Challenges in Clinical Metagenomics: Identifying Pathogenic Organisms in the Background of a Variable Microbiome

Clinical metagenomics using next-generation sequencing has the potential to create a seismic shift in the care of patients who suffer from infections. The detection of non-human nucleic acids from patient samples can identify the etiology of infections faster and more precisely than standard of care techniques leading to precision treatment of infections. However, since humans have a host of commensal organisms, separating the pathogenic bacteria from natural colonizers can be a major challenge to the clinical use of metagenomics. 

To be able to do this effectively, clinicians must make judgements based upon patient presentation, sample type and understanding of the analysis performed. Tools such as machine learning, host transcriptomics and well curated databases can help laboratories in assisting clinicians in accomplish these tasks in clinically actionable timelines to provide rapid precision medicine for infectious disease.

Lauge Farnaes, MD, Ph.D.
Head of Medical Affairs
IDbyDNA

Lauge Farnaes is the Head of Medical Affairs at IDbyDNA. His work has focused on rapid diagnostics using next generation sequencing in critically ill infants to determine a diagnosis that would optimize medical management. He obtained a Master’s degree in Biology studying antibody response in auto-immune diseases. He obtained a doctor of medicine and a Ph.D in Oceanography/marine chemistry researching small molecules from marine microorganisms that could be used to treat infections and cancer. He received pediatric training at UCSD in general pediatrics and Pediatric Hematology Oncology and Infectious Disease.

Lauge helped to pioneer the use of rapid whole genome sequencing in critically ill infants leading multiple large multi-site studies. Lauge now works at IDbyDNA to develop the clinical and economic evidence to drive Metagenomic sequencing into standard of care testing.