Publications

Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection

Zaborskyte, Greta; Coelho, Patrícia; Wrande, Marie; Sandegren, Linus

Part of Nature Communications, 2026

• DOI for Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection
• Download full text (pdf) of Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection

When Does Evidence Create a Moral Obligation to Depart from Antibiotic Guidelines?

Ancillotti, Mirko; Andersson, Dan I.; Sandegren, Linus

Part of American Journal of Bioethics, p. 109-111, 2026

• DOI for When Does Evidence Create a Moral Obligation to Depart from Antibiotic Guidelines?
• Download full text (pdf) of When Does Evidence Create a Moral Obligation to Depart from Antibiotic Guidelines?

A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes

Lee, Danna; Muir, Petra; Lundberg, Sara; Lundholm, August et al.

Part of Scientific Reports, 2025

• DOI for A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes
• Download full text (pdf) of A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes

DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach

Dvirnas, Albertas; Leal-Garza, Luis Mario; Abbaspour, Zahra; Frobrant, Erik et al.

Part of PLOS ONE, 2025

• DOI for DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach
• Download full text (pdf) of DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach

Evaluation of ceftazidime/avibactam in combination with colistin against KPC-2-producing Klebsiella pneumoniae in static and dynamic time-kill experiments

Allander, Lisa; Vikdahl, Emma; Chatzopoulou, Margarita; O'Jeanson, Amaury et al.

Part of JAC - Antimicrobial Resistance, 2025

• DOI for Evaluation of ceftazidime/avibactam in combination with colistin against KPC-2-producing Klebsiella pneumoniae in static and dynamic time-kill experiments
• Download full text (pdf) of Evaluation of ceftazidime/avibactam in combination with colistin against KPC-2-producing Klebsiella pneumoniae in static and dynamic time-kill experiments

Parallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak

Zaborskyte, Greta; Hjort, Karin; Lytsy, Birgitta; Sandegren, Linus

Part of Nature Communications, 2025

• DOI for Parallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak
• Download full text (pdf) of Parallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak

Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping

Kunnath, Radhika N.; Abbaspour, Zahra; Johnning, Anna; Frykholm, Karolin et al.

Part of ACS - Infectious Diseases, p. 3085-3092, 2025

• DOI for Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping

Impact of porin deficiency on the synergistic potential of colistin in combination with β-lactam/β-lactamase inhibitors against ESBL- and carbapenemase-producing Klebsiella pneumoniae

Allander, Lisa; Vickberg, Karin; Fermér, Elin; Söderhäll, Thomas et al.

Part of Antimicrobial Agents and Chemotherapy, 2024

• DOI for Impact of porin deficiency on the synergistic potential of colistin in combination with β-lactam/β-lactamase inhibitors against ESBL- and carbapenemase-producing Klebsiella pneumoniae
• Download full text (pdf) of Impact of porin deficiency on the synergistic potential of colistin in combination with β-lactam/β-lactamase inhibitors against ESBL- and carbapenemase-producing Klebsiella pneumoniae

Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Örmälä-Tiznado, Anni-Maria; Allander, Lisa; Maatallah, Makaoui; Kabir, Muhammad Humaun et al.

Part of Microbiology Spectrum, p. 1-14, 2024

• DOI for Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae
• Download full text (pdf) of Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae

Reduced amplification by phi29 DNA polymerase in the presence of unbound oligos during reaction in RCA

Sánchez Martín, Darío; Li, Tingting; Wrande, Marie; Sandegren, Linus et al.

Part of Biosensors and Bioelectronics: X, 2024

• DOI for Reduced amplification by phi29 DNA polymerase in the presence of unbound oligos during reaction in RCA
• Download full text (pdf) of Reduced amplification by phi29 DNA polymerase in the presence of unbound oligos during reaction in RCA

Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches

Ahlstrom, Christina A. A.; Woksepp, Hanna; Sandegren, Linus; Ramey, Andrew M. M. et al.

Part of Applied and Environmental Microbiology, 2023

• DOI for Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches

Strain-level bacterial typing directly from patient samples using optical DNA mapping

Nyblom, My; Johnning, Anna; Frykholm, Karolin; Wrande, Marie et al.

Part of Communications Medicine, 2023

• DOI for Strain-level bacterial typing directly from patient samples using optical DNA mapping
• Download full text (pdf) of Strain-level bacterial typing directly from patient samples using optical DNA mapping

A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy

Goyal, Gaurav; Ekedahl, Elina; Nyblom, My; Krog, Jens et al.

