal development and homeostasis require activation and apoptosis of diet-reactive T cells.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Nat Microbiol. 2019. Intracellular bacteria engage a STING-TBK1-MVB12b pathway to enable paracrine cGAS-STING signalling.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Methods Mol Biol. 2019. ncRNAs in Inflammatory and Infectious Diseases.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Mol Biol Evol. 2021. Pneumococcal Colonization and Virulence Factors Identified Via Experimental Evolution in Infection Models.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Sci Rep. 2020. Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity.
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Annals of Intensive Care, 2021. Association between delay in intensive care unit admission and the host response in patients with community-acquired pneumonia
2016	Transmission Dynamics	SpARK	G3 (Bethesda). 2021. Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae.
2016	Transmission Dynamics	ST131TS	Front Microbiol. 2019. Association Between Kinetics of Early Biofilm Formation and Clonal Lineage in Escherichia coli.
2016	Transmission Dynamics	ST131TS	Infect Immun. 2020. Success of Escherichia coli O25b:H4 Sequence Type 131 Clade C Associated with a Decrease in Virulence.
2016	Transmission Dynamics	ST131TS	J Antimicrob Chemother. 2021. Spatial distribution of Escherichia coli ST131 C subclades in a centralized Canadian urban region.
2016	Transmission Dynamics	ST131TS	Emerg Infect Dis. 2020. Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-2016.
2016	Transmission Dynamics	ST131TS	Infect Genet Evol. 2020. The evolutionary puzzle of Escherichia coli ST131.
2016	Transmission Dynamics	ST131TS	Appl Environ Microbiol. 2020. A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains.
2016	Transmission Dynamics	ST131TS	Clin Microbiol Rev. 2019. Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.
2016	Transmission Dynamics	ST131TS	Diagn Microbiol Infect Dis. 2018. The population structure of clinical extra-intestinal Escherichia coli in a teaching hospital from Nigeria.
2016	Transmission Dynamics	ST131TS	Antimicrob Agents Chemother. 2021. Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination.
2016	Transmission Dynamics	ST131TS	Antimicrob Resist Infect Control, 2018. Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence.
2016	Transmission Dynamics	ST131TS	J Antimicrob Chemother. 2021. Effect of RecA inactivation on quinolone susceptibility and the evolution of resistance in clinical isolates of Escherichia coli.
2016	Transmission Dynamics	ST131TS	Antimicrob Agents Chemother. 2021. Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination.
2016	Transmission Dynamics	ST131TS	Antimicrob Agents Chemother.2020. Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model.
2016	Transmission Dynamics	ST131TS	Nat Microbiol. 2019. Prediction of the intestinal resistome by a three-dimensional structure-based method.
2016	Transmission Dynamics	ST131TS	J Antimicrob Chemother. 2021. Detection in livestock of the human pandemic Escherichia coli ST131 fimH30(R) clone carrying blaCTX-M-27.
2016	Transmission Dynamics	ST131TS	Front Microbiol. 2021. The Origin of Niches and Species in the Bacterial World.
2016	Transmission Dynamics	ST131TS	Nat Microbiol. 2019. Defining and combating antibiotic resistance from One Health and Global Health perspectives.
2016	Transmission Dynamics	ST131TS	Front Microbiol. 2019. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance.
2016	Transmission Dynamics	ST131TS	Methods Mol Biol. 2020. Statistical Analysis of Accessory Genome.
2016	Transmission Dynamics	ST131TS	Methods Mol Biol. 2020. Statistical Analysis of Accessory Genome.
2016	Transmission Dynamics	STARCS	mBio. 2020. Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.
2016	Transmission Dynamics	STARCS	Microb Genom. 2020. Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium.
2016	Transmission Dynamics	STARCS	Nat Commun. 2021. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.
2016	Transmission Dynamics	STARCS	J Antimicrob Chemother. 2021. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17).
2016	Transmission Dynamics	STARCS	Front Microbiol. 2021. The Origin of Niches and Species in the Bacterial World.
2016	Transmission Dynamics	STARCS	Front Microbiol. 2019. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance.
2016	Transmission Dynamics	STARCS	Nat Microbiol. 2019. Defining and combating antibiotic resistance from One Health and Global Health perspectives.
2016	Transmission Dynamics	STARCS	Methods Mol Biol. 2020. Statistical Analysis of Accessory Genome.
2016	Transmission Dynamics	STARCS	Antimicrob Agents Chemother. 2021. Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment.
2016	Transmission Dynamics	STARCS	Microbiol Resour Announc. 2021. Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community.
