Molecular-based Optimization of Pathogen Identification in Sepsis Patients in the Indonesian National Referral Hospital

NCT07841535 | Recruiting

• 1 other identifier: 26-07-1027
• Study Type: interventional
• Target: 415
• Locations: 1 country
• Sites: 1

Brief Summary

This study aims to compare the diagnostic performance of conventional blood culture with two molecular-based diagnostic approaches, Hybrispot DNA Flow and metagenomic next-generation sequencing (mNGS), for the identification of microorganisms in patients with sepsis. The study will evaluate the turnaround time of each diagnostic method and assess their potential impact on the time to definitive antimicrobial therapy and subsequent clinical outcomes. The study is led by Robert Sinto, an infectious disease physician at Dr. Cipto Mangunkusumo National Referral Hospital (RSCM), the national referral hospital in Indonesia. Conventional blood culture, which serves as the standard microbiological diagnostic method, may require about 5 to 7 days to obtain a final result. In comparison, Hybrispot DNA Flow and mNGS detect microbial genetic material and may provide microbiological results within approximately 2 to 3 days. By comparing these diagnostic strategies, the study seeks to determine whether molecular-based approaches can facilitate more rapid pathogen identification and support earlier optimization of antimicrobial therapy. Participation in the study is voluntary. Participants may withdraw from the study at any time without affecting the medical care they receive. Participants may also request information about their diagnostic results and may ask the research team to clarify any aspect of the study that they do not understand.

Conditions

Sepsis; Antimicrobial Resistance (AMR)

Keywords

Sepsis; Molecular; antimicrobial resistance; diagnostic stewardship; metagenomic

Outcome Measures

Primary Outcomes (1)

• All-cause mortality

  28 days after study enrollment

Secondary Outcomes (10)

• Length of hospital stay

  Within a single hospital admission or within 28 days of sepsis diagnosis

• Diagnostic turnaround time

  Within 28 days of study enrollment, or within the same hospital stay

• Duration of antimicrobial therapy

  From study enrollment up to 28 days after enrollment, within a single hospital stay and one episode of sepsis

• Time from empirical antimicrobial therapy to definitive therapy

  Within same hospital stay, from enrollment up to 28 days

• Use of mechanical ventilation within 28 days of enrollment

  28 days after study enrollment

Study Arms (3)

Standard-of-care

EXPERIMENTAL

Blood culture will be performed for identification and antimicrobial susceptibility testing as standard care in accordance with the hospital's current standard operating procedures (SOPs).

Diagnostic Test: Standard-of-care blood culture

PCR

EXPERIMENTAL

Multiplex PCR will be performed in addition to standard care using standard blood culture. Blood samples will be incubated using BACT/ALERT system. As soon as a signal is detected from the respective sample (either positive or negative signal), multiplex PCR using Hybrispot will be performed.

Diagnostic Test: Standard-of-care blood culture; Diagnostic Test: Hybrispot DNA Flow

Metagenomic

EXPERIMENTAL

16s metagenomic will be performed in addition to standard care using standard blood culture. Following blood collection in an EDTA tube, DNA extraction, targeted PCR, electrophoresis, and metagenomic NGS will be performed. Only PCR-positive sample will continued to the mNGS process. PCR-negative sample will be reported as negative.

Diagnostic Test: Standard-of-care blood culture; Diagnostic Test: Metagenomic 16s RNA

Interventions

Standard-of-care blood culture DIAGNOSTIC_TEST

Participants will undergo standard blood culture using the BACT/ALERT system. Cultures will be monitored until a final result of either microbial growth or no growth is obtained.

Metagenomic; PCR; Standard-of-care

Hybrispot DNA Flow DIAGNOSTIC_TEST

Hybrispot DNA Flow is a diagnostic tool combining multiplex polymerase chain reaction (PCR) and flow-through hybridization.

PCR

Metagenomic 16s RNA DIAGNOSTIC_TEST

The metagenomic approach using the 16S rRNA platform enables comprehensive identification of microorganisms, including fastidious bacteria, low-abundance microorganisms, and unexpected or previously unrecognized pathogens.

Metagenomic

Eligibility Criteria

• Age: 18 Years+
• Sex: all
• Healthy Volunteers: No
• Age Groups: Adult (18-64), Older Adult (65+)

You may qualify if:

• Age ≥18 years.
• Hospitalized at RSCM and undergoing microbiological testing, including blood culture as part of standard care.
• At least one risk factor for multidrug-resistant (MDR) pathogens according to the 2026 Surviving Sepsis Campaign, including:
• Previous colonization or infection with a relevant MDR pathogen.
• Prolonged exposure to broad-spectrum antibiotics.
• Prolonged hospitalization in a setting with a high prevalence of MDR pathogens, such as the ICU or a ward with a high antimicrobial resistance burden.
• Written informed consent from the patient or legal representative, where applicable for prospective enrollment.

You may not qualify if:

• Unable to provide specimens according to the study protocol.
• Received intravenous antimicrobial regimen for more than 24 hours prior to study enrollment, with the regimen continued as empirical therapy for the current sepsis diagnosis.
• Opt out of best treatment according to medical advice.
• Dropout criteria:
• \- Discharge from the hospital or death within 24 hours after blood collection.

Sponsors & Collaborators

• Dr Cipto Mangunkusumo General Hospital: lead

Study Sites (1)

Dr Cipto Mangunkusumo General Hospital

Jakarta, DKI Jakarta, 10430, Indonesia

RECRUITING

MeSH Terms

Conditions

Sepsis

Condition Hierarchy (Ancestors)

Infections; Systemic Inflammatory Response Syndrome; Inflammation; Pathologic Processes; Pathological Conditions, Signs and Symptoms

Study Officials

• Robert Sinto, MD, MSc.Clin.Ed, D.Phil

  Dr Cipto Mangunkusumo General Hospital

  PRINCIPAL INVESTIGATOR

Central Study Contacts

Robert Sinto, MD, MSc.Clin.Ed, D.Phil

CONTACT

+628158835432; robert.sinto01@ui.ac.id

Selvi N Shahab, MD

CONTACT

+6285770564595; selvishahab@rscm.co.id

Study Design

• Study Type: interventional
• Phase: not applicable
• Allocation: RANDOMIZED
• Masking: DOUBLE
• Who Masked: PARTICIPANT, OUTCOMES ASSESSOR
• Purpose: DIAGNOSTIC
• Intervention Model: PARALLEL
• Sponsor Type: OTHER
• Responsible Party: PRINCIPAL INVESTIGATOR
• PI Title: Principal Investigator

Study Record Dates

• First Submitted: August 20, 2026
• First Posted: September 25, 2026
• Study Start: September 1, 2026
• Primary Completion (Estimated): August 31, 2027
• Study Completion (Estimated): December 31, 2027
• Last Updated: September 25, 2026

Record last verified: 2026-08

Data Sharing

• IPD Sharing: Will not share

Locations

ID (1)