Publications

Integrated conjugative elements drive the formation of pandemic clones of Escherichia coli with hybrid chromosomes

Berruga Fernández, Talia; Huseby, Douglas L.; Koshla, Oksana; Shaukat, Anum et al.

Part of Molecular biology and evolution, 2026

• DOI for Integrated conjugative elements drive the formation of pandemic clones of Escherichia coli with hybrid chromosomes
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The COMBINE pneumonia model: a multicenter study to standardize a mouse pneumonia model with Pseudomonas aeruginosa and Klebsiella pneumoniae for antibiotic development

Hansen, Jon U.; Arrazuria, Rakel; Hoover, Jennifer L.; Kerscher, Bernhard et al.

Part of Microbiology Spectrum, 2026

• DOI for The COMBINE pneumonia model: a multicenter study to standardize a mouse pneumonia model with Pseudomonas aeruginosa and Klebsiella pneumoniae for antibiotic development
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Impact of early-life human microbiota on the murine host metabolome: insights from a two-generation HMA mouse model and implications for allergic disease

de Jong, Ymke A.; Seren, Rana M.; Ramsak Marceta, Vida; Checa, Antonio et al.

Part of BMC Microbiology, 2025

• DOI for Impact of early-life human microbiota on the murine host metabolome: insights from a two-generation HMA mouse model and implications for allergic disease
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Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections

Hernández-Lozano, Irene; Aranzana-Climent, Vincent; Cao, Sha; Matias, Carina et al.

Part of Journal of Antimicrobial Chemotherapy, p. 301-310, 2025

• DOI for Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections
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Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria

Huseby, Douglas L.; Cao, Sha; Zamaratski, Edouard; Sooriyaarachchi, Sanjeewani et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2024

• DOI for Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria
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Apramycin efficacy against carbapenem- and aminoglycoside-resistant Escherichia coli and Klebsiella pneumoniae in murine bloodstream infection models

Frimodt-Møller, Niels; Hansen, Jon U.; Plattner, Michel; Huseby, Douglas L. et al.

Part of International Journal of Antimicrobial Agents, 2024

• DOI for Apramycin efficacy against carbapenem- and aminoglycoside-resistant Escherichia coli and Klebsiella pneumoniae in murine bloodstream infection models
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Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors

Benediktsdottir, Andrea; Sooriyaarachchi, Sanjeewani; Cao, Sha; Ottosson, Nina E. et al.

Part of European Journal of Medicinal Chemistry, 2024

• DOI for Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors
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Quantifying combined effects of colistin and ciprofloxacin against Escherichia coli in an in silico pharmacokinetic-pharmacodynamic model

Zhao, Chenyan; Kristoffersson, Anders N.; Khan, David D.; Lagerbäck, Pernilla et al.

Part of Scientific Reports, 2024

• DOI for Quantifying combined effects of colistin and ciprofloxacin against Escherichia coli in an in silico pharmacokinetic-pharmacodynamic model
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Repurposing zidovudine and 5-fluoro-2′-deoxyuridine as antibiotic drugs made possible by synergy with both trimethoprim and the mitochondrial toxicity–reducing agent uridine

Levenfors, Jolanta J.; Bjerketorp, Joakim; Guss, Bengt; Nord, Christina et al.

Part of Journal of Antimicrobial Chemotherapy, p. 509-517, 2024

• DOI for Repurposing zidovudine and 5-fluoro-2′-deoxyuridine as antibiotic drugs made possible by synergy with both trimethoprim and the mitochondrial toxicity–reducing agent uridine
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Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold- Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa

Cotman, Andrej Emanuel; Durcik, Martina; Tiz, Davide Benedetto; Fulgheri, Federica et al.

Part of Journal of Medicinal Chemistry, p. 1380-1425, 2023

• DOI for Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold- Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa
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New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus

Durcik, Martina; Cotman, Andrej Emanuel; Toplak, Zan; Mozina, Stefan et al.

Part of Journal of Medicinal Chemistry, p. 3968-3994, 2023

• DOI for New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and In Vivo Efficacy against Vancomycin-Intermediate Staphylococcus aureus
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Evolution of Bacterial Interspecies Hybrids with Enlarged Chromosomes

Bartke, Katrin; Huseby, Douglas L; Brandis, Gerrit; Hughes, Diarmaid

Part of Genome Biology and Evolution, 2022

• DOI for Evolution of Bacterial Interspecies Hybrids with Enlarged Chromosomes
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Expert workshop summary: Advancing toward a standardized murine model to evaluate treatments for antimicrobial resistance lung infections

Arrazuria, Rakel; Kerscher, Bernhard; Huber, Karen E.; Hoover, Jennifer L. et al.

