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

Abstract

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.

Interactions and effects of a stannous-containing sodium fluoride dentifrice on oral pathogens and the oral microbiome

“…While these results also suggest that host factors and behavior, rather than treatment, are major factors that shape the oral microbiome, the long-term effect of such products and its influence on the host gingival cells needs to be further investigated. Future larger scale studies utilizing spatial-omics and microbial single-cell technologies while taking into account of biofilms from patients with caries and/or periodontitis can better illustrate the complex microbial dynamics at the micro and macroscale with higher resolution while maintaining the structural integrity of the biofilm ( Borisy and Valm, 2021 ; Dar et al, 2021 ; Xu et al, 2023 ) to provide a more comprehensive understanding of the impact of different treatments on oral biofilms.…”

From bench to bedside: Opportunities and challenges for iLABMED

“…Xu et al. described a novel single cell metabolic phenome and genome technology via the ramanome technology platform, which can achieve rapid, sensitive, accurate, and comprehensive diagnosis for bacterial and fungal infections [10]. Lin et al.…”

“…This was reflected by several articles published in iLABMED as well. Xu et al described a novel single cell metabolic phenome and genome technology via the ramanome technology platform, which can achieve rapid, sensitive, accurate, and comprehensive diagnosis for bacterial and fungal infections [10]. Lin et al reviewed the stumbling blocks in detecting the HIV/Mtb co-infection.…”