R Kaiser(1,2,*), R Dewender(1,2), M Joppich(3), M Schmid(1), L Kääb(1), A Droste zu Senden(1), A Akhalkatsi(1), C Gold(1,2), S Saha(4), J Büch(4), A Gottschlich(5,6), M Lorenz(1), O Popp(7), M Lox(8), V Knottenberg(1), A Martinez-Navarro(1), L Eivers(1), R Escaig(1,2), J Erber(9), C Spinner(9), F Kur(4), S Peterss(2,4), N Hubner(7,10,11), R Draenert(12), P Verhamme(8,14), H Schulz(15), M Rudelius(15), S Kobold(5,6), P Mertins(7), R Zimmer(3), C Hagl(2,4), S Massberg(1,2), K Martinod(8,14,16), LB Joosten(17), K Stark(1,2), L Nicolai(1,2,#), and K Pekayvaz(1,2,#)

1. Medizinische Klinik und Poliklinik I, University Hospital Ludwig-Maximilians University, Munich, Germany; 2. DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany; 3. LFE Bioinformatik, Department of Informatics, Ludwig-Maximilians Universität München, Munich, Germany; 4. Department of Cardiac Surgery, University Hospital Ludwig-Maximilians University, Munich, Germany; 5. Department of Medicine III, University Hospital, LMU Munich, Munich, Germany; 6. Division of Clinical Pharmacology, University Hospital, LMU Munich, Munich, Germany; 7. Max Delbrück Center for Molecular Medicine (MDC) and Berlin Institute of Health (BIH), Berlin, Germany; 8. Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; 9. Department of Internal Medicine II, Technical University of Munich, School of Medicine, University Hospital rechts Der Isar, 81675, Munich, Germany; 10. Charite-Universitätsmedizin Berlin, Berlin, German; 11. German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany; 12. Antibiotic Stewardship Programme, University Hospital Ludwig-Maximilians University, Munich, Germany; 13. Max-von-Pettenkofer-Institute Munich, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 München, Germany; 14. Vascular Medicine and Haemostasis, University of Leuven, Leuven, Belgium; 15. Department of Pathology, Ludwig-Maximilians University, Munich, Germany; 16. University of Rochester, Rochester, New York, USA; 17. Department of Internal Medicine and Radboud Community for Infectious diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands

*Correspondence to rainer.kaiser@med.uni-muenchen.de, Medizinische Klinik und Poliklinik I, University Hospital Ludwig-Maximilian-University Munich, Marchioninistr. 15 81377, Munich, Germany.

#These authors contributed equally.

Infective endocarditis (IE) is among the most relevant pathogen-induced cardiovascular diseases. While the incidence of IE has nearly doubled during the past two decades, treatment options are mostly restricted to antibiotics and surgical valve repair, highlighting the urgent need for new therapeutic strategies. However, our understanding of the systemic immune response to IE is limited.

Here, we enrolled patients with clinically confirmed infective endocarditis in a prospective immunophenotyping study to systemically assess the host response to IE. Using both clinical data and multi-omics methods, we identify endocarditisspecific immune responses at single-cell resolution. We detect the upregulation of IE-specific circulating factors, including the broad expression of complement proteins and the expansion of distinct T cell clusters in IE. Among these clusters, we reveal CD4⁺ T cells characterized by a pro-inflammatory phenotype that upregulate IE-specific transcriptional programs with elevated cytokine expression. In vitro, we confirm that these T-cell-derived factors (e.g. IL-32 and TNF), activate myeloid cells and facilitate bacterial clearance through myeloid cell co-activation. Finally, blocking CD4⁺ T cell responses in a murine model of Staphylococcus aureus-induced IE aggravates disease severity and mortality, highlighting CD4⁺ Tcells as master regulators of the myeloid response to bacterial IE in vivo.

Our in-depth immune profile of IE patients provides mechanistic evidence of an unexpectedly fundamental role of T cells in mounting the endocarditis-specific host defense by orchestrating myeloid responses. Our study further provides the first comprehensive immune atlas of human IE and represents the foundation for the development of novel immunomodulatory treatment approaches in IE.