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Publications

 

2018

 

Jonsson V, Österlund T, Nerman O, Kristiansson E. (2018). Modelling of zero-inflation improves inference of metagenomic gene count data. Stat Methods Med Res. 2018. doi: https://doi.org/10.1177/0962280218811354

Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E. (2018). The resistomes of six carbapenem-resistant pathogens – a critical genotype–phenotype analysis. Microbial Genomics. doi: 10.1099/mgen.0.000233

Munthe, C, El-Alti, L, Hartvigsson, T, Nijsingh, N (2018). Disputing with patients in person-centered care: Ethical aspects in standard care, pediatrics, psychiatry, and public health. Journal of Argumentation in Context 2(2): 231-244. DOI: https://doi.org/10.1075/jaic.18022.mun

Karp J, Edman-Wallér J, Toepfer M, Lundqvist A, G Jacobsson. (2018). Clostridioides difficile incidence related to in-hospital cephalosporin use: a tale of two highly comparable hospitals. J Antimicrob Chemother. https://doi.org/10.1093/jac/dky408

Graf FE, Palm M, Warringer J, Farewell A. (2018). Inhibiting conjugation as a tool in the fight against antibiotic resistance. Drug development research. https://doi.org/10.1002/ddr.21457

Pärnänen K, Karkman A, Hultman J, Lyra C, Bengtsson-Palme J, Larsson DGJ, Rautava S, Salminen S, Kumar H, Satokari R, Isolauri E, Virta M. (2018). Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements. Nature Communications. https://doi.org/10.1038/s41467-018-06393-w

Flach CF, Genheden M, Fick J, DGJ Larsson. (2018). A comprehensive screening of E. coli isolates from Scandinavia’s largest sewage treatment plant indicates no selection for antibiotic resistance. Environmental Science & Technology. https://pubs.acs.org/doi/10.1021/acs.est.8b03354

Bengtsson-Palme, J. (2018). The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants—but not always. Microbiome. 6:125. microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0508-2 https://doi.org/10.1186/s40168-018-0508-2

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P. (2018). Structure and function of the global topsoil microbiome. Nature. DOI: 10.1038/s41586-018-0386-6

Walujkar SA, Kumbhare SV, Marathe NP, Patangia DV, Lawate PS, Bharadwaj RS, Shouche YS. (2018). Molecular profiling of mucosal tissue associated microbiota in patients manifesting acute exacerbations and remission stage of ulcerative colitis. World J Microbiol Biotechnol. 34:76. DOI: 10.1007/s11274-018-2449-0

Lindgren Å, Karami N, Karlsson R, Åhrén C, Welker M, Moore ERB, Stadler LS. (2018). Development of a rapid MALDI-TOF MS based epidemiological screening method using MRSA as a model organism. Eur J Clin Microbiol Infect Dis. DOI: 10.1007/s10096-017-3101-x

Karkman A, Pärnänen K, Larsson DGJ. (2018). Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments. CSH bioRxi doi: https://doi.org/10.1101/341487

Munthe C, Nijsingh N, de Fine Licht K, Larsson DGJ. (2018). Health-related research and drastic public health threats: social value, pragmatic risks and drug resistance. In review (preprint online: https://www.researchgate.net/publication/325694548_Cutting_red_tape_to_manage_drastic_public_health_threats_Should_antimicrobial_drug_innovation_be_expedited

Nijsingh N, Larsson, DGJ, Persson de Fine-Licht K, Munthe C. (2018). Justifying Antibiotic Resistance Interventions: Uncertainty, Precaution and Ethics. In Jamrozik, E. & Selgelid, M. (Eds.). Ethics and Antimicrobial Resistance. Cham: Springer. Accepted & in press.

Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J, Parts L. (2018). Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences. CSH bioRxi doi: https://doi.org/10.1101/338194

Munthe C, Nijsingh N. (2018). Cutting red tape to manage drastic public health threats: Should antimicrobial drug innovation be expedited? In review. (Preprint online: https://www.researchgate.net/publication/325694548_Cutting_red_tape_to_manage_drastic_public_health_threats_Should_antimicrobial_drug_innovation_be_expedited )

Larsson DGJ, Andremont A, Bengtsson-Palme J, Koefoed Brandt K, de Roda Husman AM, Fagerstedt P, Fick J, Flach CF, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Plant L, Ploy MC, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson AS. (2018). Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environ Int. 117:132-138. https://doi.org/10.1016/j.envint.2018.04.041

Wahlgren WY, Dunevall E, North RA, Paz A, Scalise M, Bisignano P, Bengtsson-Palme J, Goyal P, Claesson E, Caing-Carlsson R, Andersson R, Beis K, Nilsson UJ, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, Friemann R. (2018). Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+ site. Nat Commun. 1;9(1):1753. doi: 10.1038/s41467-018-04045-7.

Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ. (2018). Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms. Environ Int. 116:255-268. https://doi.org/10.1016/j.envint.2018.04.029

Lindblom A, Karami N, Magnusson T, Åhrén C. (2018). Subsequent infection with extended-spectrum β-lactamase-producing Enterobacteriaceae in patients with prior infection or fecal colonization. Eur J Clin Microbiol Infect Dis. https://doi.org/10.1007/s10096-018-3275-x

Pereira MB, Wallroth M, Jonsson V, Kristiansson E. (2018). Comparison of normalization methods for the analysis of metagenomic gene abundance data, BMC Genomics 19(274). https://doi.org/10.1186/s12864-018-4637-6
 

Munthe C, El-Alti L, Hartvigsson T, Nijsingh N (2018). Disputing with Patients in Person-Centered Care: Ethical Aspects in Standard Care, Pediatrics, Psychiatry, and Public Health. Journal of Argumentation in Context, Accepted and in press

Topp E, Larsson DGJ, Miller DN, Van den Eede C, Virta MPJ. (2018). Antimicrobial resistance and the environment: assessment of advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing. FEMS Microbiol Ecol. 2018 Mar 1;94(3). doi: 10.1093/femsec/fix185

Hanna Alalam, Fabrice E. Graf, Martin Palm, Marie Abadikhah, Martin Zackrisson, Matilda Mattsson, Chris Hadjineophytou, Linnéa Persson, Simon Stenberg, Payam Ghiaci, Per Sunnerhagen, Jonas Warringer, Anne Farewell. (2018). Conjugation factors controlling F-plasmid antibiotic resistance transmission. CSH bioRxi doi: https://doi.org/10.1101/271254

Robertson F, Jagers S, Rönnerstrand B. (2018). Managing Sustainable Use of Antibiotics—The Role of Trust. Sustainability. doi:10.3390/su10010143

Larsson DGJ. (2018). Risks of using the natural defense of commensal bacteria as antibiotics call for research and regulation. Int J Antimicrob Agents. https://doi.org/10.1016/j.ijantimicag.2017.12.018

Bengtsson-Palme J, Gunnarsson L, Larsson DGJ. (2018). Can branding and price of pharmaceuticals guide informed choices towards improved pollution control during manufacturing? J Clean Prod. 171:137 https://doi.org/10.1016/j.jclepro.2017.09.247

Bengtsson-Palme J, Larsson DGJ. (2018). Protection goals must guide risk assessment for antibiotics. Environment international. In press. http://dx.doi.org/10.1016/j.envint.2017.10.019

Bengtsson-Palme J, Kristiansson E, Larsson DGJ. (2018). Environmental factors influencing the development and spread of antibiotic resistance. FEMS Micro Rev. 1;42. https://doi.org/10.1093/femsre/fux053

 

2017

 

Razavi M, Marathe NP, Gillings MR, Flach CF, Kristiansson E, Larsson DGJ. (2017). Discovery of the fourth mobile sulfonamide resistance gene. Microbiome. 5:160. https://doi.org/10.1186/s40168-017-0379-y

Mölstad S, Löfmark S, Carlin K, Erntell M, Aspevall O, Blad L, Hanberger H, Hedin K, Hellman J, Norman C, Skoog G, Stålsby-Lundborg C, Tegmark Wisell K, Åhrén C, Cars O. (2017) Lessons learnt during 20 years of the Swedish strategic programme against antibiotic resistance. Bull World Health Organ. 2017:95(11):764-773. doi: 10.2471/BLT.16.184374

North RA, Horne CR, Davies JS, Remus DM, Muscroft-Taylor AC, Goyal P, Wahlgren WY, Ramaswamy S, Friemann R, Dobson RCJ. "Just a spoonful of sugar...": import of sialic acid across bacterial cell membranes. Biophys Rev. 2017 Dec 8. doi: 10.1007/s12551-017-0343-x. [Epub ahead of print] Review.

