A 12-target diarrhea pathogen panel uses multiplex nucleic-acid testing (NAAT) to detect high-prevalence viral, bacterial, and protozoal enteric pathogens in a single run. The objective is fast rule-in/rule-out during suspected gastroenteritis, supporting infection control and clinical decisions especially in hospitals, long-term care, and outbreak investigations.
Coverage (Representative, non-exhaustive)
- Vir uses: Norovirus (GI/GII), Rotavirus A, Adenovirus (enteric types), Sapovirus, Astrovirus
- Bacteria: Salmonella enterica, Shigella spp./EIEC marker, Campylobacter spp., Clostridioides difficile toxin gene(s), Vibrio spp. (region-dependent), heat-labile/heat-stable toxin markers for ETEC/EAEC (as applicable)
- Protozoa: Giardia duodenalis, Cryptosporidium spp., Entamoeba histolytica
The exact 12 targets should reflect local epidemiology, travel patterns, and regulatory labeling.
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Gut Microbiota and Diarrhea
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Common Pathogens causing acute diarrhea and their transmission
Specimens & Pre-analytics
- Specimens: Fresh stool or preserved stool (per collection guidelines)
- Collection: Avoid urine/water contamination; record onset date/time; ensure adequate volume
- Transport/Stability: Maintain cold chain where possible; avoid repeated freeze–thaw; aliquot for re-tests
- Pre-processing: Homogenize to minimize matrix variability; include extraction controls to detect inhibition
Workflow (Same-Day Feasible)
- Lysis & extraction (manual or automated) with an extraction control spike-in
- Multiplex amplification across 12 targets using probe-based chemistry
- Controls: Positive control (multi-analyte or panelled), non-template control (NTC), negative extraction blank
- Detection & calling: Per-target qualitative calls (Detected/Not Detected/Invalid) ± Ct values (assay-dependent)
- Review & report: Apply run-acceptance rules; issue same-day results when batching allows
Typical TAT: 2–6 hours end-to-end, platform-dependent.
Reporting & Interpretation
- Per-target results: Detected / Not Detected / Invalid, with control status
- Optional Ct metrics: Include only if validated; clarify that Ct ≠ organism viability
- Co-detections: List clearly; interpret with symptoms, duration, and exposure history to avoid over-calling colonization
- Limitations: Finite target list; stool matrix inhibition risk; no antimicrobial susceptibility
Example snippet:
- Detected: Norovirus GII (Ct 21.4)
- Not Detected: Rotavirus A, Adenovirus (enteric), Sapovirus, Astrovirus, Salmonella, Shigella/EIEC, Campylobacter, C. difficile toxin, Giardia, Cryptosporidium, E. histolytica
- Controls: Extraction IC PASS; PCR IC PASS; NTC PASS
- Interpretation: Consistent with acute viral gastroenteritis; implement contact precautions per policy; antibiotics typically not indicated for isolated norovirus.
Validation & Quality
- LoD per target in the stool matrix
- Inclusivity/Exclusivity: Circulating strains and near-neighbor cross-reactivity
- Precision: Inter-run, inter-operator, inter-instrument
- Interference: Mucus, blood, bismuth compounds, antidiarrheals
- Stability: Time/temperature studies for preserved and unpreserved stool
- EQA/PT: Enrollment and trending with CAPA for deficiencies
Clinical Value
- Rapid rule-in/rule-out for isolation and cohorting
- Stewardship: Distinguish viral from bacterial/protozoal etiologies
- Outbreak response: Same-day insights into clusters and transmission dynamics
- Reflex pathway: Negative or incongruent cases escalate to culture, antigen PCR add-ons, or mNGS