{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T17:13:34Z","timestamp":1791047614828,"version":"4.1.0"},"reference-count":28,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T00:00:00Z","timestamp":1758067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Jordan","award":["DRGS-2024-8"],"award-info":[{"award-number":["DRGS-2024-8"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Introduction: 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. Methods: 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. Results: Among 83 HAP patients (median age 63, 61.45% male), 48.15% died. Culture identified Klebsiella (25.53%), Acinetobacter (22.34%), and Candida (24.47%) as the most common pathogens, while qPCR showed higher detection rates, including for A. baumannii (62.20%, p = 0.02) and K. pneumoniae (45.12%, p &lt; 0.001). Carbapenem resistance was high; A. baumannii showed 100% resistance to most antibiotics except colistin (92.31%). The resistance genes ndm (60%) and oxa-48 (58.46%) were frequently detected and significantly associated with phenotypic resistance (p &lt; 0.001). The qPCR identified resistance genes in all carbapenem-resistant cases. No gene significantly predicted mortality. Conclusions: 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.<\/jats:p>","DOI":"10.3390\/antibiotics14090937","type":"journal-article","created":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T05:59:51Z","timestamp":1758088791000},"page":"937","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Beyond Culture: Real-Time PCR Performance in Detecting Causative Pathogens and Key Antibiotic Resistance Genes in Hospital-Acquired Pneumonia"],"prefix":"10.3390","volume":"14","author":[{"given":"Lana Hani","family":"Abu Khadija","sequence":"first","affiliation":[{"name":"Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shatha M.","family":"Alomari","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Science, Zarqa University, Zarqa 13110, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1324-7884","authenticated-orcid":false,"given":"Ahmad R.","family":"Alsayed","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heba A.","family":"Khader","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andi Dian","family":"Permana","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5810-0915","authenticated-orcid":false,"given":"Luai Z.","family":"Hasoun","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9880-1305","authenticated-orcid":false,"given":"Manar Saleh","family":"Zraikat","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walaa","family":"Ashran","sequence":"additional","affiliation":[{"name":"Department of Surgical Critical Care, The University of Jordan Hospital, The University of Jordan, Amman 11942, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8005-3908","authenticated-orcid":false,"given":"Malek","family":"Zihlif","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1128\/CMR.00051-05","article-title":"Ventilator-Associated Pneumonia: Diagnosis, Treatment, and Prevention","volume":"19","author":"Koenig","year":"2006","journal-title":"Clin. 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