Jutkina J, Marathe NP, Flach C-F, Larsson DGJ. 2017. Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations. Sci Total Environ. 2017 Nov 4;616-617:172-178. https://doi.org/10.1016/j.scitotenv.2017.10.312

Ljungström L, Pernestig A-K, Jacobsson G, Andersson R, Usener B, Tilevik D. 2017. Diagnostic accuracy of procalcitonin, neutrophil-lymphocyte count ratio, C-reactive protein, and lactate in patients with suspected bacterial sepsis. PLoS ONE 12(7): e0181704. https://doi.org/10.1371/journal.pone.0181704

Berglund F, Nachiket MP, Österlund T, Bengtsson-Palme J, Kotsakis S, Flach CF, Larsson DGJ, Kristiansson E. (2017). Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome. 2017 5:134. https://doi.org/10.1186/s40168-017-0353-8.

Lindgren Å, Karami N, Karlsson R, Åhrén C, Welker M, Moore ERB, Stadler LS. Development of a rapid MALDI-TOF MS based epidemiological screening method using MRSA as a model organism. Eur J Clin Microbiol Infect Dis. 2017 Sep 18. https://doi.org/10.1007/s10096-017-3101-x


Boulund F, Berglund F, Flach C-F, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E. 2017. Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics 18:682
https://doi.org/10.1186/s12864-017-4064-0
 

Monika Djerf-Pierre och Adam Shehata. (2017) Medierna och människors oro för antibiotikaresistens. Larmar och gör sig till. Sid. 169-186. SOM-institutets böcker. ISBN 978-91-89673-39-7.

Nachiket P.Marathe, ChandanPal, Swapnil S.Gaikwad, ViktorJonsson, ErikKristiansson, and D.G. JoakimLarsson. Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics. Water Res. Nov 1;124:388-397. https://doi.org/10.1016/j.watres.2017.07.060.
 

Bengtsson-Palme J., Larsson DGJ., Kristiansson E. 2017. Using metagenomics to investigate human and environmental resistomes. J Antimicrob Chemother. https://doi.org/10.1093/jac/dkx199

 

Mark Davis, Andrea Whittaker, Mia Lindgren, Monika Djerf-Pierre, Lenore Manderson & Paul Flowers. Understanding media publics and the antimicrobial resistance crisis. Global Public Health. P ages 1-11 | Received 29 Nov 2016, Accepted 22 May 2017, Published online: 08 Jun 2017. http://dx.doi.org/10.1080/17441692.2017.1336248
 

Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, Al-Bayati O, Åhrén C, Moore ERB, Kristiansson E. Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. Mol Cell Proteomics. 2017 Jun;16(6):1052-1063. doi: 10.1074/mcp.M116.061721. Epub 2017 Apr 18.

 

Ljungström LR, Jacobsson G, Claesson BEB, Andersson R, Enroth H. Respiratory viral infections are underdiagnosed in patients with suspected sepsis. Eur J Clin Microbiol Infect Dis. 2017 May 17. doi: 10.1007/s10096-017-2990-z.


Jakobsson HE, Salvà-Serra F, Thorell K, Karlsson R, Gonzales-Silès L, Boulund F, Engstrand L, Kristiansson E, Moore ER. Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F. Genome Announc. 2017 Apr 6;5(14). pii: e00125-17. doi: 10.1128/genomeA.00125-17.

 

J. Bengtsson-Palme. Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Curr Opin Food Sci. Volume 14, April 2017, Pages 66–71. http://dx.doi.org/10.1016/j.cofs.2017.01.010.

 

Flach CF, Pal C, Svensson CJ, Kristiansson E, Östman M, Bengtsson-Palme J, Tysklind M, Larsson DGJ. (2017). Does antifouling paint select for antibiotic resistance? Science of the Total Environment. Volumes 590–591, 15 July 2017, Pages 461–468. doi: 10.1016/j.scitotenv.2017.01.213.

 

Hao X*, Li X*, Pal C*, Hobman J, Rosen BP, Larsson DGJ, Saquib Q, Alwathnani HA, Zhu Y-G, Rensing C. (2017). Bacterial resistance to arsenic protects against protist killing. Biometals. Biometals. Volume 30, Issue 2, pp 307–311. doi: 10.1007/s10534-017-0003-4 (*-co-first authors).

 

Pal C, Asiani K, Arya S, Rensing C, Stekel DJ, Larsson DGJ, Hobman JL. (2017). Metal resistance and its association with antibiotic resistance. Advances in Microbial Physiology. Volume 70, Chapter 7, Pages 261-313. ISBN: 9780128123867.

 

Helldal L, Karami N, Welinder-Olsson C, Moore ER, Åhren C. (2017) Evaluation of MLVA for epidemiological typing and outbreak detection of ESBL-producing Escherichia coli in Sweden. BMC Microbiol. 2017 Jan 6;17(1):8. doi: 10.1186/s12866-016-0922-1. PMID:28061803

 

Rönnerstrand, B. och V. Lapurente. Corruption and use of antibiotics in regions of Europe. Health Policy. 2017 Mar;121(3):250-256. doi: 10.1016/j.healthpol.2016.12.010. Epub 2017, Jan 7.

 


2016

 

Ballard MS, Schønheyder HC, Knudsen JD, Lyytikäinen O, Dryden M, Kennedy KJ, Valiquette L, Pinholt M, Jacobsson G, Laupland KB; International Bacteremia Surveillance Collaborative. The changing epidemiology of group B streptococcus bloodstream infection: a multi-national population-based assessment. Infect Dis (Lond). 2016;48(5):386-91. doi: 10.3109/23744235.2015.1131330.


North RA, Watson AJ, Pearce FG, Muscroft-Taylor AC, Friemann R, Fairbanks AJ, Dobson RC. Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. FEBS Lett. 2016 Dec;590(23):4414-4428. doi: 10.1002/1873-3468.12462.


Bengtsson-Palme J and Larsson DGJ. (2016) Time to limit antibiotic pollution. The medicine maker, April issue, pp 17-18. (opinion paper).


Bengtsson-Palme J, Larsson DGJ (2016). Why limit antibiotic pollution? The role of environmental selection in antibiotic resistance development. APUA Newsletter, 34(2), 6-9.


Bengtsson-Palme J, Hammarén R, Pal C, Östman M, Björlenius B, Flach C-F, Fick J, Kristiansson E, Tysklind M, Larsson DGJ. (2016). Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Science of the Total Environment. doi: 10.1016/j.scitotenv.2016.06.228.


De Roda Husman A-M, Larsson DGJ (2016). Risk assessment and risk management of antimicrobial resistance in the environment. AMR control 2016. Pages 104-107. Global Health Dynamics, UK.


Edman-Wallér J, Ljungström L, Jacobsson G, Andersson R, Werner M. Systemic symptoms predict presence or development of severe sepsis and septic shock. Infect Dis (Lond). 2016;48(3):209-14. doi: 10.3109/23744235.2015.1104719.


Gao C, Uzelac I, Gottfries J, Eriksson LA. Exploration of multiple Sortase A protein conformations in virtual screening. Sci Rep. 2016 Feb 5;6:20413. doi: 10.1038/srep20413.


Johnning A, Jakobsson H, Boulund F, Salvà Serra F, Moore ERB, Åhrén C, Karami N, Kristiansson E. Draft genome sequence of extended-spectrum β-lactamase-producing Escherichia coli, strain CCUG 62462, isolated from a urine sample" Genome Announc. 2016 Dec 15;4(6). pii: e01382-16. doi: 10.1128/genomeA.01382-16.


Jonsson V, Österlund T, Nerman O, Kristiansson E. Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics. BMC Genomics. 2016 Jan 25;17:78. doi: 10.1186/s12864-016-2386-y.


Jonsson V, Österlund T, Nerman O, Kristiansson E. Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes. J Comput Biol. 2016 Nov 28.


Karami N, Wold AE, Adlerberth I. Antibiotic resistance is linked to carriage of papC and iutA virulence genes and phylogenetic group D background in commensal and uropathogenic Escherichia coli from infants and young children. Eur J Clin Microbiol Infect Dis. 2016 Dec 6.


Kwiecinski J, Peetermans M, Liesenborghs L, Na M, Björnsdottir H, Zhu X, Jacobsson G, Johansson BR, Geoghegan JA, Foster TJ, Josefsson E, Bylund J, Verhamme P, Jin T. Staphylokinase Control of Staphylococcus aureus Biofilm Formation and Detachment Through Host Plasminogen Activation. J Infect Dis. 2016 Jan 1;213(1):139-48. doi: 10.1093/infdis/jiv360.


