Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV InfectionSENTINELNCT07603453
Performance of Clinical Metagenomics in Stool and Urine Samples for Unexplained Diseases Diagnostic and Emerging Diseases Surveillance in Immunocompromised Patients
An observational study of Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV Infection, run by Assistance Publique - Hôpitaux de Paris at 1 site in France.
Trial 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). Read more about this study
- Who is it for?
- Any age
- Conditions the study is for
- Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV Infection
- What is being tested?
- Metagenomics
- How many people
- 120 participants
- Where
- 1 siteFrance
- Study dates
- 1 Jun 2026to 1 Sep 2028
- Phase
- Observational
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages Any age
- All sexes
- No healthy volunteers
- Child, Adult, Older adult
Study population: Pediatric or adult patient with a primary or secondary immune deficiency
Who may be able to join
- 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)
Who cannot join
- No healthcare insurance
Trial locations and contacts
1 site in 1 country. Contact the study team or a site near you to ask about taking part.
France1 site
Hôpital Necker - Enfants Malades
Paris, Île-de-France Region, 75015
Jacques FOURGEAUD, PharmD, PhD, 01 44 49 56 11 ext. +33, jacques.fourgeaud@aphp.fr
Aminata TRAORE, Project advisor, 01 42 19 27 34 ext. +33, aminata.traore6@aphp.fr
About this study
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).
Read the 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.
- Being tested
- Metagenomics
- Keywords
- Metagenomics, Emerging diseases, Immunocompromised patients
- Medical subject headings
- HIV Infections
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
MetagenomicsDiagnostic test
The intervention aims to increase pathogen detection of mNGS with the addition of non-invasive samples compared with invasive sampling alone
| Study group | Role | What they receive |
|---|---|---|
| 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. Receives: Diagnostic Test: Metagenomics |
What is being measured
The primary outcome is the main question the study is designed to answer.
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.
Measured: 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)
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.
Measured: 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
Measured: 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.
Measured: 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
Measured: 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
Measured: 14 days
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted22 May 2026
- Study start1 Jun 2026 (estimated)
- Primary completion1 Jun 2028 (estimated)
- Study completion1 Sep 2028 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV InfectionStudies of the same condition, open and under way.
- More trials run by Assistance Publique - Hôpitaux de ParisThe sponsor's other registered studies.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Cohort
- Time perspective
- Prospective
- Enrolment
- 120 participants (estimated)
Sponsor and investigators
- Lead sponsor
- Assistance Publique - Hôpitaux de Paris
- Sponsor type
- University, hospital or other
- Collaborators
- URC-CIC Paris Descartes Necker Cochin
- Responsible party
- Sponsor
- Investigators
- Jacques FOURGEAUD, PharmD, PhD, Principal investigator, Assistance Publique - Hôpitaux de ParisPierre FRANGE, MD, PhD, Study chair, Assistance Publique - Hôpitaux de Paris
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT07603453
- Sponsor's protocol ID
- APHP241015
- Acronym
- SENTINEL
- Status last verified
- May 2026
- First submitted
- 18 May 2026
- Last updated
- 22 May 2026
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No
Study at a glance
From the registry record, last updated by the sponsor on 22 May 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Performance of Clinical Metagenomics in Stool and Urine Samples for Unexplained Diseases Diagnostic and Emerging Diseases Surveillance in Immunocompromised Patients
- ClinicalTrials.gov ID
- NCT07603453
- Acronym / sponsor ID
- SENTINEL / APHP241015
- Keywords
- Metagenomics, Emerging diseases, Immunocompromised patients
- Study type
- Observational
- Recruitment status
- Not yet recruiting
- Enrolment
- 120 participants (estimated)
- Lead sponsor
- Assistance Publique - Hôpitaux de ParisUniversity, hospital or other
- Collaborators
- URC-CIC Paris Descartes Necker Cochin
- Study start
- 1 Jun 2026 (estimated)
- Primary completion
- 1 Jun 2028 (estimated)
- Study completion
- 1 Sep 2028 (estimated)
- First posted
- 22 May 2026 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
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).
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 design
- Observational model
- Cohort
- Time perspective
- Prospective
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Pediatric or adult patient with a primary or secondary immune deficiency | – | Diagnostic Test: MetagenomicsPediatric 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. |
Who may qualify
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult, Older adult
- Study population
- Pediatric or adult patient with a primary or secondary immune deficiency
Key inclusion criteria (3 listed)
- 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)
Key exclusion criteria (1 listed)
- No healthcare insurance
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| MetagenomicsThe intervention aims to increase pathogen detection of mNGS with the addition of non-invasive samples compared with invasive sampling alone | Diagnostic test | Pediatric or adult patient with a primary or secondary immune deficiency |
Primary outcome
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)
Time frame: 14 days
* 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.
5 secondary outcomes
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)
Time frame: 14 days
Changes in patient management
Time frame: 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
Time frame: 14 days
Detection of "causative" or "possibly causative" Pathogens by mNGS in Non-Invasive Samples in different subgroups
Time frame: 14 days
Cost of performing mNGS in invasive, stool and urine samples
Time frame: 14 days
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 22 May 2026.
- Individual participant dataSharing planned: No
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Jacques FOURGEAUD, PharmD, PhD principal investigator
Assistance Publique - Hôpitaux de Paris
Pierre FRANGE, MD, PhD study chair
Assistance Publique - Hôpitaux de Paris
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
An observational study of Primary or Secondary Immune Deficiency Including Immunosuppressive Therapy, Chemotherapy, HIV Infection, run by Assistance Publique - Hôpitaux de Paris at 1 site in France.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 3 inclusion and 1 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: opening soon, as of the sponsor's last update on 22 May 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in France. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Jacques FOURGEAUD, PharmD, PhD (01 44 49 56 11 ext. +33, jacques.fourgeaud@aphp.fr), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
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) (time frame: 14 days). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 22 May 2026.