Transcriptomics of Bordetella and Human Phagocytes Interplay

Bordetella pertussis is the causative agent of human whooping cough (pertussis), a highly contagious respiratory disease that is currently again on the rise even in highly vaccinated populations. B. pertussis has been traditionally viewed as a typical extracellular pathogen that colonizes B. pertussis cells upon ciliated respiratory epithelia. Recently, it was demonstrated that infection of human macrophages escape killing and persists within macrophages, suggesting B. pertussis can be considered as a facultative intracellular pathogen. In order to further that explore this observation we will apply parallel comparative transcriptomic analysis of gene B. pertussis simultaneously (dual expression profiles of human phagocytes and internalized RNAseq). Using this approach we plan to identify phagocytespecific adaptation responses to the infection as well as specific responses of the pathogen cells in the process of adaptation to intracellular environment in phagocytes. This analysis should reveal novel factors promoting intracellular survival of B. pertussis, as well as assign new functions for already known virulence factors. To analyse the data produced within this project, we plan to develop a tailor made bioinformatics tool which would link both host and pathogenspecific gene expression B. pertussis patterns and which would allow us to reconstruct the human macrophage infectome.

Whooping cough (pertussis) is a highly contagious infectious disease of the respiratory tract caused by the pathogen Bordetella pertussis. Despite the availability of an effective vaccine and although humans are the sole host of B. pertussis, whooping cough never disappeared. Especially newborns are at risk, even in societies with high vaccination rate. In recent years, even a rise in the number of cases in Western industrialized countries could be observed. Whooping cough is considered one of the most common vaccine-preventable diseases in the Western world. It is therefore important to deepen our understanding about the pathogen, its dissemination and its interaction with its host. Traditionally, B. pertussis has been considered an extracellular bacterium which colonizes the mucous membranes of the lower respiratory tract. Recent research suggests that B. pertussis can also survive within human immune cells, whose actual purpose is to clear the pathogen. Whether this also plays a relevant role in the course of the disease or in the transmission of disease is still controversial. This FWF research project aimed to help answer this question. For this purpose, our Czech cooperation partner, Dr. Vecerek, developed a system in which human immune cells can be infected with B. pertussis in cell culture. These cultures were subsequently studied using a technique called dual RNA-seq. Thereby the transcriptome, i.e. the totality of all transcribed genes, are quantified in the host and the pathogen, simultaneously. Thus, one gets a snapshot of how active each gene is. This should allow us to understand how the host defends himself (unsuccessfully) against the intruder, or how the intruder hides from the host or undermines his attacks, but requires sophisticated analysis methods, some of which have been developed as part of this project. Using these techniques, we were able to show that during the intracellular infection, B. pertussis greatly reduces the formation of much of its armory, also called virulence factors. This indicates that B. pertussis is actively hiding from the host. For the host cells, we found that infected macrophages, which normally initiate specific defense programs adapted to the type of infection, are modulated by the pathogens to activate different, contradicting programs simultaneously. Potentially, the pathogen hereby hinders the host to defend himself against the infection, which may also benefit bacteria that multiply extracellularly. If subsequent studies confirm that these processes observed in the simplified model of infection also occur in patients who are suffering from whooping cough, these new discoveries could help to develop improved treatment and prevention measures.