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

NCT07603453 | Not Yet Recruiting

• 1 other identifier: APHP241015
• Study Type: observational
• Target: 120
• Locations: 1 country
• Sites: 1

Brief Summary

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).

Conditions

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

Keywords

Metagenomics; Emerging diseases; Immunocompromised patients

Outcome Measures

Primary Outcomes (1)

• 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 Outcomes (5)

• 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)

  14 days

• Changes in patient management

  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

  14 days

• Detection of "causative" or "possibly causative" Pathogens by mNGS in Non-Invasive Samples in different subgroups

  14 days

• Cost of performing mNGS in invasive, stool and urine samples

  14 days

Study Arms (1)

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

Interventions

Metagenomics DIAGNOSTIC_TEST

The intervention aims to increase pathogen detection of mNGS with the addition of non-invasive samples compared with invasive sampling alone

Pediatric or adult patient with a primary or secondary immune deficiency

Eligibility Criteria

• Sex: all
• Healthy Volunteers: No
• Age Groups: Child (0-17), Adult (18-64), Older Adult (65+)
• Sampling Method: Non-Probability Sample

Study Population

Pediatric or adult patient with a primary or secondary immune deficiency

You may qualify if:

• 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)

You may not qualify if:

• No healthcare insurance

Sponsors & Collaborators

• Assistance Publique - Hôpitaux de Paris: lead
• URC-CIC Paris Descartes Necker Cochin: collaborator

Study Sites (1)

Hôpital Necker - Enfants Malades

Paris, Île-de-France Region, 75015, France

Location

MeSH Terms

Conditions

HIV Infections

Condition Hierarchy (Ancestors)

Blood-Borne Infections; Communicable Diseases; Infections; Sexually Transmitted Diseases, Viral; Sexually Transmitted Diseases; Lentivirus Infections; Retroviridae Infections; RNA Virus Infections; Virus Diseases; Genital Diseases; Urogenital Diseases; Immunologic Deficiency Syndromes; Immune System Diseases

Study Officials

• Jacques FOURGEAUD, PharmD, PhD

  Assistance Publique - Hôpitaux de Paris

  PRINCIPAL INVESTIGATOR

• Pierre FRANGE, MD, PhD

  Assistance Publique - Hôpitaux de Paris

  STUDY CHAIR

Central Study Contacts

Jacques FOURGEAUD, PharmD, PhD

CONTACT

01 44 49 56 11; jacques.fourgeaud@aphp.fr

Aminata TRAORE, Project advisor

CONTACT

01 42 19 27 34; aminata.traore6@aphp.fr

Study Design

• Study Type: observational
• Observational Model: COHORT
• Time Perspective: PROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: May 18, 2026
• First Posted: May 22, 2026
• Study Start (Estimated): June 1, 2026
• Primary Completion (Estimated): June 1, 2028
• Study Completion (Estimated): September 1, 2028
• Last Updated: May 22, 2026

Record last verified: 2026-05

Data Sharing

• IPD Sharing: Will not share

Locations

FR (1)