Kyle G. Rodino, Ph.D., D(ABMM)
Assistant Professor of Clinical Pathology and Laboratory Medicine
Assistant Director, Clinical Microbiology
Hospital of the University of Pennsylvania and Perelman School of Medicine, University of Pennsylvania

Next-Generation Sequencing in Clinical Microbiology: Current Applications and What’s Next

Advanced molecular diagnostics, including next-generation sequencing (NGS)-based technologies, are increasingly integrating into the clinical microbiology laboratory. These new technologies have the ability to provide information not previously attainable, with current applications including organism identification, outbreak investigation and mutation surveillance, and detection of resistance determinants. Of particular interest to the diagnosis of infectious diseases is the use of metagenomic NGS (mNGS), targeted or unbiased, for pathogen detection direct from patient specimens. Case reports have shown the undeniable power of mNGS to provide diagnostic evidence where other methods have failed. However, a number of hurdles to routine use remain, including technical performance characteristics and clinical utility. Addressing these issues will be important to broad adoption of mNGS methods for infectious disease testing in the clinical microbiology laboratory, particularly as we look toward future applications, including rapid sequencing assays, antimicrobial susceptibility modeling, and disease-predictive host biomarkers.