Part of Scientific Reports, 2022

• DOI for A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy
• Download full text (pdf) of A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy

Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment

Hjort, Karin; Jurén, Pontus; Toro, Juan Carlos; Hoffner, Sven et al.

Part of Journal of Infectious Diseases, p. 1011-1020, 2022

• DOI for Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment
• Download full text (pdf) of Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment

Evaluation of In Vitro Activity of Double-Carbapenem Combinations against KPC-2-, OXA-48-and NDM-Producing Escherichia coli and Klebsiella pneumoniae

Allander, Lisa; Vickberg, Karin; Lagerbäck, Pernilla; Sandegren, Linus et al.

Part of Antibiotics, 2022

• DOI for Evaluation of In Vitro Activity of Double-Carbapenem Combinations against KPC-2-, OXA-48-and NDM-Producing Escherichia coli and Klebsiella pneumoniae
• Download full text (pdf) of Evaluation of In Vitro Activity of Double-Carbapenem Combinations against KPC-2-, OXA-48-and NDM-Producing Escherichia coli and Klebsiella pneumoniae

Evolutionary Trajectories toward High-Level β-Lactam/β-Lactamase Inhibitor Resistance in the Presence of Multiple β-Lactamases

Rajer, Fredrika; Allander, Lisa; Karlsson, Philip A.; Sandegren, Linus

Part of Antimicrobial Agents and Chemotherapy, 2022

• DOI for Evolutionary Trajectories toward High-Level β-Lactam/β-Lactamase Inhibitor Resistance in the Presence of Multiple β-Lactamases

Genomically diverse carbapenem resistant Enterobacteriaceae fromwild birds provide insight into global patterns of spatiotemporal dissemination

Ahlstrom, Christina A.; Woksepp, Hanna; Sandegren, Linus; Mohsin, Mashkoor et al.

Part of Science of the Total Environment, 2022

• DOI for Genomically diverse carbapenem resistant Enterobacteriaceae fromwild birds provide insight into global patterns of spatiotemporal dissemination
• Download full text (pdf) of Genomically diverse carbapenem resistant Enterobacteriaceae fromwild birds provide insight into global patterns of spatiotemporal dissemination

Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters

Palica, Katarzyna; Vorácová, Manuela; Skagseth, Susann; Andersson Rasmussen, Anna et al.

Part of ACS Omega, p. 4550-4562, 2022

• DOI for Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters
• Download full text (pdf) of Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters

Modular 3D-Printed Peg Biofilm Device for Flexible Setup of Surface-Related Biofilm Studies

Zaborskyte, Greta; Wistrand-Yuen, Erik; Hjort, Karin; Andersson, Dan I. et al.

Part of Frontiers in Cellular and Infection Microbiology, 2022

• DOI for Modular 3D-Printed Peg Biofilm Device for Flexible Setup of Surface-Related Biofilm Studies
• Download full text (pdf) of Modular 3D-Printed Peg Biofilm Device for Flexible Setup of Surface-Related Biofilm Studies

Naked-eye detection of antibiotic resistance gene sul1 based on aggregation of magnetic nanoparticles and DNA amplification products

Sánchez Martín, Darío; Wrande, Marie; Sandegren, Linus; Zardán Gómez de la Torre, Teresa

Part of Biosensors and Bioelectronics: X, 2022

• DOI for Naked-eye detection of antibiotic resistance gene sul1 based on aggregation of magnetic nanoparticles and DNA amplification products
• Download full text (pdf) of Naked-eye detection of antibiotic resistance gene sul1 based on aggregation of magnetic nanoparticles and DNA amplification products

The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids

Rajer, Fredrika; Sandegren, Linus

Part of mBio, 2022

• DOI for The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids
• Download full text (pdf) of The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids

A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids

KK, Sriram; Lin, Yii-Lih; Sewunet, Tsegaye; Wrande, Marie et al.

Part of Micromachines, 2021

• DOI for A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids
• Download full text (pdf) of A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids

Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach

Dvirnas, Albertas; Stewart, Callum; Müller, Vilhelm; Bikkarolla, Santosh Kumar et al.

Part of PLOS ONE, 2021

• DOI for Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach
• Download full text (pdf) of Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach

Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment

Atterby, Clara; Nykvist, Marie; Lustig, Ulrika; Andersson, Dan I. et al.

Part of Antimicrobial Agents and Chemotherapy, 2021

• DOI for Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment

Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

Muller, Vilhelm; Nyblom, My; Johnning, Anna; Wrande, Marie et al.

