Abstract
Background:Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics.Methods:We extracted RNA from fecal samples of patients with CDI and profiled human mRNA using amplicon-based next-generation sequencing (NGS). We compared the fecal host mRNA transcript expression profiles of patients with CDI to controls with non-CDI diarrhea.Results:We found that the ratio of human actin gamma 1 (ACTG1) to 16S ribosomal RNA (rRNA) was highly correlated with NGS quality as measured by percentage of reads on target. Patients with CDI could be differentiated from those with non-CDI diarrhea based on their fecal mRNA expression profiles using principal component analysis. Among the most differentially expressed genes were ones related to immune response (IL23A, IL34) and actin-cytoskeleton function (TNNT1, MYL4, SMTN, MYBPC3, all adjusted P-values < 1 x 10-3).Conclusions:In this proof-of-concept study, we used host fecal transcriptomics for non-invasive profiling of the mucosal immune response in CDI. We identified differentially expressed genes with biological plausibility based on animal and cell culture models. This demonstrates the potential of fecal transcriptomics to uncover host-based biomarkers for enteric infections.
Highlights
Clostridium difficile is a spore-forming, toxin-producing bacterium that causes diarrhea and colitis, most often associated with antibiotic use
Adoption of nucleic acid amplification tests (NAATs) has led to an increase in Clostridium difficile infection (CDI) diagnoses worldwide, and concerns of over-diagnosis of CDI resulting in unnecessary use of antibiotics have sparked renewed interest in improved diagnostic strategies [4, 5]
Human Feces mRNA Yield and Effect on Transcriptome Profiling The AmpliSeq Transcriptome Human Gene Expression kit is intended for analysis of 10 ng of human RNA
Summary
Clostridium (or Clostridioides) difficile is a spore-forming, toxin-producing bacterium that causes diarrhea and colitis, most often associated with antibiotic use. It is the most common hospital-associated infection in the United States, with an estimated 453,000 cases and more than 29,000 deaths annually [1]. The most commonly used diagnostics for CDI are based on detection of the toxin or toxin genes Due to their high sensitivity and rapid turnaround times, nucleic acid amplification tests (NAATs) have been widely adopted for the diagnosis of CDI. Adoption of NAATs has led to an increase in CDI diagnoses worldwide, and concerns of over-diagnosis of CDI resulting in unnecessary use of antibiotics have sparked renewed interest in improved diagnostic strategies [4, 5]. Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics
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