Investigation of the Delve Detect Cerebrospinal Fluid (CSF) Metagenomic Next-generation Sequencing (mNGS) Test When Used for the Initial Diagnostic Workup of Patients With Suspected Central Nervous System (CNS) Infection (IMPACT)

Delve Bio, Inc.

Status: Not yet enrolling

Conditions: Central Nervous System Infection

Treatments: Diagnostic Test: Delve Detect CSF mNGS Test; Other: Real-World Data

Study type: Interventional

Funder types: Industry

Identifiers

NCT07435649

CLN-GEN-PLN-004

Details and patient eligibility

About

Delve Bio, Inc. is a developer of novel mNGS tests with the goal of aiding in the diagnosis of infectious diseases in several clinical indications that may not have alternative traditional diagnostic methods routinely available. A proof of concept for the clinical utility of this mNGS testing methodology has been described in several seminal publications.1,2,3,4 Delve Bio is currently offering one of these assays as a laboratory-developed test (LDT) performed in a CLIA-certified, CAP-accredited laboratory. The test is called Delve Detect CSF. Delve Detect CSF is an mNGS in vitro diagnostic test intended for the simultaneous detection and differentiation of nucleic acids from multiple bacteria, viruses, fungi, and parasites in CSF from individuals suspected of meningitis or encephalitis. Delve Detect CSF identifies microbial nucleic acid in an unbiased and pathogen-agnostic manner.

Historically, due to its cost and turnaround times, which can be on the order of 14 days, CSF mNGS testing is typically employed as a "test of last resort" for patients with suspected infectious meningitis and encephalitis, and is often used when traditional diagnostic methods cannot identify the cause of infection. In the IMPACT Study, we seek to investigate the diagnostic and clinical utility of mNGS testing if it is employed earlier in the diagnostic workup of patients with suspected CNS infection and unknown etiology in conjunction with a more rapid turnaround time for test results on the order of two business days from sample receipt by the laboratory. Participants who meet the inclusion/exclusion criteria and undergo informed consent (and assent as applicable) will be enrolled in the study, assigned to the appropriate subpopulation category, and obtain CSF testing with Delve Detect CSF in addition to other SOC testing. In addition to the Delve Detect CSF test results, associated clinical information and health economic data for the participants will be obtained through chart abstraction. Clinical information will be de-identified wherever possible, and any PHI being collected will not be individually reported as part of the intended analysis. The site investigator or their designee at each site will complete a survey to provide a consensus view of the treatment team regarding how the availability of Delve Detect CSF test results in early diagnostic workup affected clinical decision-making.

Analyses of the test results from Delve Detect CSF and other SOC diagnostic methods, in addition to the clinical information, will not be used to identify any participant. Information generated through the study will be recorded in such a manner that the identity of the human participants cannot readily be ascertained directly or through identifiers linked to the participants, and the participants will not be contacted. The results from this study could be used to support publications in scientific white papers, manuscripts, posters, and/or presentations.

Enrollment: 400 estimated patients

Sex: All

Volunteers: No Healthy Volunteers

Inclusion and exclusion criteria

Inclusion Criteria:

1. Must be willing and able to provide informed consent or have a legally authorized representative (LAR) willing and able to provide informed consent for participation in the study:

   a. Adults, 18 years of age or older, must provide informed consent, or if unable to provide consent, must have voluntary informed consent provided by a LAR b. Children < 18 years of age must have informed consent provided by a parent, guardian, or LAR, and: i. If 7 years of age or older, must provide voluntary assent for participation, unless unable to do so If less than 7 years of age, assent should also be obtained, if feasible.