Part of ACS - Infectious Diseases, p. 1076-1084, 2020

• DOI for Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
• Download full text (pdf) of Cultivation-Free Typing of Bacteria Using Optical DNA Mapping

Efficacy of Antibiotic Combinations against Multidrug-Resistant Pseudomonas aeruginosa in Automated Time-Lapse Microscopy and Static Time-Kill Experiments

Olsson, Anna; Wistrand-Yuen, Pikkei; Nielsen, Elisabet I.; Friberg, Lena et al.

Part of Antimicrobial Agents and Chemotherapy, 2020

• DOI for Efficacy of Antibiotic Combinations against Multidrug-Resistant Pseudomonas aeruginosa in Automated Time-Lapse Microscopy and Static Time-Kill Experiments
• Download full text (pdf) of Efficacy of Antibiotic Combinations against Multidrug-Resistant Pseudomonas aeruginosa in Automated Time-Lapse Microscopy and Static Time-Kill Experiments

Dynamics of Resistance Plasmids in Extended-Spectrum-beta-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization

Brolund, Alma; Rajer, Fredrika; Giske, Christian G.; Melefors, Öjar et al.

Part of Antimicrobial Agents and Chemotherapy, 2019

• DOI for Dynamics of Resistance Plasmids in Extended-Spectrum-beta-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization

Genome and plasmid diversity of Extended-Spectrum beta-Lactamase-producing Escherichia coli ST131-tracking phylogenetic trajectories with Bayesian inference

Ny, Sofia; Sandegren, Linus; Salemi, Marco; Giske, Christian G.

Part of Scientific Reports, 2019

• DOI for Genome and plasmid diversity of Extended-Spectrum beta-Lactamase-producing Escherichia coli ST131-tracking phylogenetic trajectories with Bayesian inference
• Download full text (pdf) of Genome and plasmid diversity of Extended-Spectrum beta-Lactamase-producing Escherichia coli ST131-tracking phylogenetic trajectories with Bayesian inference

Low sub-minimal inhibitory concentrations of antibiotics generate new types of resistance

Sandegren, Linus

Part of Sustainable Chemistry and Pharmacy, p. 46-48, 2019

• DOI for Low sub-minimal inhibitory concentrations of antibiotics generate new types of resistance

Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak

Bikkarolla, Santosh K.; Nordberg, Viveka; Rajer, Fredrika; Mueller, Vilhelm et al.

Part of mBio, 2019

• DOI for Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak
• Download full text (pdf) of Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak

Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

Dvirnas, Albertas; Pichler, Christoffer; Stewart, Callum L.; Quaderi, Saair et al.

Part of PLOS ONE, 2018

• DOI for Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
• Download full text (pdf) of Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

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

Sandegren, Linus; Stedt, Johan; Lustig, Ulrika; Bonnedahl, Jonas et al.

Part of Environmental Microbiology Reports, p. 576-582, 2018

• DOI for 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
• Download full text (pdf) of 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

A bla(OXA-181)-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance

Nahid, Fouzia; Zahra, Rabaab; Sandegren, Linus

Part of PLOS ONE, 2017

• DOI for A bla(OXA-181)-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance
• Download full text (pdf) of A bla(OXA-181)-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance

A pharmacokinetic-pharmacodynamic model characterizing the emergence of resistant Escherichia coli subpopulations during ertapenem exposure

Ungphakorn, Wanchana; Tängdén, Thomas; Sandegren, Linus; Nielsen, Elisabet I.

Part of Journal of Antimicrobial Chemotherapy, p. 2521-2533, 2016

• DOI for A pharmacokinetic-pharmacodynamic model characterizing the emergence of resistant Escherichia coli subpopulations during ertapenem exposure

Characterization of ESBL disseminating plasmids

Brolund, Alma; Sandegren, Linus

Part of Infectious Diseases, p. 18-25, 2016

• DOI for Characterization of ESBL disseminating plasmids

Combinations of mutations in envZ, ftsI, mrdA, acrB and acrR can cause high-level carbapenem resistance in Escherichia coli

Adler, Marlen; Anjum, Mehreen; Andersson, Dan I.; Sandegren, Linus

Part of Journal of Antimicrobial Chemotherapy, p. 1188-1198, 2016

• DOI for Combinations of mutations in envZ, ftsI, mrdA, acrB and acrR can cause high-level carbapenem resistance in Escherichia coli

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

Mueller, Vilhelm; Rajer, Fredrika; Frykholm, Karolin; Nyberg, Lena K. et al.

