This clinical case study evaluates the use of droplet digital PCR (ddPCR) for bloodstream infection detection, incorporating Meridian’s Lyo-Ready qPCR Mix (MDX024) to support robust and reproducible assay performance.
CASE STUDY
Rapid Sepsis Detection Enabled by ddPCR and Lyophilized PCR Chemistry INTRODUCTION Bloodstream infection (BSI) , caused by pathogens entering the bloodstream, can lead to sepsis (a systemic infection associated with high mortality). Sepsis, which progresses in severity from bacteremia to septic shock, represents a critical global health concern. Each year, approximately 30 million cases of sepsis result in an estimated 5.3 million deaths worldwide, placing a substantial burden on healthcare systems. 1 It has been estimated that for every hour of delay in the treatment of BSI, the mortality rate increases by 8%, 2 and that a six-hour delay can raise mortality to as high as 58%. 3 Blood culture is widely recognized as the “gold standard” for sepsis diagnosis. However, significant challenges remain in achieving rapid and precise diagnosis, including low positivity rates, prolonged detection times (3–5 days) and a high risk of contamination (e.g., coagulase-negative staphylococci (CoNS) and other bacteria). In addition, traditional blood culture and other laboratory approaches lack the ability to provide quantitative pathogen detection. Therefore, there is an urgent need for diagnostic tools with shorter reporting times and higher detection rates that can support timely, targeted treatment strategies and ultimately reduce sepsis- related mortality. 4 From Concept to Clinic:
Droplet digital PCR (ddPCR) has recently demonstrated strong potential for pathogen detection and has been shown to offer ultra-high sensitivity and specificity in studies of BSI, 5 owing to its ability to rapidly and sensitively detect specific DNA fragments from common sepsis-associated pathogens. In this paper, we present a case study from Pilot Gene (Hangzhou, China) evaluating Meridian’s Lyo-Ready 1-Step RT-qPCR Mix (MDX024) on a ddPCR platform for sepsis testing. The study demonstrates rapid and accurate pathogen detection, highlighting the ability to detect pathogens within 24 hours, provide early sepsis warning, and enable precise quantitative monitoring throughout the course of sepsis. The report also compares Meridian’s Lyo-Ready qPCR Mix (MDX024) with a reference mix, showing improved amplification efficiency, specificity, inhibitor tolerance and compatibility with lyophilization.
Sensitive & Rapid Identification of Pathogens by Droplet Digital PCR in Septic Patients with Meridian's Lyo-Ready qPCR Chemistry
STUDY 1
By comparing with blood culture for pathogen detection, this study demon- strated ddPCR with higher sensitivity, faster turnaround time and the ability to detect AMR genes compared to blood culture. It also showed potential for dynamic monitoring of pathogen load, making it a promising tool for early and accurate sepsis diagnosis.
A prospective pilot diagnostic study was conducted to clinically validate the multiplex ddPCR panel in diagnosing suspected septic patients using Meridian's Lyo-Ready 1-Step RT-qPCR Mix (MDX024) . A total of 100 sepsis episodes of 89 patients were included in the study. This study aimed to establish a method that can rapidly diagnose the causative microorganisms and antimicrobial resistance (AMR) markers of septic patients in the intensive care unit, thereby improving the prognosis.
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STUDY WORKFLOW
Sample Collection 1 Blood Culture 2 & ddPCR Testing 3
Blood samples (5 mL) were collected for both blood culture and ddPCR testing. Samples were stored in cell-free DNA preservation tubes and processed within 24 hours. Two blood culture samples were collected per patient for aerobic and anaerobic culture. Antibiotic susceptibility tests were performed manually according to Clinical and Laboratory Standards Institute (CLSI) guidelines. ddPCR was performed using a 7-fluorescent-channel fully-automated droplet digital PCR system AD3207 (Pilot Gene Technology Co., Ltd., Hangzhou, China), an optimized platform for clinical infectious disease testing. DNA was extracted from plasma and analyzed using multiplex ddPCR panels (Pilot Gene, Hangzhou, China) targeting specific pathogens and antimicrobial resistance genes. The platform enables rapid, multiplexed, and absolute quantitative detection with robust performance on complex blood-derived samples, supporting early sepsis diagnosis and dynamic pathogen load monitoring in clinical settings. Synthesized DNA fragments were used as positive controls, while DNase-free water or blood samples from three healthy subjects served as negative controls. The entire ddPCR workflow required approximately 2.5 hours, delivering actionable clinical results within the same timeframe.
