AN RNA-BASED CLINICAL DIAGNOSTIC ASSAY USED TO IDENTIFY ACTIVE MICROBIAL INFECTIONS
Studies reveal the clinical efficacy of the CSI-Dx assay.

APPLIED RESEARCH

Studies reveal the efficacy of the CSI-Dx technology in a variety of clinical applications.

Clostridium difficile infection (CDI) is the most common nosocomial infection in the United States, being associated with high recurrence and persistence rates. Though the relationship between intestinal dysbiosis and CDI is well known, it is unclear whether different forms of dysbiosis may potentially affect the course of CDI. How this is further influenced by C. difficile-directed antibiotics is virtually uninvestigated.

Read the Study

Novel culture independent technologies have further elucidated the composition of the human mycobiome, though the role of fungi in human health and disease remains largely unknown. Recent studies have suggested conflicting roles for fungi in the gastrointestinal tract, underscoring the complexity of the interactions between the mycobiome, its bacterial counterpart, and the host. One key example is the observation that fungal taxa are overrepresented in patients with Clostridioides difficile infection (CDI), suggesting a role for fungi in this disease.

Read the Study

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.

Read the Study

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.

Read the Study