Part of Scientific Reports, 2016

• DOI for Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
• Download full text (pdf) of Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

Fitness of Escherichia coli mutants with reduced susceptibility to tigecycline

Linkevicius, Marius; Anderssen, Jytte Mark; Sandegren, Linus; Andersson, Dan I.

Part of Journal of Antimicrobial Chemotherapy, p. 1307-1313, 2016

• DOI for Fitness of Escherichia coli mutants with reduced susceptibility to tigecycline

Potential of tetracycline resistance proteins to evolve tigecycline resistance

Linkevicius, Marius; Sandegren, Linus; Andersson, Dan I.

Part of Antimicrobial Agents and Chemotherapy, p. 789-796, 2016

• DOI for Potential of tetracycline resistance proteins to evolve tigecycline resistance
• Download full text (pdf) of Potential of tetracycline resistance proteins to evolve tigecycline resistance

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Nyberg, Lena K.; Quaderi, Saair; Emilsson, Gustav; Karami, Nahid et al.

Part of Scientific Reports, 2016

• DOI for Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
• Download full text (pdf) of Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Fast size-determination of intact bacterial plasmids using nanofluidic channels

Frykholm, K.; Nyberg, L. K.; Lagerstedt, E.; Noble, C. et al.

Part of Lab on a Chip, p. 2739-2743, 2015

• DOI for Fast size-determination of intact bacterial plasmids using nanofluidic channels

High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms

Adler, Marlen; Anjum, Mehreen; Berg, Otto, G.; Andersson, Dan I. et al.

Part of Molecular biology and evolution, p. 1526-1535, 2014

• DOI for High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms

Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals

Gullberg, Erik; Albrecht, Lisa M; Karlsson, Christoffer; Sandegren, Linus et al.

Part of mBio, 2014

• DOI for Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals

Selection of antibiotic resistance at very low antibiotic concentrations

Sandegren, Linus

Part of Upsala Journal of Medical Sciences, p. 103-107, 2014

• DOI for Selection of antibiotic resistance at very low antibiotic concentrations

Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium

Koskiniemi, Sanna; Garza-Sanchez, Fernando; Sandegren, Linus; Webb, Julia S. et al.

Part of PLOS Genetics, 2014

• DOI for Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium
• Download full text (pdf) of Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium

Silver resistance genes are overrepresented among Escherichia coli isolates with CTX-M production

Sütterlin, Susanne; Edquist, Petra; Sandegren, Linus; Adler, Marlen et al.

Part of Applied and Environmental Microbiology, p. 6863-6869, 2014

• DOI for Silver resistance genes are overrepresented among Escherichia coli isolates with CTX-M production

The Gull (Chroicocephalus brunnicephalus) as an Environmental Bioindicator and Reservoir for Antibiotic Resistance on the Coastlines of the Bay of Bengal

Hasan, Badrul; Melhus, Åsa; Sandegren, Linus; Alam, Munirul et al.

Part of Microbial Drug Resistance, p. 466-471, 2014

• DOI for The Gull (Chroicocephalus brunnicephalus) as an Environmental Bioindicator and Reservoir for Antibiotic Resistance on the Coastlines of the Bay of Bengal

Time lapse investigation of antibiotic susceptibility using a microfluidic linear gradient 3D culture device

Hou, Zining; An, Yu; Hjort, Karin; Hjort, Klas et al.

Part of Lab on a Chip, p. 3409-3418, 2014

• DOI for Time lapse investigation of antibiotic susceptibility using a microfluidic linear gradient 3D culture device

Frequent emergence of porin-deficient subpopulations with reduced carbapenem susceptibility in ESBL-producing Escherichia coli during exposure to ertapenem in an in vitro pharmacokinetic model

Tängdén, Thomas; Adler, Marlen; Cars, Otto; Sandegren, Linus et al.

Part of Journal of Antimicrobial Chemotherapy, p. 1319-1326, 2013

• DOI for Frequent emergence of porin-deficient subpopulations with reduced carbapenem susceptibility in ESBL-producing Escherichia coli during exposure to ertapenem in an in vitro pharmacokinetic model

Influence of acquired β-lactamases on the evolution of spontaneous carbapenem resistance in Escherichia coli

Adler, Marlen; Anjum, Mehreen; Andersson, Dan I.; Sandegren, Linus

Part of Journal of Antimicrobial Chemotherapy, p. 51-59, 2013

• DOI for Influence of acquired β-lactamases on the evolution of spontaneous carbapenem resistance in Escherichia coli