Rapid and sensitive sequence-based methods for diagnosis of bacterial and viral respiratory infections and corresponding host responses

Respiratory tract infections, including pneumonia, are major causes of morbidity and mortality globally.

However, many of the potential pathogens that cause pneumonia also colonizes healthy individuals without disease symptoms.

Thus, findings of microbes in upper respiratory tract samples cannot distinguish harmless colonizers from potential pathogens within the same species.

Current diagnostic tools rely upon sampling from the lower respiratory tract, which is difficult in children, and on culturing of respiratory samples and using genomic-based methods that only identify specific pathogens.

It is difficult to state the disease-causing pathogen, bacteria or viruses, and predict the infectious disease development.

In this project we aim at developing and evaluate a novel ultrasensitive sequence-based methodology where we analyze the expression of bacteria, viruses and host responses in nasal and blood samples.

We will evaluate this platform as a diagnostic tool to identify the causative agents of respiratory tract infections focusing on pneumonia.

With this method we can sequence down to nucleotide level and identify virulence properties and antibiotic resistance markers and mutations in viruses such as SARS-Cov-2 and associate the findings to host responses in the same sample. Our preliminary data suggest that we can find host signatures for pneumonia that could be used as a prediction tool.

We also aim at developing and validate a home test kit for diagnosis of pneumonia.