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

Обзор

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.

Вмешательства

• Диагностический тест Delve Detect CSF mNGS Test
  This cohort consists of patients admitted with suspected CNS infection, who will receive Delve Detect CSF mNGS testing from a prospectively collected CSF specimen. The results of the Delve Detect CSF mNGS Test will be returned to the patient's treatment team for clinical decision making.
• Другое Real-World Data
  For the analysis of secondary and exploratory outcomes, a control population of patients who were diagnosed and treated without the use of CSF mNGS testing will be constructed using real-world data (RWD). The control population will have approximately equal proportions of demographics, disease severity, and subpopulation categories as the prospective enrollment population. RWD will be used to examine the potential effect that testing with Delve Detect CSF had on the selected outcomes with the pr

Первичные конечные точки

• Overall Diagnostic Yield [Срок оценки: From Enrollment to 90 Days Post-Discharge for Each Patient]

Критерии участия

Критерии включения

• 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.

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

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

• Bulging fontanel (soft spot)
• Lethargy or irritability
• Refusing to feed or poor feeding
• Apnea
• Hypotonia or Hypertonia

Exclusionary participant characteristics:

• Unable to obtain consent (or assent, as applicable) from potential participant or legally authorized representative (LAR)
• Established diagnosis of non-infectious etiology responsible for symptoms of meningitis/encephalitis/myelitis, with confirmation prior to lumbar puncture (LP) being performed
• Established diagnosis of infectious etiology responsible for symptoms with microbiologic confirmation prior to LP being performed
• 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.

• 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:

• Trauma
• Ischemic or hemorrhagic stroke unless suspected to be due to infectious etiology
• Postictal or metabolic encephalopathy
• Malignancy without present infection symptoms
• Demyelinating disease

Exclusionary CSF sample characteristics:

• 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.

• Insufficient residual CSF volume available for Delve Detect testing (< 500 μL)
• The residual CSF sample available for testing with Delve Detect CSF was not the first diagnostic LP for the participant's current admission
• Residual CSF was stored at room temperature for ≥ 6 hours
• Residual CSF was stored refrigerated (2-8 °C) for ≥ 7 days
• Residual CSF was stored frozen (≤ -70 °C) for ≥ 90 days
• Residual CSF experienced more than a cumulative two freeze-thaw cycles

Критерии приведены из реестра в оригинале (на английском). Окончательную оценку соответствия проводит исследовательский центр.

Здоровые добровольцы: Нет

Дизайн исследования

Распределение

Нерандомизированное

Модель

Одна группа

Маскирование

Открытое

Основная цель

Диагностика

Центры проведения

США · 4 центра

• University of California at San Francisco at Zuckerberg San Francisco General — San Francisco
• Emory University Hospital — Atlanta
• Lahey Hospital & Medical Center — Burlington
• Vanderbilt University Medical Center — Nashville

Публикации

• Benoit P, Brazer N, de Lorenzi-Tognon M, Kelly E, Servellita V, Oseguera M, Nguyen J, Tang J, Omura C, Streithorst J, Hillberg M, Ingebrigtsen D, Zorn K, Wilson MR, Blicharz T, Wong AP, O'Donovan B, Murray B, Miller S, Chiu CY. Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections. Nat Med. 2024 Dec;30(12):3522-3533. doi PMID 39533109
• Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dal PMID 31189036
• Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 2019 May;29(5):831-842. doi: 10.1101/gr.238170.118. Epub 2019 Apr 16. PMID 30992304
• Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19;370(25):2408-17. doi: 10.1056/NEJMoa1401268. Epub 2014 J PMID 24896819

Идентификаторы

NCT: NCT07435649 · CLN-GEN-PLN-004

Первоисточники (государственные реестры)

• ClinicalTrials.gov (NIH, США)

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