Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Conventional diagnostics miss many pathogens and genes.
• Metagenomic next-generation sequencing (mNGS) offers broader pathogen and gene detection.
• This study assesses a fecal mNGS assay's performance.

Purpose of the Study:

• Evaluate the clinical, analytical, and in silico performance of a fecal mNGS assay.
• Assess detection of bacteria, eukaryotes, viruses, virulence factors (VF), and antimicrobial resistance (AMR) genes.
• Compare mNGS to conventional methods for gastrointestinal infections.

Main Methods:

• Clinical performance evaluated on 510 fecal samples against conventional testing.
• Analytical performance assessed using contrived samples to determine limit of detection.
• In silico samples used to evaluate performance across 176 targets.

Main Results:

• Clinical specificity ≥96%, median pathogen sensitivity 91%.
• VF and AMR gene detection sensitivity was lower (median 58.7%).
• Assay highly reproducible (99.5% concordance); increased diagnostic yield by detecting additional targets and AMR genes in over 50% and 35% of samples, respectively.

Conclusions:

• Fecal mNGS assay is competitive with existing diagnostics, expanding actionable detection.
• Supports stool mNGS as a high-yield test for gastrointestinal infections.
• Enables better identification of rare pathogens, co-infections, and resistance determinants.