Young Investigator Group "Infectious Diseases"

Current Projects

Bacterial and viral co-infections of the upper and lower respiratory tract

supported by Federal Excellence Initiative of Mecklenburg Western Pomerania and European Social Fund (ESF) Grant KoInfekt

Bacterial and viral co-infections of the respiratory tract are life-threatening and present a global burden to the global community. Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes are frequent colonizers of the upper respiratory tract. Imbalances through acquisition of seasonal viruses, e.g. Influenza A virus, can lead to bacterial dissemination to the lower respiratory tract, which in turn can result in severe pneumonia. It is estimated that around 95% of all severe cases and deaths were attributed to secondary infections with bacterial pathogens. We are trying to gain insight into immunology and microbiology of this highly lethal disease; how hyper-inflammatory conditions of the lungs at the onset are promoted, which immunological and microbiological factors are contributing to immune paralysis afterwards, and how tissue pathology is promoted. 

This research is performed with a number of local national collaborators, including: Sven Hammerschmidt, Katharina Riedel, Tim Urich, Dörthe Becher, Uwe Völker, Frank Schmidt, Ulrike Seifert, Michael Lalk, Barbara Bröker, Lars Kaderalli (University of Greifswald), Bernd Kreikemeyer, Sonja Oehmcke-Hecht, Brigitte Müller-Hilke (University of Rostock), Thomas C. Mettenleiter (Friedrich Loeffler-Institute (FLI), Island Riems).


Resistance and persistence strategies by Gram-positive bacteria in necrotizing skin and soft tissue infections

supported by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)

This project focuses on severe acute infections caused by Gram-positive bacteria: group A, B, and G streptococci (GAS; GBS, and GGS) and Staphylococcus aureus. These microorganisms are associated with a variety of diseases ranging from superficial skin and throat infections to life-threatening sepsis, toxic shock syndrome and necrotizing soft tissue infections (NSTIs). The latter are rapidly progressing infections associated with high mortality and morbidity. In this project we will apply tissue engineering to generate in vitro skin, which will allow us to study bacterial persistence and resistance phenotypes at the tissue site, including phenotypic switches of the bacteria and biofilm formation. Further, we are aiming to identify potential virulence mechanisms, therapy targets, and host pathways contributing to the severity of infection.

This research is performed with a number of international and national collaborators, including: Anna Norrby-Teglund, Mattias Svensson (Karolinska Institutet, Stockholm, Sweden), Slavena Vylkova (Septomics, Jena, Germany), Matthias Mörgelin (Lund University, Lund, Sweden), Bernd Kreikemeyer (University of Rostock, Rostock, Germany).

Lab Members

Nikolai Siemens, group leader

Nikolai received his Dipl.-Biol. and PhD degrees from University of Rostock (Germany) in 2009 and 2012, respectively. After working in the lab of Anna Norrby-Teglund at the Center for Infectious Medicine, Karolinska Institutet in Stockholm (Sweden) for four years, he moved back to Germany. His laboratory is located within the Department Molecular Genetics and Infection Biology.


Dr. rer. nat. Nikolai Siemens
University of Greifswald
Center for Functional Genomics of Microbes
Interfaculty Institute for Genetics and Functional Genomics
Dept. Molecular Genetics and Infection Biology
Felix-Hausdorff-Straße 8
17087 Greifswald, Germany
Phone +49 3834 420 5711

Fabian Cuypers, PhD student

Fabian received his Masters degree in Human Biology from University of Greifswald (Germany) in 2016. His work focuses on understanding how S. aureus and Influenza A Virus infections are contributing to the pathogenesis of respiratory infections.


Phone +49 3834 420 5716

Surabhi Surabhi, PhD student

Surabhi completed her Master studies in Microbiology (Friedrich-Schiller University Jena, Germany) in 2017. In her doctoral studies she is conducting comparative characterizations of human lung cells and their responses towards different viral and bacterial respiratory pathogens.


Phone +49 3834 420 5716

Patience Shumba, PhD student

Patience received her Master degree in Medical Sciences from University of KwaZulu Natal (South Africa). In her doctoral studies she focuses on phenotypic switches of bacteria in tissue environment and how these are contributing to the severity of infection.


Phone +49 3834 420 5716

Lea Tölken, PhD student

Lea received her Bachelor and Master degrees in Biochemistry from University of Greifswald. In her studies she analyzes immune responses in bacterial and viral co-infections. Furthermore, she is interested in evasion strategies of group G streptococci in NSTIs.


Phone +49 3834 420 5751

Antje Paulikat, PhD student

Antje received her Bachelor and Master degrees in Human Biology from University of Greifswald. Her work focuses on understanding how Gram-positive bacteria and Influenza A virus impact dendritic cell function.


