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

Sponsor: Dr Cipto Mangunkusumo General Hospital • ClinicalTrials.gov ID: NCT07841535

Registry updated: 2026-09-25

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Description

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.

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

Eligibility criteria

Inclusion Criteria: * Age ≥18 years. * Sepsis or septic shock according to Sepsis-3 criteria, defined as suspected or confirmed infection with acute organ dysfunction (SOFA score increase ≥2 points from baseline) within 24 hours of inclusion. * 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. Exclusion Criteria: * 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.

Conditions

Sepsis Antimicrobial Resistance (AMR)

Locations

Dr Cipto Mangunkusumo General Hospital — Jakarta, DKI Jakarta, Indonesia

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Official Source

Data sourced from ClinicalTrials.gov, a service of the U.S. National Institutes of Health.

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