Researchers have developed a new sequencing-based approach for pathogen discovery from challenging samples.

Infectious diseases are caused by pathogenic viruses, bacteria, fungi or parasites. The treatment of bacterial and fungal infections relies particularly on antimicrobial drugs, while the focus in treating viral infections is the alleviation of symptoms.

Initial therapy for infection is often empiric and guided by clinical presentation. Its efficacy on the pathogen is, however, only seldom understood at therapy initiation. Although methods for assessing treatment responses exist, the effectiveness is mainly determined through monitoring symptoms and signs of infections.

Advances in sequencing technology have made characterization of genomes and gene expression products increasingly practical. The technology has also made it possible to identify microbiota components up to species- and gene-level. Nevertheless, microbiota sequencing is only occasionally employed in infection treatment.

Now, researchers at the University of Helsinki have, together with their collaborators at the Helsinki University Hospital, developed a new sequencing-based approach for pathogen discovery from challenging samples. The approach and preliminary results on its usage in burn wound infection clearance assessment have been published in the Clinical Microbiology and Infection journal.

«The approach enables to capture the real-time functional activities of even minuscule amounts of microbes. It can be used to reliably investigate the activity of microbial drug resistance mechanisms and other microbial mechanisms relevant to infection or its treatment. This helps to understand whether causative microbes are alive or dying and what they do,» says bioinformatician Matti Kankainen, PhD, from the University of Helsinki.

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