Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision?

Due to the limitations of existing approaches, a rapid, sensitive, accurate, comprehensive, and generally applicable strategy to diagnose and treat bacterial and fungal infections remains a major challenge. Here, based on the ramanome technology platform, we propose a culture-free, one cell resolution, phenome-genome-combined strategy called single-cell identification, viability and vitality tests and source tracking (SCIVVS). For each cell directly extracted from a clinical specimen, the fingerprint region of the D₂O-probed single cell Raman spectrum (SCRS) enables species-level identification based on a reference SCRS database of pathogen species, whereas the C-D band accurately quantifies viability, metabolic vitality, phenotypic susceptibility to antimicrobials, and their intercellular heterogeneity. Moreover, to source track a cell, Raman-activated cell sorting followed by sequencing or cultivation proceeds, producinging an indexed, high coverage genome assembly or a pure culture from precisely one pathogenic cell. Finally, an integrated SCIVVS workflow that features automated profiling and sorting of metabolic and morphological phenomes can complete the entire process in only a few hours. Because it resolves heterogeneity for both the metabolic phenome and genome, targets functions, can be automated, and is orders-of-magnitude faster while cost-effective, SCIVVS is a new technological and data framework to diagnose and treat bacterial and fungal infections in various clinical and disease control settings.