Part of Frontiers in Microbiology, 2022

• DOI for Expert workshop summary: Advancing toward a standardized murine model to evaluate treatments for antimicrobial resistance lung infections
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Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria

Cao, Sha; Brandis, Gerrit; Huseby, Douglas L; Hughes, Diarmaid

Part of Molecular biology and evolution, 2022

• DOI for Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria
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Synthesis and in vitro biological evaluation of quinolinyl pyrimidines targeting type II NADH-dehydrogenase (NDH-2)

Lu, Lu; Åkerbladh, Linda; Ahmad, Shabbir; Konda, Vivek et al.

Part of ACS - Infectious Diseases, p. 482-498, 2022

• DOI for Synthesis and in vitro biological evaluation of quinolinyl pyrimidines targeting type II NADH-dehydrogenase (NDH-2)
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Translational in vitro and in vivo PKPD modelling for apramycin against Gram-negative lung pathogens to facilitate prediction of human efficacious dose in pneumonia

Aranzana-Climent, Vincent; Hughes, Diarmaid; Cao, Sha; Tomczak, Magdalena et al.

Part of Clinical Microbiology and Infection, p. 1367-1374, 2022

• DOI for Translational in vitro and in vivo PKPD modelling for apramycin against Gram-negative lung pathogens to facilitate prediction of human efficacious dose in pneumonia
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Variability of murine bacterial pneumonia models used to evaluate antimicrobial agents

Arrazuria, Rakel; Kerscher, Bernhard; Huber, Karen E.; Hoover, Jennifer L. et al.

Part of Frontiers in Microbiology, 2022

• DOI for Variability of murine bacterial pneumonia models used to evaluate antimicrobial agents
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Antibacterial activity of apramycin at acidic pH warrants wide therapeutic window in the treatment of complicated urinary tract infections and acute pyelonephritis

Becker, Katja; Cao, Sha; Nilsson, Anna; Erlandsson, Maria et al.

Part of EBioMedicine, 2021

• DOI for Antibacterial activity of apramycin at acidic pH warrants wide therapeutic window in the treatment of complicated urinary tract infections and acute pyelonephritis
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Antibacterial sulfonimidamide-based oligopeptides as type I signal peptidase inhibitors: Synthesis and biological evaluation

Benediktsdottir, Andrea; Lu, Lu; Cao, Sha; Zamaratski, Edouard et al.

Part of European Journal of Medicinal Chemistry, 2021

• DOI for Antibacterial sulfonimidamide-based oligopeptides as type I signal peptidase inhibitors: Synthesis and biological evaluation
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Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination in Salmonella

Garmendia, Eva; Brandis, Gerrit; Guy, Lionel; Cao, Sha et al.

Part of mBio, 2021

• DOI for Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination in Salmonella
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Efficacy of EBL-1003 (apramycin) against Acinetobacter baumannii lung infections in mice

Becker, Katja; Aranzana-Climent, Vincent; Cao, Sha; Nilsson, Anna et al.

Part of Clinical Microbiology and Infection, p. 1315-1321, 2021

• DOI for Efficacy of EBL-1003 (apramycin) against Acinetobacter baumannii lung infections in mice
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ENABLE: an engine for European antibacterial drug discovery and development

Olliver, Marie; Griestop, Laura; Hughes, Diarmaid; Belfrage, Anna Karin et al.

Part of Nature reviews. Drug discovery, p. 407-408, 2021

• DOI for ENABLE: an engine for European antibacterial drug discovery and development

Evaluating the potential efficacy and limitations of a phage for joint antibiotic and phage therapy of Staphylococcus aureus infections

Berryhill, Brandon A.; Huseby, Douglas L; McCall, Ingrid C.; Hughes, Diarmaid et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2021

• DOI for Evaluating the potential efficacy and limitations of a phage for joint antibiotic and phage therapy of Staphylococcus aureus infections
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Expression of the qepA1 gene is induced under antibiotic exposure

Brandis, Gerrit; Gockel, Jonas; Garoff, Linnéa; Guy, Lionel et al.

Part of Journal of Antimicrobial Chemotherapy, p. 1433-1440, 2021

• DOI for Expression of the qepA1 gene is induced under antibiotic exposure
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Genetic Architecture and Fitness of Bacterial Interspecies Hybrids

Bartke, Katrin; Garoff, Linnéa; Huseby, Douglas L; Brandis, Gerrit et al.

