Publikationer

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

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

Ingår i Nature Communications, 2026

• DOI för Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection
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When Does Evidence Create a Moral Obligation to Depart from Antibiotic Guidelines?

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

Ingår i American Journal of Bioethics, s. 109-111, 2026

• DOI för When Does Evidence Create a Moral Obligation to Depart from Antibiotic Guidelines?
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A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes

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

Ingår i Scientific Reports, 2025

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

Ingår i PLOS ONE, 2025

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

Ingår i JAC - Antimicrobial Resistance, 2025

• DOI för Evaluation of ceftazidime/avibactam in combination with colistin against KPC-2-producing Klebsiella pneumoniae in static and dynamic time-kill experiments
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Parallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak

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

Ingår i Nature Communications, 2025

• DOI för Parallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak
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Strain-Level Typing of Streptococcus pyogenes Using Optical DNA Mapping

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

Ingår i ACS - Infectious Diseases, s. 3085-3092, 2025

• DOI för 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.

Ingår i Antimicrobial Agents and Chemotherapy, 2024

• DOI för 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
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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.

Ingår i Microbiology Spectrum, s. 1-14, 2024

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

Ingår i Biosensors and Bioelectronics: X, 2024

• DOI för Reduced amplification by phi29 DNA polymerase in the presence of unbound oligos during reaction in RCA
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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.

Ingår i Applied and Environmental Microbiology, 2023

• DOI för 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.

Ingår i Communications Medicine, 2023

• DOI för Strain-level bacterial typing directly from patient samples using optical DNA mapping
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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.

Ingår i Scientific Reports, 2022

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

Ingår i Journal of Infectious Diseases, s. 1011-1020, 2022

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

Ingår i Antibiotics, 2022

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

Ingår i Antimicrobial Agents and Chemotherapy, 2022

• DOI för 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.

Ingår i Science of the Total Environment, 2022

• DOI för Genomically diverse carbapenem resistant Enterobacteriaceae fromwild birds provide insight into global patterns of spatiotemporal dissemination
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Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters

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

Ingår i ACS Omega, s. 4550-4562, 2022

• DOI för Metallo-β-Lactamase Inhibitor Phosphonamidate Monoesters
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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.

Ingår i Frontiers in Cellular and Infection Microbiology, 2022

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

Ingår i Biosensors and Bioelectronics: X, 2022

• DOI för Naked-eye detection of antibiotic resistance gene sul1 based on aggregation of magnetic nanoparticles and DNA amplification products
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The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids

Rajer, Fredrika; Sandegren, Linus

Ingår i mBio, 2022

• DOI för The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids
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A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids

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

Ingår i Micromachines, 2021

• DOI för A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids
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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.

Ingår i PLOS ONE, 2021

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

Ingår i Antimicrobial Agents and Chemotherapy, 2021

• DOI för 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.

Ingår i ACS - Infectious Diseases, s. 1076-1084, 2020

• DOI för Cultivation-Free Typing of Bacteria Using Optical DNA Mapping
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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.

Ingår i Antimicrobial Agents and Chemotherapy, 2020

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

Ingår i Antimicrobial Agents and Chemotherapy, 2019

• DOI för 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.

Ingår i Scientific Reports, 2019

• DOI för Genome and plasmid diversity of Extended-Spectrum beta-Lactamase-producing Escherichia coli ST131-tracking phylogenetic trajectories with Bayesian inference
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Low sub-minimal inhibitory concentrations of antibiotics generate new types of resistance

Sandegren, Linus

Ingår i Sustainable Chemistry and Pharmacy, s. 46-48, 2019

• DOI för 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.

Ingår i mBio, 2019

• DOI för Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak
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Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

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

Ingår i PLOS ONE, 2018

• DOI för Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach
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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.

Ingår i Environmental Microbiology Reports, s. 576-582, 2018

• DOI för 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
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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

Ingår i PLOS ONE, 2017

• DOI för A bla(OXA-181)-harbouring multi-resistant ST147 Klebsiella pneumoniae isolate from Pakistan that represent an intermediate stage towards pan-drug resistance
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A pharmacokinetic-pharmacodynamic model characterizing the emergence of resistant Escherichia coli subpopulations during ertapenem exposure

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

Ingår i Journal of Antimicrobial Chemotherapy, s. 2521-2533, 2016

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

Characterization of ESBL disseminating plasmids

Brolund, Alma; Sandegren, Linus

Ingår i Infectious Diseases, s. 18-25, 2016

• DOI för 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

Ingår i Journal of Antimicrobial Chemotherapy, s. 1188-1198, 2016

• DOI för 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.

Ingår i Scientific Reports, 2016

• DOI för Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
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Fitness of Escherichia coli mutants with reduced susceptibility to tigecycline

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

Ingår i Journal of Antimicrobial Chemotherapy, s. 1307-1313, 2016

• DOI för 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.

Ingår i Antimicrobial Agents and Chemotherapy, s. 789-796, 2016

• DOI för Potential of tetracycline resistance proteins to evolve tigecycline resistance
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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.

Ingår i Scientific Reports, 2016

• DOI för Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
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Fast size-determination of intact bacterial plasmids using nanofluidic channels

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

Ingår i Lab on a Chip, s. 2739-2743, 2015

• DOI för 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.

Ingår i Molecular biology and evolution, s. 1526-1535, 2014

• DOI för 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.

Ingår i mBio, 2014

• DOI för 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

Ingår i Upsala Journal of Medical Sciences, s. 103-107, 2014

• DOI för 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.

Ingår i PLOS Genetics, 2014

• DOI för Selection of Orphan Rhs Toxin Expression in Evolved Salmonella enterica Serovar Typhimurium
• Ladda ner fulltext (pdf) av 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.

Ingår i Applied and Environmental Microbiology, s. 6863-6869, 2014

• DOI för 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.

Ingår i Microbial Drug Resistance, s. 466-471, 2014

• DOI för 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.

Ingår i Lab on a Chip, s. 3409-3418, 2014

• DOI för 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.

Ingår i Journal of Antimicrobial Chemotherapy, s. 1319-1326, 2013

• DOI för 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

Ingår i Journal of Antimicrobial Chemotherapy, s. 51-59, 2013

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