Plasma DNA Extraction
STUDY RESULTS Compared with blood culture, the ddPCR panel demonstrated an overall sensitivity of 75.0% and specificity of 68.7%, yielding an additional detection rate of 17.0% for sepsis cases, with a turnaround time of 2.5 h [ Figure 1 ]. Antimicrobial resistance genes were identified in 13 samples. Whenever ddPCR detected the ß -lactamase—Klebsiella pneumoniae carbapenemase (blaKPC) or ß -lactamase—New Delhi metallo (blaNDM) genes, these findings corresponded to the cultivation of carbapenem- resistant Gram-negative bacteria. Dynamic ddPCR monitoring revealed a consistent correlation between quantitative ddPCR results and trends in C-reactive protein and procalcitonin levels [ Figure 2 ].
This study also highlighted the versatility of Meridian's chemistry: one mix, multiple applications, including digital PCR. Digital platforms require finely-tuned reagent formulations to ensure precise droplet partitioning and consistent amplification without inhibition. Meridian's Lyo-Ready 1-Step RT-qPCR Mix (MDX024) demon- strated strong compatibility with ddPCR workflows and robust performance in this case study, confirming its flexibility across diverse molecular testing workflows.
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1
Figure 1. Distribution of detected pathogens by ddPCR and blood culture . Pathogens detected by ddPCR and blood culture within the range of ddPCR targeted organisms. Reproducible performance across both PCR mixes. Figure 2. The value of ddPCR in the dynamic surveillance of sepsis . The quantitative results of ddPCR align with the trends seen in CRP and PCT levels.
2
Comparative Performance of Meridian's Chemistry Versus Commercial Alternatives on ddPCR
STUDY 2
Parallel tests were conducted using the same samples and reaction conditions with MDX024 and a mix from a second supplier, to assess amplification efficiency, specificity, inhibitor tolerance and stability after lyophilized.
STUDY RESULTS Under identical reaction conditions and thermal cycling protocols, templates of the same concentration were tested to compare the number of positive droplets and their fluorescence intensity distribution. MDX024 demonstrated higher amplification efficiency and improved uniformity [ Figure 3A ]. Negative samples were evaluated based on fluorescence intensity distribution to assess non- specific amplification. The MDX024 enzyme exhibited superior specificity, with no false positives arising from non-specific amplification [ Figure 3B ].
To evaluate inhibitor tolerance, 20 mg/mL of hemoglobin (a known PCR inhibitor in blood samples) was added to the reaction system. Under identical conditions, MDX024 generated more positive droplets than Supplier A, indicating greater resistance to inhibition [ Figure 3C ]. The enzyme's performance was also assessed in both liquid and lyophilized formats. MDX024 maintained its amplification performance across diverse templates before and after lyophilization, demonstrating strong compatibility with dry-down processes [ Figure 4 ].
A ddPCR AMPLIFICATION EFFICIENCY 3
SUPPLIER A
MDX024
B ddPCR AMPLIFICATION SPECIFICITY
C
INHIBITOR TOLERANCE IN ddPCR
SUPPLIER A
MDX024
SUPPLIER A
MDX024
Figure 3. Comparative results using Meridian MDX024 and a reference mix from Supplier A in the same reaction settings . (A) ddPCR amplification efficiency; (B) ddPCR amplification specificity; (C) Inhibitor tolerance to samples.
4
LYOPHILIZATION COMPATIBILITY
SUPPLIER A
MDX024
Liquid Lyophilized
Figure 4. Lyophilization compatibility. Comparative results using Meridian MDX024 and a reference mix from Supplier A in the same reaction settings.
Meridian’s Lyo-Ready 1-Step RT-qPCR Mix (MDX024) demonstrated strong amplification performance, high specificity, and compatibility with inhibitor-challenged samples and lyophilized formats in this ddPCR-based sepsis case study. These results support its suitability as a flexible reagent for ddPCR assay development in demanding molecular testing workflows.