Part of Molecular biology and evolution, p. 1472-1481, 2021

• DOI for Genetic Architecture and Fitness of Bacterial Interspecies Hybrids
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Model-Informed Drug Development for Antimicrobials: Translational PK and PK/PD Modeling to Predict an Efficacious Human Dose for Apramycin

Sou, Tomás; Hansen, Jon; Liepinsh, Edgars; Backlund, Maria et al.

Part of Clinical Pharmacology and Therapeutics, p. 1063-1073, 2021

• DOI for Model-Informed Drug Development for Antimicrobials: Translational PK and PK/PD Modeling to Predict an Efficacious Human Dose for Apramycin
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Mutant RNA polymerase can reduce susceptibility to antibiotics via ppGpp-independent induction of a stringent-like response

Brandis, Gerrit; Granström, Susanna; Leber, Anna T.; Bartke, Katrin et al.

Part of Journal of Antimicrobial Chemotherapy, p. 606-615, 2021

• DOI for Mutant RNA polymerase can reduce susceptibility to antibiotics via ppGpp-independent induction of a stringent-like response
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Phenotypic and genetic barriers to establishment of horizontally transferred genes encoding ribosomal protection proteins

Yadav, Kavita; Garoff, Linnea; Huseby, Douglas L; Hughes, Diarmaid

Part of Journal of Antimicrobial Chemotherapy, p. 1441-1447, 2021

• DOI for Phenotypic and genetic barriers to establishment of horizontally transferred genes encoding ribosomal protection proteins

Resistance/fitness trade-off is a barrier to the evolution of MarR inactivation mutants in Escherichia coli

Praski Alzrigat, Lisa; Huseby, Douglas L.; Brandis, Gerrit; Hughes, Diarmaid

Part of Journal of Antimicrobial Chemotherapy, p. 77-83, 2021

• DOI for Resistance/fitness trade-off is a barrier to the evolution of MarR inactivation mutants in Escherichia coli
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Antibiotic resistance by high-level intrinsic suppression of a frameshift mutation in an essential gene

Huseby, Douglas L; Brandis, Gerrit; Praski Alzrigat, Lisa; Hughes, Diarmaid

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 3185-3191, 2020

• DOI for Antibiotic resistance by high-level intrinsic suppression of a frameshift mutation in an essential gene
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Isopedopeptins A-H: Cationic Cyclic Lipodepsipeptides from Pedobacter cryoconitis UP508 Targeting WHO Top-Priority Carbapenem-Resistant Bacteria

Nord, Christina; Bjerketorp, Joakim; Levenfors, Jolanta J.; Cao, Sha et al.

Part of ACS Chemical Biology, p. 2937-2944, 2020

• DOI for Isopedopeptins A-H: Cationic Cyclic Lipodepsipeptides from Pedobacter cryoconitis UP508 Targeting WHO Top-Priority Carbapenem-Resistant Bacteria
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Population Bottlenecks Strongly Influence the Evolutionary Trajectory to Fluoroquinolone Resistance in Escherichia coli

Garoff, Linnéa; Pietsch, Franziska; Huseby, Douglas L; Lilja, Tua et al.

Part of Molecular biology and evolution, p. 1637-1646, 2020

• DOI for Population Bottlenecks Strongly Influence the Evolutionary Trajectory to Fluoroquinolone Resistance in Escherichia coli
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Structure-activity relationship studies on the inhibition of the bacterial translation of novel Odilorhabdins analogues

Loza, Einars; Sarciaux, Matthieu; Ikaunieks, Martins; Katkevics, Martins et al.

Part of Bioorganic & Medicinal Chemistry, 2020

• DOI for Structure-activity relationship studies on the inhibition of the bacterial translation of novel Odilorhabdins analogues

Synthesis of New N-Acyl-1,2,3-triazole Chalcones and Determination of Their Antibacterial Activity

Odin, I. S.; Cao, Sha; Hughes, Diarmaid; Zamaratskii, E. V. et al.

Part of Doklady. Chemistry, p. 89-92, 2020

• DOI for Synthesis of New N-Acyl-1,2,3-triazole Chalcones and Determination of Their Antibacterial Activity

The SNAP hypothesis: Chromosomal rearrangements could emerge from positive Selection during Niche Adaptation

Brandis, Gerrit; Hughes, Diarmaid

Part of PLOS Genetics, 2020

• DOI for The SNAP hypothesis: Chromosomal rearrangements could emerge from positive Selection during Niche Adaptation
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In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii

Juhas, Mario; Widlake, Emma; Teo, Jeanette; Huseby, Douglas L et al.

