Background and objective <p>Droplet digital polymerase chain reaction (ddPCR) is increasingly being applied in clinical practice, with absolute quantification as one of its key advantages. This study aims to explore the significance of pathogen DNA load in evaluating the therapeutic efficacy of bloodstream infection (BSI).</p> Methods <p>A total of 25 hospitalized patients with bloodstream infection were enrolled as research subjects. These patients were confirmed by ddPCR testing in the Department of Infectious Diseases, Fuyang People's Hospital, and admitted between November 2024 and April 2025. All patients showed clinical improvement after treatment and were discharged. Based on ddPCR results, they were divided into the Escherichia coli (E. coli) group (n=15) and the Klebsiella pneumoniae (K. pneumoniae) group (n=10). Each patient underwent consecutive ddPCR testing three times, and data including general clinical information, laboratory test results, and sequential organ failure assessment (SOFA) scores were collected and analyzed. The study further aimed to investigate the value of dynamic changes in pathogen DNA load for evaluating efficacy of treatment in BSI and other potential clinical implications.</p> Results <p>Among the baseline data of two groups, the alanine aminotransferase（ALT）level in the K. pneumoniae group (52.8 U/L) was higher than that in the E. coli group (21.0U/L), and the medianl DNA load in the K.pneumoniae group(8329.2 copies/mL,[IQR]: 291.8–47722.4 copies/mL) was higher than that in the E. coli group (310.2 copies/mL,[IQR]: 129.0–1838.0 copies/mL). Meanwhile, Pearson correlation analysis showed no strong correlation between the initial DNA load and SOFA score in patients of the two groups. Dynamic observation indicated that the pathogen DNA load of BSI patients in both groups showed a decreasing trend; at the same time, the proportion of patients with normalized body temperature increased in each group. Further verification demonstrated a strong correlation between the changing trend of DNA load and C-reactive protein(CRP) as well as procalcitonin(PCT)(r ＞0.9).In addition, the rate of reduction in pathogen DNA load in the two groups was comparable to CRP and PCT. Finally, in the K. pneumoniae group, it was found when the DNA load cut-off value was set at 8329.23 copies/mL, it exhibited high sensitivity and high specificity for identifying the formation of secondary abscesses(AUC=1).</p> Conclusion <p>Our study demonstrates that DNA load levels of BSI vary significantly among different pathogens. More importantly, the dynamic changes in pathogen DNA load closely correlate with clinical outcomes, serving as a reliable and objective indicator to directly evaluate therapeutic efficacy in BSI patients. This highlights the practical clinical value of pathogen DNA load monitoring for real-time assessment of treatment response and optimization of clinical management strategies.</p> Clinical trial number <p>Not applicable.</p>