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MARCH | 2026
CASE STUDY RAPID SEPSIS DETECTION WITH ddPCR
Meridian's Chemistry Elevates ddPCR-Based Sepsis Testing
DRIVING DIAGNOSTIC INNOVATION
Lyo-Ready 1-Step RT-qPCR Mix (MDX024) , which exhibited high amplification efficiency, enhanced specificity, strong inhibitor tolerance and excellent lyophilization compatibility. These features support the use of MDX024 as a suitable reagent for ddPCR- based sepsis assay development. Its versatile formulation underscores Meridian’s commitment to advancing molecular diagnostics, providing high-performing reagents that deliver consistency, flexibility and confidence across diverse platforms and clinical applications. 4. Gaieski, D. F., et al . (2010). Impact of time to antibiotics on survival in patients with severe sepsis or septic shock in whom early goal-directed therapy was initiated in the emergency department*. Critical Care Medicine, 38 (4), 1045–1053. https://doi.org/10.1097/ccm.0b013e3181cc4824 5. Hu, B., et al. (2021). A comparison of blood pathogen detection among droplet digital PCR, metagenomic Next-Generation sequencing, and blood culture in critically ill patients with suspected bloodstream infections. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.641202 6. Wu, Z., et al. (2024). Sensitive and rapid identification of pathogens by droplet digital PCR in a cohort of septic patients: a prospective diagnostic study. Infectious Diseases, 56 (10), 830–841. https:// doi.org/10.1080/23744235.2024.2354312
Sepsis remains a leading cause of mortality among critically ill patients and early, accurate pathogen detection is essential for effective clinical intervention. Traditional blood culture methods are time-consuming and often lack sensitivity, highlighting the need for faster and more reliable diagnostic approaches. This case study evaluated the clinical utility of droplet digital PCR (ddPCR), demonstrating earlier pathogen detection compared with conventional blood culture workflows in patients with suspected sepsis. The study also highlighted the exceptional performance of Meridian’s REFERENCES 1. Fleischmann, C., et al. (2015). Assessment of global incidence and mortality of hospital-treated sepsis. Current estimates and limitations. American Journal of Respiratory and Critical Care Medicine , 193 (3), 259–272. https://doi.org/10.1164/rccm.201504- 0781oc 2. Kumar, A., et al. (2006). Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock*. Critical Care Medicine , 34 (6), 1589–1596. https://doi.org/10.1097/01.ccm.0000217961.75225.e9 3. Kumar, A. (2014). Antimicrobial delay and outcome in severe sepsis. Critical Care Medicine, 42 (12), e802. https://doi.org/10.1097/ ccm.0000000000000620
TO LEARN MORE | Discover how Meridian's molecular solutions can help you optimize your sepsis workflows. From high-performance PCR chemistries to custom formulations and scalable manufacturing, we provide the tools and expertise to accelerate your assay development. VISIT | www.meridianbioscience.com/lifescience
ABOUT MERIDIAN
Pilot Gene is an innovative high-tech company specializing in molecular diagnostics, molecular biology, and genetics. Headquartered in Hangzhou, China, it is committed to becoming a leading global provider of molecular diagnostics and life science solutions. With a strong focus on droplet digital PCR (ddPCR) technology, Pilot Gene has developed high-throughput, fully automated digital PCR systems widely used in clinical diagnostics, life sciences, and public health. Backed by over 10 years of experience, the company continues to strengthen its R&D capabilities and expand its global presence through continuous innovation. ABOUT PILOT GENE
Meridian is a global provider of innovative diagnostic solutions and critical raw materials for molecular and immunoassay development. We design, manufacture and deliver components that enable fast, accurate and reliable diagnostics—from early research through commercial testing. As part of our molecular focus, we offer a comprehensive portfolio of: • Enzymes for isothermal, qPCR and NGS sample prep Our solutions, engineered for workflow efficiency, sensitivity and reproducibility, enable applications from infectious disease detection to precision oncology. Backed by deep technical expertise and global manufacturing capabilities, we deliver consistent quality, rapid turnaround and scalable supply—empowering diagnostic innovators to accelerate development and bring products to market with confidence. • Optimized master mixes for LAMP and qPCR • Nucleotides and other supporting reagents
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