Author

P. J. Johnsen

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 9 Evolutionary Biology· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Organism:E. coli· 7 Research Focus:host-pathogen & immune response· 4 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:drug response / drug discovery· 2 Assay:long-read sequencing· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1

Frequent Co-Authors

O. Samuelsen· 8 shared K. Harms· 4 shared C. Frohlich· 3 shared J. Corander· 3 shared R. A. Gladstone· 3 shared A. K. Pöntinen· 2 shared H. A. Thorpe· 2 shared H.-K. S. Leiros· 2 shared

Activity by Year

2018-2023 · peak 4/yr

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10 top collaborators · 25 mutual co-author links

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8 shared papersMicrobiology

O. Samuelsen

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11 papers

Recent·Most cited

Plasmid-driven strategies for clone success in Escherichia coli

S. Arredondo-Alonso, A. K. Pontinen, J. Gama, R. A. Gladstone, K. Harms, G. Tonkin-Hill, H. A. Thorpe, G. S. Simonsen, O. Samuelsen, P. J. Johnsen, J. Corander

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

bioRxiv · Oct 14, 2023 · PreprintMicrobiology

The Biofilm Lifestyle Shapes the Evolution of β-Lactamases

O. M. Lorentzen, A. S. B. Haukefer, P. J. Johnsen, C. Frohlich

This study shows that biofilm lifestyle selects for mutations in β-lactamases that reduce biofilm inhibition while maintaining antibiotic resistance.

bioRxiv · Oct 2, 2023Microbiology

Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

C. Frohlich, H. A. Bunzel, K. Buda, A. J. Mulholland, M. W. van der Kamp, P. J. Johnsen, H.-K. S. Leiros, N. Tokuriki

This study shows that epistasis in enzyme evolution arises from shifting the rate-limiting step in the catalytic cycle, leading to substantial activity enhancements through synergistic mutations.

bioRxiv · Jun 29, 2023Evolutionary Biology

Testing for the fitness benefits of natural transformation during community-embedded evolution

M. R. Winter, K. Harms, P. J. Johnsen, A. Buckling, M. Vos

The paper tests if natural transformation provides fitness benefits in community-embedded evolution but finds no significant effect on fitness.

bioRxiv · Mar 20, 2023Microbiology

Strong pathogen competition in neonatal gut colonisation

T. Mäklin, H. A. Thorpe, A. K. Pöntinen, R. A. Gladstone, Y. Shao, M. Pesonen, A. McNally, P. J. Johnsen, O. Samuelsen, T. D. Lawley, A. Honkela, J. Corander

This study quantifies strain-level colonisation dynamics of gut pathogens in neonates, finding strong competition and some synergies, and reveals pathogenic potential differences among ExPEC clones.

bioRxiv · Jun 19, 2022Microbiology

Evolutionary instability of collateral susceptibility networks in ciprofloxacin resistant clinical Escherichia coli strains

V. Sorum, E. L. Oynes, A. S. Moller, K. Harms, O. Samuelsen, N. L. Podnecky, P. J. Johnsen

This study shows that collateral networks in ciprofloxacin-resistant E. coli strains are evolutionarily unstable due to compensatory mutations, particularly affecting rpoS.

bioRxiv · Oct 26, 2021Microbiology

A high-throughput multiplexing and selection strategy to complete bacterial genomes

S. Arredondo-Alonso, A. K. Pöntinen, F. Cleon, R. A. Gladstone, A. C. Schürch, P. J. Johnsen, O. Samuelsen, J. Corander

This paper evaluates a high-throughput multiplexing strategy using Oxford Nanopore Technologies to complete bacterial genomes, showing improved assembly contiguity and completeness.

bioRxiv · Jun 14, 2021Microbiology

Cryptic β-lactamase evolution is driven by low β-lactam concentrations

C. Frohlich, J. A. Gama, K. Harms, V. H. A. Hirvonen, B. A. Lund, M. W. van der Kamp, P. J. Johnsen, O. Samuelsen, H.-K. S. Leiros

The paper shows that low β-lactam concentrations drive cryptic evolution of β-lactamases through fitness benefits in competition experiments, not increased resistance.

bioRxiv · Dec 1, 2020Evolutionary Biology

The chemotherapeutic drug methotrexate selects for antibiotic resistance

J. S. Guthmundsdottir, E. G. A. Fredheim, C. I. M. Koumans, J. Hegstad, P.-C. Tang, D. I. Andersson, O. Samuelsen, P. J. Johnsen

This study shows methotrexate can select for antibiotic resistance genes in E. coli when linked to trimethoprim resistance, at sub-inhibitory concentrations.

bioRxiv · Nov 12, 2020Microbiology

Piggybacking on niche-adaptation reduces the cost of multidrug resistance plasmids

J. Kloos, J. A. Gama, J. Hegstad, O. Samuelsen, P. J. Johnsen

The paper shows that chromosomal mutations in E. coli reduce the cost of multidrug resistance plasmids by downregulating plasmid gene expression during niche adaptation.

bioRxiv · Oct 23, 2020Microbiology

Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli.

N. L. Podnecky, E. G. Fredheim, J. Kloos, V. Sorum, R. Primicerio, A. P. Roberts, D. E. Rozen, O. Samuelsen, P. J. Johnsen

The paper examines collateral susceptibility networks in diverse E. coli strains to inform antimicrobial resistance treatment strategies.

bioRxiv · Jan 17, 2018Microbiology