Part of Journal of Antimicrobial Chemotherapy, p. 944-952, 2019

• DOI for In vitro activity of apramycin against multidrug-, carbapenem- and aminoglycoside-resistant Enterobacteriaceae and Acinetobacter baumannii
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Measuring Homologous Recombination Rates between Chromosomal Locations in Salmonella

Brandis, Gerrit; Cao, Sha; Hughes, Diarmaid

Part of Bio-protocol, 2019

• DOI for Measuring Homologous Recombination Rates between Chromosomal Locations in Salmonella

Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes

Brandis, Gerrit; Cao, Sha; Hughes, Diarmaid

Part of Molecular biology and evolution, p. 1990-2000, 2019

• DOI for Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes
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Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase

Szałaj, Natalia; Lu, Lu; Benediktsdottir, Andrea; Zamaratski, Edouard et al.

Part of European Journal of Medicinal Chemistry, p. 1346-1360, 2018

• DOI for Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase

Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella

Brandis, Gerrit; Cao, Sha; Hughes, Diarmaid

Part of Molecular Microbiology, p. 697-710, 2018

• DOI for Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella
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Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli

Garoff, Linnéa; Huseby, Douglas L; Praski Alzrigat, Lisa; Hughes, Diarmaid

Part of Journal of Antimicrobial Chemotherapy, p. 3285-3292, 2018

• DOI for Effect of aminoacyl-tRNA synthetase mutations on susceptibility to ciprofloxacin in Escherichia coli
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Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones

Jeannot, Frédéric; Taillier, Thomas; Despeyroux, Pierre; Renard, Stéphane et al.

Part of Journal of Medicinal Chemistry, p. 3565-3581, 2018

• DOI for Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones

Increased expression of Qnr is sufficient to confer clinical resistance to ciprofloxacin in Escherichia coli

Garoff, Linnéa; Yadav, Kavita; Hughes, Diarmaid

Part of Journal of Antimicrobial Chemotherapy, p. 348-352, 2018

• DOI for Increased expression of Qnr is sufficient to confer clinical resistance to ciprofloxacin in Escherichia coli
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Mechanisms of fitness cost reduction for rifampicin-resistant strains with deletion or duplication mutations in rpoB.

Brandis, Gerrit; Hughes, Diarmaid

Part of Scientific Reports, 2018

• DOI for Mechanisms of fitness cost reduction for rifampicin-resistant strains with deletion or duplication mutations in rpoB.
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Methods to determine mutational trajectories after experimental evolution of antibiotic resistance.

Huseby, Douglas L; Hughes, Diarmaid

Part of Methods in Molecular Biology, p. 95-103, 2018

• DOI for Methods to determine mutational trajectories after experimental evolution of antibiotic resistance.

Muramyl Endopeptidase Spr Contributes to Intrinsic Vancomycin Resistance in Salmonella enterica Serovar Typhimurium

Vestö, Kim; Huseby, Douglas L; Snygg, Lina; Wang, Helen et al.

Part of Frontiers in Microbiology, 2018

• DOI for Muramyl Endopeptidase Spr Contributes to Intrinsic Vancomycin Resistance in Salmonella enterica Serovar Typhimurium
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Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site

Pantel, Lucile; Florin, Tanja; Dobosz-Bartoszek, Malgorzata; Racine, Emilie et al.

Part of Molecular Cell, p. 83-94, 2018

• DOI for Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site

Predicting mutant selection in competition experiments with ciprofloxacin-exposed Escherichia coli

Khan, David; Lagerbäck, Pernilla; Malmberg, Christer; Kristoffersson, Anders et al.

Part of International Journal of Antimicrobial Agents, p. 399-406, 2018

• DOI for Predicting mutant selection in competition experiments with ciprofloxacin-exposed Escherichia coli

Transcriptional Regulation Buffers Gene Dosage Effects on a Highly Expressed Operon in Salmonella

Garmendia, Eva; Brandis, Gerrit; Hughes, Diarmaid

Part of mBio, 2018

• DOI for Transcriptional Regulation Buffers Gene Dosage Effects on a Highly Expressed Operon in Salmonella
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Alternative Evolutionary Pathways for Drug-Resistant Small Colony Variant Mutants in Staphylococcus aureus

Cao, Sha; Huseby, Douglas L; Brandis, Gerrit; Hughes, Diarmaid

Part of mBio, 2017

• DOI for Alternative Evolutionary Pathways for Drug-Resistant Small Colony Variant Mutants in Staphylococcus aureus
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