RNA-based infection testing used to identify bacteria, virus, and fungal species
Applying the same technology as CSI-Dx™ in other applications to assist physicians

Applications of RNA-based Infection Testing

Contamination Source Identification technology and physicians have been applying the same technology as CSI-Dx™ in other applications to assist physicians in identifying microbial species in different applications. For more information on this technology’s research and application, please reference any of the studies listed below.

While metagenomic (microbial DNA) sequencing technologies can detect the presence of microbes in a clinical sample, it is unknown whether this signal represents dead or live organisms within a microbial community, and also if it maps expressed genes to a functional pathway of interest (e.g. antibiotic resistance.) After RNA metratranscriptomic analysis of synovial fluid and peripheral blood, differential metatranscrptomic signatures for infected vs. noninfected cohorts enabled us to train machine learning algorithms to 84.9% predictive accuracy for infection. A variety of antibiotic resistance genes were also expressed, with high concordance to conventional antibiotic sensitivity data.

There has been no prior application of matched metagenomics and meta-transcriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from inpatients and utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative co-occurring relationships with several bacterial taxa.

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