Clinical Scorecard: Can Omics Improve Parasite Surveillance?

At a Glance

Key Highlights

• Metagenomics enables simultaneous detection of multiple microorganisms, including low-abundance parasites.
• Current testing methods may miss unexpected pathogens due to reliance on microscopy and targeted PCR.
• Standardized workflows and high-quality reference genomes are critical for reliable metagenomic results.
• Metagenomics supports longitudinal monitoring of parasitic infections.
• Population-scale surveillance can reveal geographic differences in parasite prevalence.

Guideline-Based Recommendations

Diagnosis

• Use species-specific computational pipelines for detecting eukaryotic parasites.

Management

• Implement metagenomics alongside traditional methods for comprehensive parasite detection.

Monitoring & Follow-up

• Utilize metagenomics for longitudinal monitoring of parasitic infections.

Risks

• Challenges include contamination, sensitivity issues, and distinguishing clinically relevant findings from background noise.

Patient & Prescribing Data

Individuals undergoing testing for parasitic infections

Metagenomics may inform treatment decisions through improved detection of parasites.

Clinical Best Practices

• Establish standardized workflows for sample collection, DNA extraction, and computational analysis.
• Validate thresholds for identifying parasite subtypes to reduce false positives and negatives.
• Incorporate proteomics to complement metagenomic findings.

Related Resources & Content

• ESCMID Global 2026 Presentation by Francesco Asnicar