Larsson DGJ, Svennerholm A-M (2016). The role of antibacterial agents in the development of antibiotic resistance (in Swedish). Läkartidningen 2016;113:D44E.


Marathe NP, Shetty SA, Shouche YS, Larsson DGJ. 2016. Limited bacterial diversity within a treatment plant receiving antibiotic-containing waste from bulk drug production. PloS One 11(11): e0165914. doi:10.1371/journal.pone.0165914.


Munthe C. Antibiotikaresistens och etik. Ord & Bild, (5)64-68, 2016.


Müller V, Karami N, Nyberg LK, Pichler C, Torche Pedreschi PC, Quaderi S, Fritzsche J, Ambjörnsson T, Åhrén C, Westerlund F. Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping. ACS Infect Dis. 2016 May 13;2(5):322-8. doi: 10.1021/acsinfecdis.6b00017.


Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping. Sci Rep. 2016 Dec 1;6:37938. doi: 10.1038/srep37938.


Nyberg LK, Quaderi S, Emilsson G, Karami N, Lagerstedt E, Müller V, Noble C, Hammarberg S, Nilsson AN, Sjöberg F, Fritzsche J, Kristiansson E, Sandegren L, Ambjörnsson T, Westerlund F. Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules. Sci Rep. 2016 Jul 27;6:30410. doi: 10.1038/srep30410.


Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. (2016). The structure and diversity of human, animal and environmental resistomes. Microbiome. 4:54. doi: 10.1186/s40168-016-0199-5.


Pereira MB, Kristiansson E, Axelsson-Fisk M, HattCI: fast and accurate attC site identification using hidden Markov models. J Comput Biol, 2016 Nov;23(11):891-902. Epub 2016 Jul 18

 
Runesson J, Shamansurova E, Jacobsson G. Antibiotics are being misused to treat diarrhoeal disease in children in Central Asia. Acta Paediatr. 2016 Dec;105(12):1382-1383. doi: 10.1111/apa.13583. PMID: 27870206.


Rönnerstrand B. Antibiotikaresistens och det kollektiva handlandets problem. Ord & Bild, (5)56-63, 2016.


Rönnerstrand B, Jagers S, Larsson DGJ (2016). Who worries about antibiotic resistance? (In Swedish). Ekvilibrium (Eds. Henrik Oscarsson, Jonas Ohlsson and Maria Solevid). SOM-institutet, University of Gothenburg. ISBN 978-91-89673-35-9.


Salvà-Serra F, Jakobsson HE, Thorell K, Gonzales-Siles L, Hallbäck ET, Jaén-Luchoro D, Boulund F, Sikora P, Karlsson R, Svensson L, Bennasar A, Engstrand L, Kristiansson E, Moore ER. Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T. Genome Announc. 2016 Mar 24;4(2). pii: e00175-16. doi: 10.1128/genomeA.00175-16.


Skyman E, Lindahl B, Bergbom I, Sjöström HT, Åhrén C. Being Met as marked - patients' experiences of being infected with community-acquired methicillin-resistant Staphylococcus aureus (MRSA). Scand J Caring Sci. 2016 Dec;30(4):813-820. doi: 10.1111/scs.12309.


Svensson J. och C. Verdinelli. Mirakellösningen som blev ett problem. Ord & Bild, (5)36-41, 2016.


Wehrli PM, Angerer TB, Farewell A, Fletcher JS, Gottfries J. Investigating the Role of the Stringent Response in Lipid Modifications during the Stationary Phase in E. coli by Direct Analysis with Time-of-Flight-Secondary Ion Mass Spectrometry. Anal Chem. 2016 Sep 6;88(17):8680-8. doi: 10.1021/acs.analchem.6b01981.


Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sanchez J, Sanli K, Thorell K. Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics. 2016 Sep;16(18):2454-60. doi: 10.1002/pmic.201600034.


Zaborowska M, Tillander J, Branemark R, Hagberg L, Thomsen P, Trobos M. Biofilm formation and antimicrobial susceptibility of staphylococci and enterococci from osteomyelitis associated with percutaneous orthopaedic implants. J Biomed Mater Res B Appl Biomater. Oct 25 2016.

 

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Utskriftsdatum: 2018-12-11