2016	Transmission Dynamics	STARCS	Elife. 2021. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut.
2016	Transmission Dynamics	STARCS	Nat Commun. 2020. Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum.
2016	Transmission Dynamics	STARCS	Front Genet. 2019. A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries.
2016	Transmission Dynamics	STARCS	J Glob Health. 2019. A cross-sectional survey of practices and knowledge among antibiotic retailers in Nairobi, Kenya.
2016	Transmission Dynamics	STARCS	Int J Antimicrob Agents. 2019. Epidemiology of antimicrobial-resistant Escherichia coli carriage in sympatric humans and livestock in a rapidly urbanizing city.
2016	Transmission Dynamics	STARCS	Clin Microbiol Infect. 2020. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics.
2016	Transmission Dynamics	STARCS	J Microbiol Methods. 2019. Potential in vivo transfer of a blaCTX-M14-harbouring plasmid established by combining long- and short-read sequencing.
2016	Transmission Dynamics	TransComp-ESC-R	Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada. Vet Microbiol. 2019
2016	Transmission Dynamics	TransComp-ESC-R	Microbiology Research. 2021. Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity.
2016	Transmission Dynamics	TransComp-ESC-R	One Health. 2021. Drivers of ESBL-producing Escherichia coli dynamics in calf fattening farms: A modelling study.
2016	Transmission Dynamics	TransPred	FEMS Microbiol Lett. 2020. Teaching about antibiotic resistance to a broad audience: a multidisciplinary approach.
2016	Transmission Dynamics	TransPred	mSphere. 2021. Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico.
2016	Transmission Dynamics	TransPred	Anal Chem. 2019. Chemical Changes On, and Through, The Bacterial Envelope in Escherichia coli Mutants Exhibiting Impaired Plasmid Transfer Identified Using Time-of-Flight Secondary Ion Mass Spectrometry.
2016	Transmission Dynamics	PREPARE	Evol Ecol, 2020. The effect of environmental heterogeneity on the fitness of antibiotic resistance mutations in Escherichia coli.
2016	Transmission Dynamics	PREPARE	Can J Microbiol. 2018. Plasmid persistence: costs, benefits, and the plasmid paradox.
2016	Transmission Dynamics	PREPARE	Genome Biol Evol. 2018. Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli.
2016	Transmission Dynamics	PREPARE	Mol Biol Evol. 2021. The Adaptive Potential of the Middle Domain of Yeast Hsp90.
2016	Transmission Dynamics	PREPARE	Elife. 2020. Comprehensive fitness maps of Hsp90 show widespread environmental dependence.
2016	Transmission Dynamics	PREPARE	EPL, 2018 Playing evolution in the laboratory: From the first major evolutionary transition to global warming.
2016	Transmission Dynamics	PREPARE	Peer Community in Evolutionary Biology, 2018. Let’s move beyond costs of resistance!
2016	Transmission Dynamics	PREPARE	Heredity (Edinb). 2018. The fitness landscape of the codon space across environments.
2016	Transmission Dynamics	PREPARE	Evolutionary Applications. 2020. Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection
2016	Transmission Dynamics	PREPARE	Nat Ecol Evol. 2020. Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut.
2016	Transmission Dynamics	PREPARE	Antimicrob Agents Chemother. 2020. Radial Expansion Facilitates the Maintenance of Double Antibiotic Resistances.
2016	Transmission Dynamics	PREPARE	Trends Microbiol. 2018. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance.
2016	Transmission Dynamics	AWARE	Front Microbiol. 2021. Multidrug Resistant Klebsiella pneumoniae ST101 Clone Survival Chain From Inpatients to Hospital Effluent After Chlorine Treatment.
2016	Transmission Dynamics	AWARE	Syst Rev. 2019. Do wastewater treatment plants increase antibiotic resistant bacteria or genes in the environment? Protocol for a systematic review.
2016	Transmission Dynamics	AWARE	Antibiotics (Basel). 2021. Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study.
2016	Transmission Dynamics	AWARE	Microb Genom. 2020. Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes.
2016	Transmission Dynamics	MACOTRA	Epidemics, 2021. Understanding MRSA clonal competition within a UK hospital; the possible importance of density dependence.
2016	Transmission Dynamics	SpARK	Wellcome Open Res, 2021. High-resolution sweep metagenomics using ultrafast read mapping and inference
2016	Transmission Dynamics	PET-Risk	J 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.
2016	Transmission Dynamics	PET-Risk	Antimicrob Agents Chemother, 2020. OXA-181-Producing Extraintestinal Pathogenic Escherichia coli Sequence Type 410 Isolated from a Dog in Portugal.
