Sequencing-based solution can help determine patients’ response to infection therapy

Pathogenic viruses, parasites, bacteria, or fungi are responsible for causing infectious diseases. The treatment of fungal and bacterial infections specifically depends on antimicrobial medications, while the treatment for viral infections focuses on the alleviation of symptoms.

Advances in sequencing technology have made the characterization of genomes and gene expression products increasingly practical. Image Credit: Mostphotos.

Initial infection therapy is usually empiric and directed by clinical presentation. But its efficacy on pathogen has been rarely understood at therapy initiation. While there are techniques for evaluating treatment responses, the effectiveness is primarily identified by tracking symptoms and signs of infections.

Developments in sequencing technology have made it increasingly practical to define genomes and gene expression products. Moreover, the technology has made it feasible to detect microbiota components up to gene- and species-level. Nonetheless, microbiota sequencing is rarely used in infection treatment.

Now, along with their collaborators from the Helsinki University Hospital, scientists from the University of Helsinki have created a new sequencing-based strategy for identifying pathogens from complex samples. The strategy and initial results on its usage in the assessment of burn wound infection clearance 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.”

Matti Kankainen, PhD, Bioinformatician, University of Helsinki

Tech­nique sheds light on pathogen activities

The fundamental principle of the method is as follows—a clinical sample is obtained from the patient and its RNA, the basic foundation of biological processes, is derived, and the microbial RNA is finally enriched to increase the information on pathogens. The RNA is sequenced and novel algorithms are used to evaluate a large amount of information gained.

The team used their solution on a complex wound infection case to better interpret the value of the new approach in clinical practice. A wound infection patient was the study subject, who had been treated with many antibiotic therapies for nearly one hundred days but without success. Despite the therapies, the infection still reappeared.

Briefly tracking the initiation of the fourth antibiotic regimen, the team obtained samples from the site of infection. These samples were examined using the new method and with the help of 16S DNA-gene profiling, which is a more common method. Corresponding samples were also obtained from a control subject.

The fourth antibiotic regimen was demonstrated to be effective and reduced symptoms. The outcomes obtained through the new method matched with the clinical presentation and confirmed the removal of pathogens. They also showed the recovery of the normal microbiota. An analogous microbiota change was not observed in the 16S DNA-gene profiling. But rather, candidate pathogens of the infection were detected because of the slow breakdown of DNA.

Metatranscriptomics may be the answer to diagnosing infectious diseases

The applied technique is called metatranscriptomics. It enables an in-depth determination of the activity of microbial genes. Its use has become more and more common, but issues related to handling and analysis of complex host-microbe specimens have prevented the more extensive clinical use of metatranscriptomics.

Our findings demonstrate that our solution suits also to challenging samples that contain minuscule amounts of microbes. On top of pathogen identification, it can be used to characterise host-microbe interaction. It may thereby shed light into yet-unidentified disease mechanisms. We will develop the technique further as a part of infection studies ongoing at our laboratory. Further work will also focus on understanding its application spectrum.”

Esko Kankuri, Docent in Pharmacology, University of Helsinki

Teija Ojala, a Postdoctoral Researcher from the University of Helsinki, designed the new technique. Ojala will later apply the method to improve one’s interpretation of COVID-19 coronavirus disease.