Mikkel M Liljegren  –  PhD Candidate

Ørjan Samuelsen  –  Professor 2

Pål Jarle Johnsen  –  Professor

Elizabeth G Aarag Fredheim  –  Associate professor

Øyvind Myrvold Lorentsen  –  MD PhD student

Klaus Harms  –  Researcher

Jonina Gudmundsdottir  –  Postdoc. Research Fellow

Christopher Frøhlich  –  Postdoc. Research Fellow, Biomolecular and Structural Chemistry

Anna Pöntinen  –  Researcher

Silje Lauksund  –  Lab manager

Miriam Kristine Karlsen  –  PhD Candidate

MicroPop publications 2015- (group members in bold)

1. Pontinen AK., Gladstone RA., Pesonen H., Pesonen H., Cleon F., Kallonen T., Simonsen GS., Croucher N., McNally A., Johnsen PJ., Samuelsen Ø., and J. Corander. Modulation of multi- drug resistant clone success in Escherichia coli populations: a longitudinal multi-country genomic and antibiotic usage cohort study. Lancet Microbe Jan 4th2024, https://doi.org/10.1016/ S2666-5247(23)00292-6.

2. Fröhlich C., Bunzel HA., Buda K., Mulholland AJ., van der Kamp MW., Johnsen PJ., Leiros HK., and N. Tokuriki. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution of a b-lactamase.Accepted for publication Nature Catalysis, January 25th, 2024

3. Arredondo-Alonso S., Gladstone RA., Pontinen AK., Gama JA., Gladstone R., Harms K., Tonkin-Hill G, Thorpe H., Simonsen GS., Norwegian E. coli study group., Johnsen PJ., Samuelsen Ø., and J. Corander. Escherichia coli plasmidome maps the game of clones. bioRxiv, doi: https://doi.org/10.1101/2023.10.14.562336 Dec. 7th. 2023, in review

4. Liljegren M., Gama JA., Johnsen PJ, and K. Harms. The recombination initiation functions DprA and RecFOR suppress microindel mutations in Acinetobacter baylyi ADP1. bioRxiv, doi:https://doi.org/10.1101/2023.11.22.568220, Nov. 22, 2023, in review.

5. Winter MR., Vos M., Buckling A., Johnsen PJ, and K. Harms. Effect of Chemotherapeutic Agents on Natural Transformation Frequency in Acinetobacter baylyi. Access Microbiology (preprint, under review)https://doi.org/10.1099/acmi.0.000733.v1, Nov. 3, 2023.

6. Lorentzen ØM., Haukefer ASB., Johnsen PJ, and C. Fröhlich. The Biofilm Lifestyle Shapes the Evolution of b-lactamases. bioRxiv, doi: https://doi.org/10.1101/2023.10.02.560492, Oct 2, 2023, in review.

7. Arredondo-Alonso S., Gladstone RA., Pontinen AK., Gama JA., Schurch AC., Lanza VF., Johnsen PJJ., Samuelsen Ø., Tonkin-Hill G., and J. Corander. Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genomics and Bioinformatics. 2023.5 (3) 1. doi: https://doi.or g/10.1093/nar gab/lqad066

8. Arredondo-Alonso S., Blundell-Hunter G., Fu Z., Gladstone RA., Filol-Salom A., Loraine, J., Johnsen PJJ., Samuelsen Ø., Pontinen AK., Cleon F., Chavez-Bueno S., De la Cruz MA., Ares MA., Vongsouvath M., Cmielarczyk A., Horner C., Klein N., McNally A., Reis JN., Penades JR., Thomson N., Corander J., Taylor PW., and AJ McCarthy. Evolutionary and functional history of the Escherichia coli K1 capsule. Nature Communications, 2023. 14, 3294. doi: https://doi.org/10.1038/s41467-023-39052-w

9. Winter M., Harms K., Johnsen PJ, and M. Vos. Collection of Annotated Acinetobacter Genome Sequences. Microbiol Res Announcements. 2023. 12 (3), e01094-2. doi: https://doi.org/10.1128/mra.01094-22

10. Sørum V., Øynes EL., Møller AS., Harms K., Samuelsen Ø., Podnecky NL., and PJ Johnsen. Evolutionary Instability of Collateral Susceptibility Networks in Ciprofloxacin-Resistant Clinical Escherichia coli Strains. mBio. 2022. 13 (4), e00441-22. doi: https://doi.org/10.1128/mbio.00441-22

