Utility of droplet digital PCR for pathogen detection in bronchoalveolar lavage fluid from mechanically ventilated ICU patients

Rapid and accurate pathogen detection in severe pneumonia remains a significant clinical challenge, as traditional diagnostic methods are often time-consuming and insensitive. Droplet digital polymerase chain reaction (ddPCR) is an emerging technology that can potentially enhance pathogen identification. This study aimed to evaluate the utility of ddPCR for pathogen detection in bronchoalveolar lavage fluid from mechanically ventilated intensive care unit (ICU) patients. A prospective study was conducted from June 2023 to September 2024 at a tertiary teaching hospital in China, enrolling 60 adult patients diagnosed with severe pneumonia requiring bronchoscopy. Bronchoalveolar lavage fluid (BALF) samples were collected for simultaneous ddPCR, metagenomic next-generation sequencing (mNGS), and conventional culture testing. A total of 92 BALF specimens from 60 patients were detected using ddPCR, mNGS, and conventional culture testing simultaneously. The most frequently detected bacteria by 3 methods were Acinetobacter baumannii , Klebsiella , Pseudomonas aeruginosa , Stenotrophomonas maltophilia , Escherichia coli , and Staphylococcus aureus , while Aspergillus spp. and Pneumocystis jirovecii . were the predominant fungal pathogens detected by ddPCR and mNGS. Based on comprehensive clinical assessment, ddPCR showed sensitivities of 83.33% to 100%, specificities of 75.38% to 100%, and AUCs of 95.67% to 100% for these common pathogens. The turnaround time of ddPCR was significantly shorter than that of mNGS and conventional culture (5.48 ± 0.78 vs. 41.81 ± 10.96 vs. 77.41 ± 16.31 h, respectively). At the sample level, ddPCR showed moderate agreement with mNGS (κ = 0.465, 95% CI 0.166–0.764; P < 0.001) but only slight agreement with conventional culture (κ = 0.112, 95% CI 0.008–0.216; P = 0.020). The AUCs of ddPCR were significantly higher than those of mNGS for Acinetobacter baumannii , Klebsiella , Pseudomonas aeruginosa , Stenotrophomonas maltophilia , Escherichia coli , and Aspergillus spp. (all P < 0.05), whereas no significant differences were observed for Staphylococcus aureus or Pneumocystis jirovecii . Our findings indicated that lung infection often involves multiple pathogens, and ddPCR in BALF is a valuable tool for detecting non-viral pathogens in ICU patients with severe pneumonia requiring mechanical ventilation. This study highlights the superior diagnostic performance of ddPCR over conventional culture, reinforcing its clinical utility in pneumonia diagnosis. Not applicable.