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Bacterial culture and drug susceptibility testing are used to identify pathogen infections. Nevertheless, the process requires several days from collection to the identification of bacterial species and drug-resistance patterns. The digital PCR system is a rapidly developing quantitative detection technology widely applied to molecular diagnosis, including copy number variations, single nucleotide variant analysis, cancer biomarker discovery, and pathogen identification. This study aimed to use a droplet digital PCR system to identify bacteria in blood samples and explore its ability to identify pathogen in bacteremia. Then, we designed primers and probes of SWG-9 and COA gene for  E. coli  and  S. aureus  to identify in blood samples with the ddPCR system. The system had demonstrated extremely high detection accuracy in blood samples, and the detection rate of  E. coli  was 13.1–21.4%, and that of  S. aureus  was 50–88.3%. Finally, blood samples containing both  E. coli  and  S. aureus  were tested to evaluate further the accuracy and applicability of this method, indicating the detection rates range from 18.1% to 97%. The ddPCR system is highly promising as a qualitatively and quantitatively screening method for rapidly detecting pathogen.

Qualitative and quantitative detection of surgical pathogenic microorganisms Escherichia coli and Staphylococcus aureus based on ddPCR system