Phone +49 3834 420 5751

Lana Jachmann, PhD student

Lana received her Bachelor and Master degrees in Biochemistry from the University of Greifswald. In her studies she analyzes epithelial cell responses to pneumococcal and influenza A virus single and co-infections.

Phone +49 3834 420 5716

Selected Publications

Show all publications (PubMed)

The role of NLRP3 inflammasome in pneumococcal infections. Surabhi S, Cuypers F, Hammerschmidt S, Siemens N. Frontiers in Immunology. 2020. doi: 10.3389/fimmu.2020.614801

Pathogenic Mechanisms of Streptococcal Necrotizing Soft Tissue Infections. Siemens N, Snäll J, Svensson M, Norrby-Teglund A. Adv Exp Med Biol. 2020;1294:127-150. doi: 10.1007/978-3-030-57616-5_9.

Adenosine Triphosphate Neutralizes Pneumolysin-induced Neutrophil Activation. Cuypers F, Klabunde B, Gesell Salazar M, Surabhi S, et al. The Journal of Infectious Diseases. 2020. doi: 10.1093/infdis/jiaa277.

16HBE Cell Lipid Mediator Responses to Mono and Co-Infections with Respiratory Pathogens. Schultz D, Surabhi S, Stelling N, Rothe M, Group KS, Methling K, Hammerschmidt S, Siemens N, Lalk M. Metabolites. 2020. doi: 10.3390/metabo10030113.

Pro-thrombotic and pro-inflammatory activities of the β-hemolytic group B streptococcal pigment. Siemens N, Oehmcke-Hecht S et al. Journal of Innate Immunity. 2019. DOI: 10.1159/000504002

Glycoconjugated Phthalocyanines as Photosensitizers for PDT –Overcoming Aggregation in Solution. Bächle F, Siemens N, Ziegler T. European Journal of Organic Chemistry. 2019.

Is it time to reconsider the group A streptococcal rheumatogenic concept? Norrby-Teglund A and Siemens N. Clinical Infectious Diseases.2019 Jul 23. pii: ciz427. doi: 10.1093/cid/ciz427.

The role of streptococcal and staphylococcal exotoxins and proteases in human necrotizing soft tissue infections. Shumba P, Mairpady Shambat S, and Siemens N. Toxins (Basel). 2019 Jun 11;11(6). pii: E332. doi: 10.3390/toxins11060332.

Port d'Entrée for Respiratory Infections - Does the Influenza A Virus Pave the Way for Bacteria? Siemens N, Oehmcke-Hecht S, Mettenleiter TC, Kreikemeyer B, Valentin-Weigand P, Hammerschmidt S. Frontiers in Microbiology. 2017 Dec 21;8:2602. doi: 10.3389/fmicb.2017.02602. eCollection 2017.

Shocking superantigens promote establishment of bacterial infection. Siemens N and Norrby-Teglund A. Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10000-10002. doi: 10.1073/pnas.1713451114. Epub 2017 Sep 12.

Biofilm in group A streptococcal necrotizing soft tissue infections. Siemens N, Chakrakodi B, Shambat SM, et al. Journal of Clinical Investigation Insight. 2016 Jul 7;1(10):e87882.

Phosphoglycerate kinase – a novel streptococcal factor involved in neutrophil activation and degranulation. Uhlmann J, Siemens N, Kai-Larsen Y, et al. Journal of Infectious Diseases. 2016 Dec 15;214(12):1876-1883.

A point mutation in AgrC determines cytotoxic or colonizing properties associated with phenotypic variants of ST22 MRSA strains. Mairpady Shambat S, Siemens N, Monk IR, et al. Scientific Reports. 2016 Aug 11;6:31360. doi: 10.1038/srep31360.

Genetic Architecture of Group A Streptococcal Necrotizing Soft Tissue Infections in the Mouse. Chella Krishnan K, Mukundan S, Alagarsamy J, Hur J, Nookala S, Siemens N, et al. PLoS Pathogens. 2016 Jul 11;12(7):e1005732. doi: 10.1371/journal.ppat.1005732. eCollection 2016 Jul.

Increased cytotoxicity and streptolysin O activity in group G streptococcal strains causing invasive tissue infections. Siemens N, Kittang BR, Chakrakodi B, et al.Scientific Reports. 2015 Nov 25;5:16945. doi: 10.1038/srep16945.

Open Positions

We always want to get in touch with talented and highly motivated potential co-workers interested in translational research aimed at understanding the mechanisms of highly lethal infectious diseases. If you are interested in doing research within our group, as a degree project, please contact the group leader Nikolai Siemens.

Contact details:

Nikolai Siemens
Phone +49 3834 420 5711