New PathSeq breakthrough for pathogen hunting

Although technologies for pathogen discovery have been substantially advanced since the early days of Koch and Pasteur, many human diseases are still being caused by undiscovered microbes. A new paper published in Nature Biotechnology describes a comprehensive computational tool for identification of nonhuman nucleic acids in high-throughput human resequencing data. This challenging PathSeq software has major biomedical implications. By Dr. Pavlica.

Massachusetts researchers performed computational subtraction method for finding pathogens in a scalable manner. This approach is superior over other genetic methods (microbial microarrays or targeted PCR) since it does not require initial sequence information about the microbes being sought. PathSeq is composed of a subtractive phase (input reads are subtracted by alignment to human reference databases sequences) followed by an analytic phase (several parallel steps where the remaining reads are aligned to microbial reference sequences) and assembled de novo.

The software is implemented in a cloud computing environment. It is freely available for the public use to help other researchers with their (“Eureka”) findings within emerging pathogen discoveries associated with both acute and chronic human and animal diseases.

For sure, this work will facilitate new scientific discoveries of infectious agents and highlight new associations of microbial organisms with health and disease conditions.

Discovery of known or novel pathogen is the early step in establishing a causal relationship with host or understanding how it causes infectious disease. Engaging clinicians and epidemiologists is the next move to support effective pathogen discovery enabling biomedical implications. In addition, this diagnostic and monitoring approach may support further efforts to achieve optimal individual health care decisions in the upcoming era of personalized medicine.

About the author : Dr. Sanja Pavlica is scientist leader in biotechnology research at the University of Leipzig, Germany, and member of the European Medical Writers Association (EMWA).