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The study of host-pathogen interactions is central to a better understanding of the human microbiome, infections and the inner workings of immune cells. One focal point of this research is how the human immune system recognises both harmful and harmless antigens, integrates the resulting signals and forms a response, and how, conversely, microbes can manipulate this reaction.
In this thesis, Pseudomonas aeruginosa (P. aeruginosa), a critical pathogen in chronic and nosocomial infections, was in the focus. The aim was to search for bacterial proteins that favour a type 2 immune response, as it is orchestrated by CD4+ type 2 T helper cells (Th2 cells). The humoral arm of a type 2 response is dominated by IgG4 and IgE. Such immune responses are typically directed against multicellular pathogens like helminths and other parasites. However, type 2 immune responses are suboptimal for the defence against extracellular bacteria like P. aeruginosa. Previous research suggests that some bacterial proteins may promote a switch to such an insufficient immune response as a mechanism of immune evasion.
To optimise the sensitivity of the search for type 2 response inducing proteins of P. aeruginosa, cystic fibrosis (CF) patients were studied, as many are exposed to the pathogen in their airways over prolonged time periods. As such, the humoral immune response of 9 CF patients to their own P. aeruginosa strain was examined. For this, the secretomes of 9 clinical P. aeruginosa isolates from CF patients and the P. aeruginosa reference strain PAO-1 were studied by 2D-immunoblotting for their ability to be bound by IgG4 and IgG1 from respective patient sera. IgG4 served as a proxy for IgE, as assays analysing IgE binding suffer from low sensitivity because of low serum concentrations of IgE. Antibody reactive P. aeruginosa proteins were then identified by liquid chromatography tandem mass spectrometry and the results were compared with proteomics data from literature.
In total, 308 distinct protein spots were analysed. These belonged to 17 bacterial proteins, which comprise the entire known P. aeruginosa secretome. Of these spots, 232 were bound by IgG4, and 24 by IgG1 only. Notably proteases like serralysin and P. aeruginosa elastase presented with an IgG4 bias. This is concordant with previous research linking proteases to a type 2 immune response. Moreover, structural proteins like
agellins were also immunodominant. Flagellins are known as common targets of immune detection in bacteria. These proteins also demonstrated a clear IgG4 bias.
Thus, the search for secreted P. aeruginosa proteins that elicit an IgG4-dominated antibody response was successful. It remains to be shown whether these bacterial proteins are also recognized by IgE and Th2 cells, meaning whether they are truly driving a type 2 immune response in CF patients. It is also an open question whether the observed IgG4 bias in the antibody response to the exoproteome of P. aeruginosa is specific to CF or a general feature of the human immune response to the pathogen.
In vitro and in vivo analyses of mono- and mixed-species biofilms formed by microbial pathogens
(2022)
Microbial biofilms can be defined as multicellular clusters of microorganisms embedded in a self-produced extracellular matrix (ECM), which is primarily composed of polymeric biomolecules. Biofilms represent one of the most severe burdens in both industry and healthcare worldwide, causing billions of dollars of treatment costs annually because biofilms are inherently difficult to prevent, treat, and eradicate. In health care settings, patients suffering from cystic fibrosis, or patients with medical implants are highly susceptible to biofilm infections. Once a biofilm is formed, it is almost impossible to quantitatively eradicate it by mechanical, enzymatical, chemical, or antimicrobial treatment. Often the only remaining option to fully eradicate the biofilm is removing of the infected implant or body part. The primary reasons for the inherent resistance of biofilms against all forms of antimicrobial treatment are (I) a reduced metabolic activity of biofilm-embedded cells climaxing in the presence of metabolic inactive persister cells, as well as (II) the protective nature of the biofilm matrix acting as a (diffusion) barrier against antimicrobials and the host immune system. Consequently, there is an urgent need to better understand microbial biofilms from a structural and (patho-) physiological point of view in order to be able to develop new treatment strategies.
Therefore, the aims of this study were to investigate fundamental physiological properties of different clinically relevant single and multi-species biofilms, both in vitro and in vivo. Furthermore, the effectiveness of a novel treatment strategy using cold atmospheric pressure plasma was evaluated in vitro to treat biofilms of the pathogenic fungus C. albicans.
In article I, the intracellular and ECM protein inventory of Staphylococcus aureus during in vitro biofilm growth in a flow reactor was analyzed by liquid-chromatography coupled to tandem mass-spectrometry (LC-MS/MS) analysis combined with metabolic footprint analysis. This analysis showed that anaerobiosis within biofilms releases organic acids lowering the ECM pH. This, in turn, leads to protonation of alkaline proteins – mostly ribosomal proteins originating from cell lysis as well as actively secreted virulence factors – resulting in a positive net charge of these proteins. As a consequence, these proteins accumulate within the ECM and form an electrostatic network with negatively charged cell surfaces, eDNA, and metabolites contributing to the overall biofilm stability.
In article II, the in vivo metaproteome of the multi-species biofilm community in cystic fibrosis sputum was investigated. To this end, an innovative protocol was developed allowing the enrichment of microbial cells, the extraction of proteins from a small amount of cystic fibrosis sputum, and subsequent metaproteome analysis. This protocol also allows 16S sequencing, metabolic footprint analysis, and microscopy of the same sample to complement the metaproteome data. Applying this protocol, we were able to significantly enhance microbial protein coverage providing first insights into important physiological pathways during CF lung infection. A key finding was that the arginine deaminase pathway as well as microbial proteases play a so far underappreciated role in CF pathophysiology.
In articles III and IV, a novel treatment strategy for biofilms formed by the important fungal pathogen Candida albicans was evaluated in vitro. Biofilms were treated with two different sources of nonthermal plasma (with the Nonthermal Plasma Jet “kINPen09” as well as with the Microwave-induced plasma torch “MiniMIP”) and the effect on growth, survival, and viability was assessed by counting colony-forming units (CFU), by cell proliferation assays, as well as by live/dead staining combined with fluorescence microscopy, confocal laser scanning microscopy, (CLSM) and atomic force microscopy (AFM). These tests revealed that biofilms were effectively inactivated mostly on the bottom side of biofilms, indicating a great potential of these two plasma sources to fight biofilms.
In einer Untersuchung von 1530 DNA-Proben Neugeborener aus Ostvorpommern wurden mittels PCR 32 Heterozygote der F508del-Mutation gefunden. Unter Berücksichtigung der CF-Allelverteilung der Region wurde eine Inzidenz der Mukoviszidose von 1:4216 errechnet. Es wurde die Notwendigkeit und die Möglichkeiten eines Neugeborenenscreenings auf Mukoviszidose diskutiert.