2016	Transmission Dynamics	PET-Risk	Journal of Clinical Microbiology, 2019. Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans.
2016	Transmission Dynamics	PET-Risk	Journal of Clinical Microbiology, 2021. Driving Laboratory Standardization of Bacterial Culture and Antimicrobial Susceptibility Testing in Veterinary Clinical Microbiology in Europe and Beyond
2016	Transmission Dynamics	ST131TS	European Journal of Clinical Microbiology & Infectious Diseases, 2021. Population-based epidemiology of Escherichia coli ST1193 causing blood stream infections in a centralized Canadian region
2016	Transmission Dynamics	ST131TS	Philosophical Transactions of the Royal Society B Biological Sciences, 2021. Translational demand is not a major source of plasmid-associated fitness costs.
2016	Transmission Dynamics	MODERN	European 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.
2016	Transmission Dynamics	MODERN	European 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
2016	Transmission Dynamics	Restrict-Pneumo-AMR	Clinical & Experimental Immunology, 2022. The PPAR-γ agonist pioglitazone exerts proinflammatory effects in bronchial epithelial cells during acute Pseudomonas aeruginosa pneumonia.
2016	Transmission Dynamics	STARCS	GigaScience, 2021. A high-throughput multiplexing and selection strategy to complete bacterial genomes
2016	Transmission Dynamics	BEAT-AMR	The ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2021. Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms
2016	Transmission Dynamics	STARCS	The Lancet Microbe, 2022. The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis
2016	Transmission Dynamics	MACOTRA	International Journal of Antimicrobial Agents, 2022. MRSA Surveillance Programmes Worldwide: Moving towards a harmonised international approach
2016	Transmission Dynamics	HECTOR	bioRxiv, 2022. Genome-wide association reveals host-specific genomic traits in Escherichia coli
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Microbiology Spectrum, 2021. Ubericin K, a New Pore-Forming Bacteriocin Targeting mannose-PTS.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Biophysical Journal, 2021. Switching off: the phenotypic transition to the uninduced state of the lactose uptake pathway
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	DISRUPT	Nature Protocols, 2022. CRISPRi-seq for genome-wide fitness quantification in bacteria.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	EMBARK	Nature, 2021. Unravelling the collateral damage of antibiotics on gut bacteria.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	MTI4MDR-TB	Organic & Biomolecular Chemistry, 2021. K2S2O8-mediated coupling of 6-amino-7-aminomethyl-thiazolino-pyridones with aldehydes to construct amyloid affecting pyrimidine-fused thiazolino-2-pyridones.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	MTI4MDR-TB	The Journal of Organic Chemistry, 2021. Tandem Ring Opening/Intramolecular [2 + 2] Cycloaddition Reaction for the Synthesis of Cyclobutane Fused Thiazolino-2-Pyridones.
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	RIBOTARGET	PNAS, 2022. A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains
2018	Innovations against antibiotic-resistant bacteria: New targets, compounds and tools	Anti-Persistence	Research Square, 2022. The structure of SpoT reveals evolutionary tuning of enzymatic output through constraint of the conformational landscape
2018	JPIAMR-VRI Network Call	NEAR-AMR	The Lancet Microbe, 2021. NIMble innovation - a networked model for public antibiotic trials.
2018	Network Call on Surveillance	WAWES	Current Opinion in Microbiology, 2021. The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment.
2018	Network Call on Surveillance	PRAISE	Journal of Hospital Infection, 2022. Automated surveillance systems for healthcare-associated infections: results from a European survey and experiences from real-life utilization.
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	J Bacteriol. 2016. Antibodies Damage the Resilience of Fimbriae, Causing Them To Be Stiff and Tangled.
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Curr Opin Syst Biol, 2017. Chemical genetics in drug discovery.
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Nature. 2018. Species-specific activity of antibacterial drug combinations.
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Front Microbiol. 2018. Enhanced Biofilm Formation and Membrane Vesicle Release by Escherichia coli Expressing a Commonly Occurring Plasmid Gene, kil.
2015	Antimicrobial Resistance through the JPIAMR	Combinatorials	Diagnostics (Basel). 2020. Guideline for Urine Culture and Biochemical Identification of Bacterial Urinary Pathogens in Low-Resource Settings.
2017	Comparison of prevention, control and intervention strategies for AMR infections through multidisciplinary studies, including One Health approaches	INART	Journal of Environmental Management, 2022. Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting