Publications Center for Infectious Medicine (CIM)

In addition to this list, publications are also listed on each research group page.

2025

Clinical Characteristics of Tick-Borne Encephalitis in Adult Patients: A 10-year Retrospective Study in Stockholm, Sweden.
Bartholdsson S, Hergens MP, Hansson KE, Ragnarsson J, Hodosi P, Kus I, Insulander M, Vene S, Lindquist L, Askling HH, Gredmark-Russ S
J Infect Dis 2025 Feb;231(1):e195-e205

Distinct MAIT cell phenotypes associated with sepsis clinical outcome in emergency department patients.
Emgård J, Filipovic I, Unge C, Palma Medina LM, Parke Å, Bergsten H, Moll K, Dzidic M, Alpkvist H, Fang H, Özenci V, Björkström NK, Svensson M, Sandberg JK, Strålin K, Norrby-Teglund A
Clin Transl Immunology 2025 ;14(3):e70028

Human MAIT cell response profiles biased toward IL-17 or IL-10 are distinct effector states directed by the cytokine milieu.
Boulouis C, Mouchtaridi E, Müller TR, Mak JYW, Fairlie DP, Bergman P, Michaëlsson J, Halfvarson J, Mjösberg J, Buggert M, Sandberg JK
Proc Natl Acad Sci U S A 2025 Feb;122(6):e2414230122

Antigen-specific T cell responses following single and co-administration of tick-borne encephalitis, Japanese encephalitis, and yellow fever virus vaccines: Results from an open-label, non-randomized clinical trial-cohort.
Wullimann D, Sandberg JT, Akber M, Löfling M, Gredmark-Russ S, Michaëlsson J, Buggert M, Blom K, Ljunggren HG
PLoS Negl Trop Dis 2025 Feb;19(2):e0012693

2024

MAIT cell heterogeneity across paired human tissues reveals specialization of distinct regulatory and enhanced effector profiles.
Kammann T, Cai C, Sekine T, Mouchtaridi E, Boulouis C, Nilsén V, Ballesteros OR, Müller TR, Gao Y, Raineri EJM, Mily A, Adamo S, Constantz C, Niessl J, Weigel W, Kokkinou E, Stamper C, Marchalot A, Bassett J, Ferreira S, Rødahl I, Wild N, Brownlie D, Tibbitt C, Mak JYW, Fairlie DP, Leeansyah E, Michaelsson J, Marquardt N, Mjösberg J, Jorns C, Buggert M, Sandberg JK
Sci Immunol 2024 Sep;9(99):eadn2362

Memory T cells effectively recognize the SARS-CoV-2 hypermutated BA.2.86 variant.
Müller TR, Gao Y, Wu J, Ribeiro O, Chen P, Bergman P, Blennow O, Hansson L, Mielke S, Nowak P, Vesterbacka J, Akber M, Söderdahl G, Smith CIE, Loré K, Chen MS, Ljungman P, Ingelman-Sundberg HM, Ljunggren HG, Österborg A, Sette A, Grifoni A, Aleman S, Buggert M
Cell Host Microbe 2024 Feb;32(2):156-161.e3

Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.
Kvedaraite E, Lourda M, Mouratidou N, Düking T, Padhi A, Moll K, Czarnewski P, Sinha I, Xagoraris I, Kokkinou E, Damdimopoulos A, Weigel W, Hartwig O, Santos TE, Soini T, Van Acker A, Rahkonen N, Flodström Tullberg M, Ringqvist E, Buggert M, Jorns C, Lindforss U, Nordenvall C, Stamper CT, Unnersjö-Jess D, Akber M, Nadisauskaite R, Jansson J, Vandamme N, Sorini C, Grundeken ME, Rolandsdotter H, Rassidakis G, Villablanca EJ, Ideström M, Eulitz S, Arnell H, Mjösberg J, Henter JI, Svensson M
Nat Commun 2024 Feb;15(1):1752

Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.
Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ
Nat Immunol 2024 Aug;25(8):1445-1459

Tissue-specific nonheritable influences drive endometrial immune system variation.
Bister J, Filipovic I, Sun D, Crona-Guterstam Y, Cornillet M, Ponzetta A, Michaëlsson J, Gidlöf S, Ivarsson MA, Strunz B, Björkström NK
Sci Immunol 2024 Apr;9(94):eadj7168

Vemurafenib inhibits the replication of diabetogenic enteroviruses in intestinal epithelial and pancreatic beta cells.
Butrym M, Byvald F, Blanter M, Ringqvist EE, Vasylovska S, Marjomäki V, Lau J, Stone VM, Flodström-Tullberg M
Antiviral Res 2024 Nov;231():106021

Clonally heritable gene expression imparts a layer of diversity within cell types.
Mold JE, Weissman MH, Ratz M, Hagemann-Jensen M, Hård J, Eriksson CJ, Toosi H, Berghenstråhle J, Ziegenhain C, von Berlin L, Martin M, Blom K, Lagergren J, Lundeberg J, Sandberg R, Michaëlsson J, Frisén J
Cell Syst 2024 Feb;15(2):149-165.e10

Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Bilev E, Wild N, Momayyezi P, Sala BM, Sun R, Sandalova T, Marquardt N, Ljunggren HG, Achour A, Hammer Q
PLoS Pathog 2024 Dec;20(12):e1012755

Real-world assessment of immunogenicity in immunocompromised individuals following SARS-CoV-2 mRNA vaccination: a two-year follow-up of the prospective clinical trial COVAXID.
Chen P, Bergman P, Blennow O, Hansson L, Mielke S, Nowak P, Gao Y, Söderdahl G, Österborg A, Smith CIE, Vesterbacka J, Wullimann D, Cuapio A, Akber M, Bogdanovic G, Muschiol S, Åberg M, Loré K, Chen MS, Ljungman P, Buggert M, Aleman S, Ljunggren HG
EBioMedicine 2024 Nov;109():105385

Coxsackievirus infection induces direct pancreatic β cell killing but poor antiviral CD8+ T cell responses.
Vecchio F, Carré A, Korenkov D, Zhou Z, Apaolaza P, Tuomela S, Burgos-Morales O, Snowhite I, Perez-Hernandez J, Brandao B, Afonso G, Halliez C, Kaddis J, Kent SC, Nakayama M, Richardson SJ, Vinh J, Verdier Y, Laiho J, Scharfmann R, Solimena M, Marinicova Z, Bismuth E, Lucidarme N, Sanchez J, Bustamante C, Gomez P, Buus S, , You S, Pugliese A, Hyoty H, Rodriguez-Calvo T, Flodstrom-Tullberg M, Mallone R
Sci Adv 2024 Mar;10(10):eadl1122

Genetic ablation of adhesion ligands mitigates rejection of allogeneic cellular immunotherapies.
Hammer Q, Perica K, Mbofung RM, van Ooijen H, Martin KE, Momayyezi P, Varady E, Pan Y, Jelcic M, Groff B, Abujarour R, Krokeide SZ, Lee T, Williams A, Goodridge JP, Valamehr B, Önfelt B, Sadelain M, Malmberg KJ
Cell Stem Cell 2024 Sep;31(9):1376-1386.e8

2023

Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia.
Palma Medina LM, Babačić H, Dzidic M, Parke Å, Garcia M, Maleki KT, Unge C, Lourda M, Kvedaraite E, Chen P, Muvva JR, Cornillet M, Emgård J, Moll K, , Michaëlsson J, Flodström-Tullberg M, Brighenti S, Buggert M, Mjösberg J, Malmberg KJ, Sandberg JK, Gredmark-Russ S, Rooyackers O, Svensson M, Chambers BJ, Eriksson LI, Pernemalm M, Björkström NK, Aleman S, Ljunggren HG, Klingström J, Strålin K, Norrby-Teglund A
Respir Res 2023 Feb;24(1):62

SARS-CoV-2 vaccination enhances the effector qualities of spike-specific T cells induced by COVID-19.
Cai C, Gao Y, Adamo S, Rivera-Ballesteros O, Hansson L, Österborg A, Bergman P, Sandberg JK, Ljunggren HG, Björkström NK, Strålin K, Llewellyn-Lacey S, Price DA, Qin C, Grifoni A, Weiskopf D, Wherry EJ, Sette A, Aleman S, Buggert M
Sci Immunol 2023 Dec;8(90):eadh0687

Additive effects of booster mRNA vaccination and SARS-CoV-2 Omicron infection on T cell immunity across immunocompromised states.
Müller TR, Sekine T, Trubach D, Niessl J, Chen P, Bergman P, Blennow O, Hansson L, Mielke S, Nowak P, Vesterbacka J, Akber M, Olofsson A, Amaya Hernandez SP, Gao Y, Cai C, Söderdahl G, Smith CIE, Österborg A, Loré K, Sällberg Chen M, Ljungman P, Ljunggren HG, Karlsson AC, Saini SK, Aleman S, Buggert M
Sci Transl Med 2023 Jul;15(704):eadg9452

The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis.
Kokkinou E, Soini T, Pandey RV, van Acker A, Theorell J, Czarnewski P, Kvedaraite E, Vandamme N, Lourda M, Sorini C, Weigel W, Carrasco A, Tibbitt CA, Schlums H, Lindforss U, Nordenvall C, Ljunggren M, Ideström M, Svensson M, Henter JI, Villablanca EJ, Bryceson YT, Rolandsdotter H, Mjösberg J
Cell Rep Med 2023 May;4(5):101038

Long-read whole-genome analysis of human single cells.
Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A
Nat Commun 2023 Aug;14(1):5164

2022

CD116+ fetal precursors migrate to the perinatal lung and give rise to human alveolar macrophages.
Evren E, Ringqvist E, Doisne JM, Thaller A, Sleiers N, Flavell RA, Di Santo JP, Willinger T
J Exp Med 2022 02;219(2): PMID: 35019940 

Broad anti-SARS-CoV-2 antibody immunity induced by heterologous ChAdOx1/mRNA-1273 vaccination.
Kaku CI, Champney ER, Normark J, Garcia M, Johnson CE, Ahlm C, Christ W, Sakharkar M, Ackerman ME, Klingström J, Forsell MNE, Walker LM. Science 2022 03;375(6584):1041-1047 PMID: 35143256; PMCID: PMC8939765.

Perturbed NK-cell homeostasis associated with disease severity in chronic neutropenia.
Sohlberg E, Pfefferle A, Heggernes Ask E, Tschan-Plessl A, Jacobs B, Netskar H, Lorenz S, Kanaya M, Kosugi-Kanaya M, Meinke S, Mörtberg A, Höglund P, Sundin M, Carlsson G, Palmblad J, Malmberg KJ
Blood 2022 02;139(5):704-716. PMID: 34699594 DOI: 10.1182/blood.2021013233

A single-cell map of vascular and tissue lymphocytes identifies proliferative TCF-1+ human innate lymphoid cells.
Gao Y, Alisjahbana A, Boey DZH, Mohammad I, Sleiers N, Dahlin JS, Willinger T
Front Immunol 2022 ;13():902881 PMID: 35967297

Ancestral SARS-CoV-2-specific T cells cross-recognize the Omicron variant.
Gao Y, Cai C, Grifoni A, Müller TR, Niessl J, Olofsson A, Humbert M, Hansson L, Österborg A, Bergman P, Chen P, Olsson A, Sandberg JK, Weiskopf D, Price DA, Ljunggren HG, Karlsson AC, Sette A, Aleman S, Buggert M
Nat Med 2022 Mar;28(3):472-476 PMID: 35042228

MAIT cell compartment characteristics are associated with the immune response magnitude to the BNT162b2 mRNA anti-SARS-CoV-2 vaccine.
Boulouis C, Kammann T, Cuapio A, Parrot T, Gao Y, Mouchtaridi E, Wullimann D, Lange J, Chen P, Akber M, Rivera Ballesteros O, Muvva JR, , Smith CIE, Vesterbacka J, Kieri O, Nowak P, Bergman P, Buggert M, Ljunggren HG, Aleman S, Sandberg JK
Mol Med 2022 May;28(1):54 PMID:35562666

Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination.
Gao Y, Cai C, Wullimann D, Niessl J, Rivera-Ballesteros O, Chen P, Lange J, Cuapio A, Blennow O, Hansson L, Mielke S, Nowak P, Vesterbacka J, Akber M, Perez-Potti A, Sekine T, Müller TR, Boulouis C, Kammann T, Parrot T, Muvva JR, Sobkowiak M, Healy K, Bogdanovic G, Muschiol S, Söderdahl G, Österborg A, Hellgren F, Grifoni A, Weiskopf D, Sette A, Loré K, Sällberg Chen M, Ljungman P, Sandberg JK, Smith CIE, Bergman P, Ljunggren HG, Aleman S, Buggert M
Immunity 2022 Sep;55(9):1732-1746.e5 PMID: 35961317

