Comparison of pathogen and resistance profiles in bloodstream infections using conventional methods and multiplex RT-PCR

Bloodstream infections (BSIs) remain a major cause of morbidity and mortality, particularly in hospitalized patients with sepsis. Rapid identification of pathogens and their resistance profiles is critical for timely initiation of effective antimicrobial therapy, as delays can substantially increase mortality. This prospective study aimed to compare conventional culture-based methods with Multiplex Real-Time PCR (RT-PCR) for the early detection of pathogens and resistance genes in blood culture samples exhibiting positive signals. A total of 100 hospitalized patients with suspected sepsis were included in the study. Blood culture samples were analyzed using both conventional culture methods and multiplex real-time PCR. Conventional methods identified 108 microorganisms, whereas RT-PCR detected pathogens in 90 samples, After the blood culture bottle signaled positive, the samples were inoculated onto culture media. Subsequently, multiplex PCR was performed, and results were obtained within approximately 2–4 h. The subcultured samples were evaluated the following day, identified using MALDI-TOF MS, and antimicrobial susceptibility testing was performed. Both identification and susceptibility results were reported on the second day.along with an additional 14 microorganisms that were not recovered by culture. Resistance gene profiles identified by RT-PCR demonstrated high concordance with phenotypic resistance results, including mecA/C, VIM, NDM, KPC, and vanA genes. Nevertheless, discrepancies such as very major errors (5.1%) were observed, indicating areas requiring further investigation. Multiplex RT-PCR serves as a valuable adjunct to conventional culture methods, enabling rapid pathogen identification and resistance profiling. Its integration into routine diagnostic workflows may enhance clinical outcomes by facilitating timely, targeted therapy for septic patients.