2. Individuals presenting with, or admitted or transferred with, suspected CNS infection with at least 2 of the following clinical signs and symptoms:

   1. Headache
   2. Photophobia
   3. Neck stiffness
   4. Nausea/vomiting
   5. Documented fever ≥ 38°C (100.4°F)
   6. Altered mental status (defined as decreased or altered level of consciousness, lethargy, or personality change) lasting ≥ 24 h with no alternative cause identified
   7. Generalized or partial seizures not fully attributable to a preexisting seizure disorder, identified toxic-metabolic derangement, or alcohol withdrawal
   8. Abnormality of brain parenchyma on neuroimaging suggestive of CNS infection that is either new from prior studies or appears acute in onset
   9. Abnormal spinal cord imaging suggestive of myelitis

Note: The clinical signs and symptoms list above applies to non-infant participants (≥ 1 year old). Infants (< 1 year old) who are suspected of CNS infection may be enrolled if they present with fever ≥ 38°C (100.4°F) OR hypothermia < 36.5°C (97.7°F) AND at least 1 of the following clinical signs and symptoms:

1. Bulging fontanel (soft spot)
2. Lethargy or irritability
3. Refusing to feed or poor feeding
4. Apnea
5. Hypotonia or Hypertonia

Exclusionary participant characteristics:

1. Unable to obtain consent (or assent, as applicable) from potential participant or legally authorized representative (LAR)

2. Established diagnosis of non-infectious etiology responsible for symptoms of meningitis/encephalitis/myelitis, with confirmation prior to lumbar puncture (LP) being performed

3. Established diagnosis of infectious etiology responsible for symptoms with microbiologic confirmation prior to LP being performed

4. Established diagnosis of infectious etiology responsible for symptoms prior to CSF sample being sent for testing with Delve Detect CSF

   Note: participants already consented and enrolled in the study who obtain a positive test result from SOC testing prior to the CSF sample being sent for testing with Delve Detect CSF will be withdrawn from the study and excluded from analysis.

5. Low clinical suspicion for infection with one of the following known diagnoses related to the patient admission prior to LP being performed. Remote history of these diagnoses does not exclude the patient from eligibility:

   1. Trauma
   2. Ischemic or hemorrhagic stroke unless suspected to be due to infectious etiology
   3. Postictal or metabolic encephalopathy
   4. Malignancy without present infection symptoms
   5. Demyelinating disease

   Exclusionary CSF sample characteristics:

6. No evidence of CSF pleocytosis (defined as CSF white blood cell count (WBC) ≥ 5 cells per μL) in the first LP collected.

   Note: Exclusion criterion 4 applies to participants who are immunocompetent or otherwise not known to have a current immunodeficiency or immunocompromised status. Individuals with a current immunodeficiency or immunocompromised status (as defined in Section 9.3) may be enrolled with or without the presence of CSF pleocytosis and continue to final analysis.

7. Insufficient residual CSF volume available for Delve Detect testing (< 500 μL)

8. The residual CSF sample available for testing with Delve Detect CSF was not the first diagnostic LP for the participant's current admission

9. Residual CSF was stored at room temperature for ≥ 6 hours

10. Residual CSF was stored refrigerated (2-8 °C) for ≥ 7 days

11. Residual CSF was stored frozen (≤ -70 °C) for ≥ 90 days

12. Residual CSF experienced more than a cumulative two freeze-thaw cycles

Trial design

Primary purpose: Diagnostic

Allocation: Non-Randomized

Interventional model: Single Group Assignment

Masking: None (Open label)

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400 participants in 2 patient groups

Prospectively Collected Patients tested with Delve Detect mNGS

Experimental group

Description:

Participants will be identified as candidates for the prospective enrollment population by clinicians who are treating the patients and/or laboratory investigators performing clinical testing on initial samples obtained from the patients through inpatient or ICU admission. Patients may be identified and enrolled in the study prior to or after CSF collection has been performed. Following informed consent and assent procedures, as applicable, participants will be enrolled in the study. Following enrollment and informed consent/assent, 500 - 1000 µL of CSF specimen collected as part of the first LP for SOC diagnostic workup will be sent for mNGS testing with the Delve Detect CSF test. Delve Detect CSF test results will be provided to treating physicians for clinical decision-making.

Treatment:

Diagnostic Test: Delve Detect CSF mNGS Test

Real-World Data Control Cohort

Active Comparator group

Description:

RWD will be used to construct a control dataset for patients who were diagnosed and treated without the use of CSF mNGS. An attempt will be made to match the calendar time period/duration, and proportions of sex, age, disease, etiology (infectious/non-infectious), and subpopulation categories as the prospective enrollment population. The intent of the control population is to enable secondary and exploratory outcome comparisons by collecting data for patients who were diagnosed and treated without the use of CSF mNGS testing.

Treatment:

Other: Real-World Data