Adaptive single-KIR+NKG2C+ NK cells expanded from select superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia.
Haroun-Izquierdo A, Vincenti M, Netskar H, van Ooijen H, Zhang B, Bendzick L, Kanaya M, Momayyezi P, Li S, Wiiger MT, Hoel HJ, Krokeide SZ, Kremer V, Tjonnfjord G, Berggren S, Wikström K, Blomberg P, Alici E, Felices M, Önfelt B, Höglund P, Valamehr B, Ljunggren HG, Björklund A, Hammer Q, Kveberg L, Cichocki F, Miller JS, Malmberg KJ, Sohlberg E. J Immunother Cancer. 2022 Nov;10 (11):e005577. doi: 10.1136/jitc-2022-005577. PMID: 36319065 Free PMC article.

SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells.
Hammer Q, Dunst J, Christ W, Picarazzi F, Wendorff M, Momayyezi P, Huhn O, Netskar HK, Maleki KT, García M, Sekine T, Sohlberg E, Azzimato V, Aouadi M; Karolinska COVID-19 Study Group; Severe COVID-19 GWAS Group, Degenhardt F, Franke A, Spallotta F, Mori M, Michaëlsson J, Björkström NK, Rückert T, Romagnani C, Horowitz A, Klingström J, Ljunggren HG, Malmberg KJ.
Cell Rep. 2022 Mar 8;38(10):110503. doi: 10.1016/j.celrep.2022.110503. Epub 2022 Feb 21.
PMID: 35235832 Free PMC article.

2021

MAIT cell activation is associated with disease severity markers in acute hantavirus infection
Maleki KT, Tauriainen J, García M, Kerkman PF, Christ W, Dias J, Wigren Byström J, Leeansyah E, Forsell MN, Ljunggren HG, Ahlm C, Björkström NK, Sandberg JK, Klingström J. Cell Rep Med 2021 Mar;2(3):100220

Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.
Mold JE, Modolo L, Hård J, Zamboni M, Larsson AJM, Stenudd M, Eriksson CJ, Durif G, Ståhl PL, Borgström E, Picelli S, Reinius B, Sandberg R, Réu P, Talavera-Lopez C, Andersson B, Blom K, Sandberg JK, Picard F, Michaëlsson J, Frisén J. Cell Rep 2021 May;35(8):109174

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.
Mazzurana L, Czarnewski P, Jonsson V, Wigge L, Ringnér M, Williams TC, Ravindran A, Björklund ÅK, Säfholm J, Nilsson G, Dahlén SE, Orre AC, Al-Ameri M, Höög C, Hedin C, Szczegielniak S, Almer S, Mjösberg J. Cell Res 2021 May;31(5):554-568

Expansion of donor-unrestricted MAIT cells with enhanced cytolytic function suitable for TCR redirection.
Parrot T, Healy K, Boulouis C, Sobkowiak MJ, Leeansyah E, Aleman S, Bertoletti A, Sällberg Chen M, Sandberg JK. JCI Insight 2021 03;6(5):

A heterozygous germline CD100 mutation in a family with primary sclerosing cholangitis.
Jiang X, Bergquist A, Löscher BS, Venkatesh G, Mold JE, Holm K, Laerdahl JK, Skånland SS, Maleki KT, Cornillet M, Taskén K, Franke A, Karlsen TH, Björkström NK, Melum E. Sci Transl Med 2021 Feb;13(582):

Distinct developmental pathways from blood monocytes generate human lung macrophage diversity.
Evren E, Ringqvist E, Tripathi KP, Sleiers N, Rives IC, Alisjahbana A, Gao Y, Sarhan D, Halle T, Sorini C, Lepzien R, Marquardt N, Michaëlsson J, Smed-Sörensen A, Botling J, Karlsson MCI, Villablanca EJ, Willinger T. Immunity 2021 Feb;54(2):259-275.e7

