Beyond Culture: Real-Time PCR Performance in Detecting Causative Pathogens and Key Antibiotic Resistance Genes in Hospital-Acquired Pneumonia

Abstract

<b>Introduction:</b> The rise in hospital-acquired pneumonia (HAP) due to antibiotic-resistant bacteria is increasing morbidity, mortality, and inappropriate empirical antibiotic use. This prospective research aimed to evaluate the performance of a real-time polymerase chain reaction (PCR) assay for detecting causative microorganisms and antibiotic-resistance genes from respiratory specimens compared to traditional methods. Additionally, we aimed to determine the molecular epidemiology of antibiotic resistance genes among HAP patients at The University of Jordan hospital. <b>Methods:</b> Lower respiratory tract samples were collected from HAP patients, including those with ventilator-associated pneumonia (VAP), between May 2024 and October 2024. Clinical data from the medical files were used to collect and analyze demographic and clinical information, including clinical outcomes. Real-time PCR was run to detect causative microbes and antibiotic resistance genes. <b>Results:</b> Among 83 HAP patients (median age 63, 61.45% male), 48.15% died. Culture identified <i>Klebsiella</i> (25.53%), <i>Acinetobacter</i> (22.34%), and <i>Candida</i> (24.47%) as the most common pathogens, while qPCR showed higher detection rates, including for <i>A. baumannii</i> (62.20%, <i>p</i> = 0.02) and <i>K. pneumoniae</i> (45.12%, <i>p</i> < 0.001). Carbapenem resistance was high; <i>A. baumannii</i> showed 100% resistance to most antibiotics except colistin (92.31%). The resistance genes <i>ndm</i> (60%) and <i>oxa-48</i> (58.46%) were frequently detected and significantly associated with phenotypic resistance (<i>p</i> < 0.001). The qPCR identified resistance genes in all carbapenem-resistant cases. No gene significantly predicted mortality. <b>Conclusions:</b> Real-time PCR diagnostic technique combined with epidemiology of antibiotic resistance genes data may be a rapid and effective tool to improve HAP management. Large, multicenter studies are needed in the future to validate the performance of real-time PCR in HAP diagnosis, and appropriate management is also required.

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