Performance of Clinical Metagenomics in Stool and Urine Samples for Unexplained Diseases Diagnostic and Emerging Diseases Surveillance in Immunocompromised Patients

Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV Infection

Metagenomics, Emerging diseases, Immunocompromised patients

The study is based on the hypothesis that the concomitant use of mNGS in non-invasive samples (stool, urine) could improve the rate of detected pathogens in immunodeficient patients compared with mNGS performed in an invasive reference sample alone (blood, CSF, broncho-alveolar lavage fluid (BAL), tissue).

Emerging and re-emerging infectious diseases require broad-spectrum diagnostic approaches capable of identifying a wide range of microorganisms without prior assumptions. This challenge is particularly relevant in immunocompromised patients, who are at high risk for opportunistic, atypical, or previously unknown infections. Conventional microbiological methods rely on targeted assays and may fail to detect uncommon or novel pathogens. Clinical metagenomics based on high-throughput sequencing (metagenomic Next-Generation Sequencing, mNGS) enables unbiased detection of viral, bacterial, fungal, and parasitic genomes directly from clinical samples. At Necker-Enfants Malades Hospital (Paris, France), implementation of a diagnostic mNGS platform between 2019 and 2022 demonstrated a higher diagnostic yield in immunocompromised patients compared with immunocompetent individuals, with particularly high positivity rates in stool samples. These findings support the evaluation of non-invasive samples as complementary diagnostic matrices. The SENTINEL study aims to assess the diagnostic performance of mNGS performed on non-invasive samples (stool and urine) compared with invasive reference samples (blood, cerebrospinal fluid, bronchoalveolar lavage fluid, or tissue) in immunocompromised pediatric and adult patients with suspected infection. The underlying hypothesis is that adding stool and/or urine mNGS to invasive sample analysis will increase the detection rate of causative or possibly causative pathogens. In this multicenter study, invasive samples collected as part of standard of care and study-specific stool and urine samples will undergo centralized mNGS analysis. Non-invasive samples will be collected preferably on the same day as the reference sample or within a maximum of five days. Clinical and laboratory data generated during routine care will be collected at inclusion. Participants will be followed for three months to evaluate the clinical impact of mNGS findings. For pathogens classified as possibly causative, confirmatory analyses will be performed to support causal attribution. Secondary analyses will examine the detection of emergent or re-emergent pathogens, including previously unknown pathogens, as well as diagnostic performance according to clinical presentation and type of immune deficiency. The impact of non-invasive mNGS results on patient management and the incremental laboratory cost associated with adding stool and urine analyses will also be evaluated. The study is sponsored by Assistance Publique - Hôpitaux de Paris and funded by the French Ministry of Health and ANRS Emerging Infectious Diseases.

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