11. Fröhlich C., Sørum V., Tokuriki N., Johnsen PJ, and Ø. Samuelsen. Evolution of b-lactamase-mediated cefiderocol resistance. J Antimicrob Chemother. 77(9) 2429-2436, 2022. doi: https://doi.org/10.1093/jac/dkac221

12. Mäklin T., Thorpe HA., Pöntinen AK., Gladstone RA., Shao Y., Pesonen M., McNally A., Johnsen PJ., Samuelsen Ø., Lawley TD., Honkela A., and J Corander. Strong pathogen competition in neonatal gut colonization. Nature Communications. 2022. 13 (1), 7417. doi: https://doi.org/10.1038/s41467-022-35178-5

13. Winter M., Buckling A., Harms K., Johnsen PJ., and M Vos. Antimicrobial resistance acquisition via natural transformation: context is everything. Curr. Op. Microbiol. 2022. 64, 133-138. doi: https://doi.org/10.1016/j.mib.2021.09.009

14. Dey, H, D Simonovic, ISFNS Hagen, T Vasskog, EGA Fredheim, HM Blencke, T Anderssen, MB Strøm, T Haug. Synthesis and antimicrobial activity of short analogues of the marine antimicrobial peptide Turgencin A: Effects of SAR optimizations, Cys-Cys cyclization and lipopeptide modifications. Interntional Journal of Molecular Sciences, 2022, 23(22). doi:https://doi.org/10.3390/ijms232213844

15. Gudmundsdóttir JS., Fredheim EGA., Koumans CIM., Hegstad J., Tang PC., Andersson DI., Samuelsen Ø.,and PJ Johnsen. The chemotherapeutic drug methotrexate selects for antibiotic resistance. EBioMedicine(2021), 74:103742. doi: https://doi.org/10.1016/j.ebiom.2021.103742

16. Arredondo-Alonso S., Pöntinen AK., Cleon F., Gladstone RA., Schürch AC., Johnsen PJ., Samuelsen Ø.,and J. Corander. A high-throughput multi-plexing strategy to complete bacterial genomes. GigaScience, 10, 2021, 1–13. doi: https://doi.org/10.1093/gigascience/giab079

17. Kloos J., Gama JA., Hegstad J., Samuelsen, Ø., and PJ Johnsen. Piggybacking on niche- adaptation reduces the cost of multidrug resistance plasmids. Mol. Biol. Evol, 2021, 38, 8, 3188–3201. doi: https://doi.org/10.1093/molbev/msab091

18. Gladstone R., McNally A., Pöntinen AK., Tonkin-Hill G., Lees JA., Skytén KO., Cléon F., Christensen MOK., Haldorsen BC., Bye KK., Gammelsrud KW., Hjetland R., Kümmel A., Larsen HE., Lindemann PC., Löhr IH., Marvik Å., Nilsen E., Noer MT., Simonsen GS., Steinbakk M., Tofteland S., Vattøy M., Bentley SD., Croucher NJ., Parkhill J., Johnsen PJ., Samuelsen Ø., Corander J. Emergence and dissemination of antimicrobial resistance in Escherichia coli bloodstream infections: a nationwide longitudinal microbial population study in Norway between 2002-2017. Lancet Microbe (2021), 2(10), e492. doi: https://doi.org/10.1016/S2666-5247(21)00031-8

19. Fröhlich C., Gama J., Harms K., Hirvonen VHA., Lund BA., van der Kamp MW., Johnsen PJ., Samuelsen Ø, and HK Leiros. Cryptic β-Lactamase Evolution Is Driven by Low β- Lactam Concentrations. 2021. mSphere, 6 (2), 10.1128/msphere. 00108-21. doi: https://doi.org/10.1128/msphere.00108-21

20. PJ Johnsen, Gama J, and K. Harms. Bacterial evolution on demand. 2021. eLife, 10,e68070, invited commentary. doi:https://doi.org/10.7554/eLife.68070

21. Kloos J., Johnsen PJ., and K. Harms. Tn1 transposition in the course of natural transformationenables horizontal antibiotic resistance spread in Acinetobacter baylyi. 2021. Microbiology, 167 (1). doi: 10.1099/mic.0.001003

