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

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).

Study Overview

• Status: Not yet recruiting
• Conditions: Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV Infection
• Intervention / Treatment: Diagnostic test: Metagenomics

Detailed Description

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.

• Study Type: Observational
• Enrollment (Estimated): 120

Contacts and Locations

• Study Contact: Name: Aminata TRAORE, Project advisor; Phone Number: +33 01 42 19 27 34; Email: aminata.traore6@aphp.fr
• Study Contact Backup: Name: Jacques FOURGEAUD, PharmD, PhD; Phone Number: +33 01 44 49 56 11; Email: jacques.fourgeaud@aphp.fr

Study Locations

• France
  • Île-de-France Region
    • Paris, Île-de-France Region, France, 75015
      • Hopital Necker - Enfants Malades
      • Contact: Aminata TRAORE, Project advisor; Phone Number: +33 01 42 19 27 34; Email: aminata.traore6@aphp.fr
      • Contact: Jacques FOURGEAUD, PharmD, PhD; Phone Number: +33 01 44 49 56 11; Email: jacques.fourgeaud@aphp.fr
      • Principal Investigator: Jacques FOURGEAUD, PharmD, PhD

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Child; Adult; Older Adult
• Accepts Healthy Volunteers: No

• Sampling Method: Non-Probability Sample

Study Population

Pediatric or adult patient with a primary or secondary immune deficiency

Description

Inclusion Criteria:

• Pediatric or adult patient with a primary or secondary immune deficiency (including immunosuppressive therapy, chemotherapy, HIV infection).
• mNGS prescription on tissue, CSF, BAL and/or blood to identify the causative pathogen in patient with symptoms or biological signs compatible with an infection as per investigator's judgment (e.g., fever, leukocytosis, increased CRP level)
• Non opposition of the participant (or parent(s)/ legal guardian(s) of infant participant)

Exclusion Criteria:

• No healthcare insurance

Study Plan

How is the study designed?

Number of groups / cohorts

1

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Pediatric or adult patient with a primary or secondary immune deficiency; Pediatric or adult populations with a primary or secondary immune deficiency following immunosuppressive treatment or an underlying disease are at increased risk of severe infection by a wide range of viruses.	Diagnostic test: Metagenomics; The intervention aims to increase pathogen detection of mNGS with the addition of non-invasive samples compared with invasive sampling alone

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Detection of a "causative" or "possibly causative" pathogens by mNGS in Non-Invasive (stool and/or urine) and invasive samples (blood, CSF, BAL and/or tissue)	Possibly causative pathogen: microorganism associated with the symptoms in literature but without formal proof of causality.; Causative pathogen: known pathogen detected and typical associated symptoms.	14 days

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Detection of emergent or re-emergent pathogens by mNGS in non-invasive samples (stool and/or urine) and invasive sample (blood and/or CSF and/or BAL and/or tissue)	Among detected "causative" or "possibly causative" pathogen", evaluation of emergent or re-emergent pathogen: Emergent or re-emergent pathogen: pathogen with no known circulation in the geographical area and during the period in which it will be identified; Pathogen X: infectious agent that is not currently known to cause human disease, but an aetiologic agent of a future outbreak with epidemic or pandemic potential.	14 days
Changes in patient management	Evaluation of the impact of stool and urine mNGS results on patient management: administration of antimicrobial therapy and/or specific or polyvalent immunoglobulins, change in the management of immunosuppression (reduction of immunosuppressive therapy, delay of solid organ or haematopoietic stem cell transplantation), hospitalization (incidence, duration) and/or additional samples collection	3 months
Detection of the "possibly causative" pathogen genomes by specific PCR in all available invasive and non-invasive samples collected at inclusion and by in situ hybridization in available tissue sample collected at inclusion	Confirmation of the role of the detected "possibly causative" pathogen in the patient's symptoms using additional investigations.	14 days
Detection of "causative" or "possibly causative" Pathogens by mNGS in Non-Invasive Samples in different subgroups	Subgroups according to symptoms, immune deficiency type and age	14 days
Cost of performing mNGS in invasive, stool and urine samples	Calculation of the cost (including laboratory personnel and reagents) of performing mNGS in invasive, stool and urine samples	14 days

Collaborators and Investigators

• Sponsor: Assistance Publique - Hôpitaux de Paris
• Collaborators: URC-CIC Paris Descartes Necker Cochin
• Investigators: Principal Investigator: Jacques FOURGEAUD, PharmD, PhD, Assistance Publique - Hôpitaux de Paris; Study Chair: Pierre FRANGE, MD, PhD, Assistance Publique - Hôpitaux de Paris

Study record dates

Study Major Dates

• Study Start (Estimated): June 1, 2026
• Primary Completion (Estimated): June 1, 2028
• Study Completion (Estimated): September 1, 2028

Study Registration Dates

• First Submitted: May 18, 2026
• First Submitted That Met QC Criteria: May 18, 2026
• First Posted (Actual): May 22, 2026

Study Record Updates

• Last Update Posted (Actual): May 22, 2026
• Last Update Submitted That Met QC Criteria: May 18, 2026
• Last Verified: May 1, 2026

More Information

Terms related to this study

• Keywords: Metagenomics; Immunocompromised patients; Emerging diseases
• Additional Relevant MeSH Terms: Blood-Borne Infections; Urogenital Diseases; Genital Diseases; Immune System Diseases; Infections; RNA Virus Infections; Virus Diseases; Communicable Diseases; Sexually Transmitted Diseases, Viral; Sexually Transmitted Diseases; Lentivirus Infections; Retroviridae Infections; Immunologic Deficiency Syndromes; HIV Infections
• Other Study ID Numbers: APHP241015

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No