Continuous human uterine NK cell differentiation in response to endometrial regeneration and pregnancy.
Strunz B, Bister J, Jönsson H, Filipovic I, Crona-Guterstam Y, Kvedaraite E, Sleiers N, Dumitrescu B, Brännström M, Lentini A, Reinius B, Cornillet M, Willinger T, Gidlöf S, Hamilton RS, Ivarsson MA, Björkström NK. Sci Immunol 2021 Feb;6(56):

Immunomodulatory agents combat multidrug-resistant tuberculosis by improving antimicrobial immunity.
Rao Muvva J, Ahmed S, Rekha RS, Kalsum S, Groenheit R, Schön T, Agerberth B, Bergman P, Brighenti S. J Infect Dis 2021 Feb;():

Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity
Egle Kvedaraite, Laura Hertwig, Indranil Sinha, Andrea Ponzetta, Ida Hed Myrberg, Magda Lourda, Majda Dzidic, Mira Akber, Jonas Klingström, Elin Folkesson, Jagadeeswara Rao Muvva, Puran Chen, Sara Gredmark-Russ, Susanna Brighenti, Anna Norrby-Teglund, Lars I. Eriksson, Olav Rooyackers, Soo Aleman, Kristoffer Strålin, Hans-Gustaf Ljunggren, Florent Ginhoux, Niklas K. Björkström, Jan-Inge Henter, Mattias Svensson, and Karolinska KI/K COVID-19 Study Group. PNAS February 9, 2021 118 (6)

Heterologous ChAdOx1 nCoV-19 and mRNA-1273 Vaccination.
Normark J, Vikström L, Gwon YD, Persson IL, Edin A, Björsell T, Dernstedt A, Christ W, Tevell S, Evander M, Klingström J, Ahlm C, Forsell M
N Engl J Med 2021 09;385(11):1049-1051 PMID: 34260850; PMCID: PMC8314734.

Coxsackievirus B Vaccines Prevent Infection-Accelerated Diabetes in NOD Mice and Have No Disease-Inducing Effect.
Stone VM, Butrym M, Hankaniemi MM, Sioofy-Khojine AB, Hytönen VP, Hyöty H, Flodström-Tullberg M
Diabetes 2021 12;70(12):2871-2878

Discriminatory plasma biomarkers predict specific clinical phenotypes of necrotizing soft-tissue infections.
Palma Medina LM, Rath E, Jahagirdar S, Bruun T, Madsen MB, Strålin K, Unge C, Hansen MB, Arnell P, Nekludov M, Hyldegaard O, Lourda M, Santos VAMD, Saccenti E, Skrede S, Svensson M, Norrby-Teglund A. J Clin Invest 2021 07;131(14):

High-dimensional immune cell profiling reveals phenotypic heterogeneity and disease-specific alterations of polymorphonuclear leukocytes in COVID-19.
M Lourda*, M Dzidic*, L Hertwig^*, H Bergsten, L M Palma Medina, E Kvedaraite, P Chen, R Muvva Jagadeeswara, J-B Gorin, M Cornillet, J Emgård, K Moll, M Garcia, K Maleki, J Klingström, J Michaelsson, M Flodström-Tullberg, S Brighenti, M Buggert, J Mjösberg, K-J Malmberg, J Sandberg, J-I Henter, E Folkesson, S Gredmark Russ, L I Eriksson, O Rooyackers, S Aleman, K Strålin, H-G Ljunggren, N K Björkström, M Svensson, A Ponzetta^#, A Norrby-Teglund^#, BJ Chambers^#; and the Karolinska COVID-19 Study Group. Proc Natl Acad Sci USA 2021; 118(40):e2109123118. # shared senior

Preferential and persistent impact of acute HIV-1 infection on CD4+ iNKT cells in colonic mucosa.
Paquin-Proulx D, Lal KG, Phuang-Ngern Y, Creegan M, Tokarev A, Suhkumvittaya S, Alrubayyi A, Kroon E, Pinyakorn S, Slike BM, Bolton DL, Krebs SJ, Eller LA, Sajjaweerawan C, Pagliuzza A, Chomont N, Rerknimitr R, Chomchey N, Phanuphak N, de Souza MS, Michael NL, Robb ML, Ananworanich J, Sandberg JK, Eller MA, Schuetz A,. Proc Natl Acad Sci U S A 2021 Nov;118(46): PMID: 34753817