22. Gama J., Kloos J., Johnsen PJ., and Ø. Samuelsen. Host dependent maintenance of blaNDM- 1-encoding plasmid in clinical Escherichia coli isolates. 2020. Scientific Reports, 10 (1), 9332.https://doi.org/10.1038/s41598-020-66239-8

23. Obuobi, SAO, K Julin, EGA Fredheim, M Johannessen, N Skalko-Basnet. Liposomal delivery of antibiotic loaded nucleic acid nanogels with enhanced drug loading and synergistic anti-inflammatory activity against S. aureus intracellular infections. Journal of Controlled Release, 2020, 324:620-632. doi: https://doi.org/10.1016/j.jconrel.2020.06.002

24. Wolden R, M Pain, R Karlsson, A Karlson, EGA Fredheim, JP Cavanagh. Identification of surface proteins in a clinical Staphylococcus haemolyticus isolate by bacterial surface shaving. BMC Microbiology, 2020, 20(80); 1-18. doi: https://doi.org/10.1186/s12866-020-01778-8

25. Gama JA, EGA Fredheim, FPA Clèon, AM Reis, R Zilhão, F. Dionisio. Dominance between plasmids determines the extent of biofilm formation. Frontiers in Microbiology, 2020. doi: https://doi.org/10.3389/fmicb.2020.02070

26. Fröhlich C., AM.Thomassen., PJ Johnsen, HKLeiros and Ø.Samuelsen.OXA-48-mediated ceftazidime-avibactam resistance is associated with evolutionary trade-offs. 2019. mSphere, 4: e00024-19. doi: https://doi.org/10.1128/msphere.00024-19

27. Granslo, HN, EGA Fredheim, E Esaiassen, L Christophersen, PØ Jensen, TE Mollnes, C Moser, T Flægstad, C Klingenberg, JP Cavanagh. The synthetic antimicrobial peptide LTX21 induces inflammatory responses in a human whole blood model and murine peritoneum model. APMIS -Journal of Pathology, Microbiology and Immunology, 2019, 127(6);475-483. Doi: https://doi.org/10.1111/apm.12946

28. Podnecky NL, Fredheim EGA, Kloos J, Sørum V, Primicerio R, Roberts AP, Rozen DE, Samuelsen Ø, PJ Johnsen. Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli. Nature Communications, 2018. 9 (1), 3673. doi: https://doi.org/10.1038/s41467-018-06143-y

29. Hülter N., Sørum V., Borch-Pedersen K., Liljegren M., Utnes A.L.G., Primicerio R., Harms K., P. J. Johnsen. Costs and benefits of natural transformation in Acinetobacter baylyi. 2017. BMC Microbiology 17 (1), 34. doi: https://doi.org/10.1186/s12866-017-0953-2

30. Di Luca MC., Sørum V., Starikova I., Kloos J., Hülter N., Naseer U., Johnsen PJ., Ø. Samuelsen. Low biological cost of carbapenemase-encoding plasmids following transfer from Klebsiella pneumoniae to Escherichia coli. 2017. J Antimicrob Chemother, 2017 72:1 85-89. doi: https://doi.org/10.1093/jac/dkw350

31. Ambur O.H., Engelstädter J., Johnsen P. J., Miller E- L., Rozen D. E. Steady at the wheel: conservative sex and the benefits of bacterial transformation. 2016. Phil. Trans. R. Soc. B 371 (1706), 20150528. doi: https://doi.org/10.1098/rstb.2015.0528

32. Harms K., Lunnan A., Hülter N., Mourier T., Vinner L., Andam CP., Martiinen P., Fridholm H., Hansen AJ., Hanage WP., Nielsen KM., Willerslev E., PJ Johnsen. Substitutions of short Heterologous DNA segements of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Nat Acad Sci U S A, 2016 113:52 15066-07. doi: https://doi.org/10.1073/pnas.1615819114

33. Engelstädter J., Harms K., and PJ Johnsen. The evolutionary dynamics of integrons in changing environments ISME J, 2016 Feb 5. doi: 10.1038/ismej.2015.222.

34. Utnes A., Sorum V., Hulter N., Primicerio R., Kloos J., Nielsen K.M., and PJ Johnsen. Growth phase specific evolutionary benefits of natural transformation in Acinetobacter baylyi. ISME J, 2015; advance online publication 7 April 2015; doi: 10.1038/ismej.2015.35