{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T08:20:29Z","timestamp":1787818829982,"version":"build-2784847793"},"reference-count":26,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Rapid diagnosis is vital for patients with sepsis. Therefore, this study was conducted to assess the diagnostic performance of rapid Real-Time PCR (rRT-PCR), which detects 32 pathogens and common resistance genes in whole blood within four hours. This study included 160 adult patients with sepsis. Whole-blood samples and BCs were collected from all patients simultaneously, and causative microorganisms were investigated using an rRT-PCR panel and an automated BC system. The panel was also used to detect common resistance genes. The microorganisms most frequently isolated from the BCs were Staphylococcus aureus, Klebsiella pneumoniae, and Escherichia coli. Among the resistance genes (7.5%) detected by rRT-PCR, mecA, OXA-48, and CTX-M were the most frequently identified. The agreement rate between the BC and rRT-PCR results was statistically significant at 79.4%. In the concordance group, the mean age was higher, while the duration of positive BC signals was significantly shorter. Additionally, the sensitivity and specificity of the rRT-PCR method were found to be 80.7% and 99.0%, respectively. Thus, the panel\u2019s ability to detect the causative bacteria and common resistance genes within four hours offers a significant clinical advantage. This allows for early diagnosis in patients with sepsis, prevents progression to septic shock, and reduces mortality rates.<\/jats:p>","DOI":"10.3390\/ijms27177669","type":"journal-article","created":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T08:02:27Z","timestamp":1787817747000},"page":"7669","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diagnosing Sepsis and Identifying Bacterial Resistance Genes Directly from Whole Blood Using a Rapid Real-Time PCR System"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3746-7227","authenticated-orcid":false,"given":"Selbi","family":"Begmyradova","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases and Clinical Microbiology, Istanbul Faculty of Medicine, 34093 Istanbul, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6722-141X","authenticated-orcid":false,"given":"L\u00fctfiye","family":"\u00d6ks\u00fcz","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Istanbul Faculty of Medicine, 34093 Istanbul, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5998-0440","authenticated-orcid":false,"given":"Zerrin","family":"Aktas","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Istanbul Faculty of Medicine, 34093 Istanbul, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oral","family":"\u00d6nc\u00fcl","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Istanbul Faculty of Medicine, 34093 Istanbul, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"key":"ref_1","first-page":"67","article-title":"Sepsis definition: What\u2019s new in the treatment guidelines","volume":"61","author":"Adam","year":"2022","journal-title":"Acta Clin. Croat."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1007\/s00134-021-06506-y","article-title":"Surviving sepsis campaign: International guidelines for management of sepsis and septic shock 2021","volume":"47","author":"Evans","year":"2021","journal-title":"Intensive Care Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1007\/s00063-023-01088-7","article-title":"Challenges of assessing the burden of sepsis","volume":"118","author":"Rudd","year":"2023","journal-title":"Med. Klin.-Intensivmed. Notfallmedizin"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Lamy, B., Darg\u00e8re, S., Arendrup, M.C., Parienti, J.-J., and Tattevin, P. (2016). How to optimize the use of blood cultures for the diagnosis of bloodstream infections? A state-of-the art. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.00697"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/cc11202","article-title":"Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection-a new frontier?","volume":"16","author":"Afshari","year":"2012","journal-title":"Crit. Care"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.diagmicrobio.2012.08.013","article-title":"Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the Film Array system","volume":"74","author":"Blaschke","year":"2012","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1097\/01.CCM.0000217961.75225.E9","article-title":"Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock","volume":"34","author":"Kumar","year":"2006","journal-title":"Crit. Care Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e00231-21","DOI":"10.1128\/jcm.00231-21","article-title":"Direct-from-blood detection of pathogens: A review of technology and challenges","volume":"61","author":"Samuel","year":"2023","journal-title":"J. Clin. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1007\/s10096-018-3255-1","article-title":"Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis","volume":"37","author":"Bos","year":"2018","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1128\/JCM.00011-09","article-title":"Molecular diagnosis of polymicrobial sepsis","volume":"47","author":"Mancini","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e157","DOI":"10.3346\/jkms.2024.39.e157","article-title":"Rapid direct identification of microbial pathogens and antimicrobial resistance genes in positive blood cultures using a fully automated multiplex PCR assay","volume":"39","author":"Kim","year":"2024","journal-title":"J. Korean Med. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments","volume":"55","author":"Bustin","year":"2009","journal-title":"Clin. Chem."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.ijid.2017.12.015","article-title":"Clinical utility of an optimised multiplex real-time PCR assay for the identification of pathogens causing sepsis in Vietnamese patients","volume":"67","author":"Trung","year":"2018","journal-title":"Int. J. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s00134-009-1705-z","article-title":"A multicenter trial to compare blood culture with polymerase chain reaction in severe human sepsis","volume":"36","author":"Bloos","year":"2010","journal-title":"Intensive Care Med."},{"key":"ref_15","unstructured":"Ferara, A.T., Mascarello, A., Merli, M., Casalicchio, G., Nava, A., Gianni, S., Bielli, A., Laratta, M., Fanti, D., and Proto, A. (2025, January 11\u201315). Sepsis on critical patients: Performance and evaluation of a new molecular test from direct whole blood. Proceedings of the 35th ESCMID Global, Vienna, Austria. P2088."},{"key":"ref_16","unstructured":"Altieri, A., Andreassi, E., Bossa, M.C., Minelli, S., Camicia, V., Fiorilla, C., D\u2019Agostini, C., and Frasinetti, S. (2025, January 19\u201322). Innovative strategies of fast microbiology for the early diagnosis of sepsis. Proceedings of the 53\u00b0 Congresso Nazionale della Societ\u00e0 Italiana di Microbiologia, Monastero dei Benedettini, Italy."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"432","DOI":"10.5578\/mb.20229705","article-title":"Comparison of the Multiplex Real Time Polymerase Chain Reaction Method Directly from Whole Blood and from Blood Culture Bottle with the Conventional Method for the Etiological Diagnosis in Patients with Pre-Diagnosis of Sepsis","volume":"56","author":"Alp","year":"2022","journal-title":"Mikrobiyoloji Bul."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Nieman, A.E., Savelkoul, P.H.M., Beishuizen, A., Henrich, B., Lamik, B., MacKenzie, C.R., Kindgen-Milles, D., Helmers, A., Diaz, C., and Sakka, S.G. (2016). A prospective multicenter evaluation of direct molecular detection of blood stream infection from a clinical perspective. BMC Infect. Dis., 16.","DOI":"10.1186\/s12879-016-1646-4"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1128\/JCM.00418-07","article-title":"Prospective comparison of eubacterial PCR and measurement of procalcitonin levels with blood culture for diagnosing septicemia in intensive care unit patients","volume":"47","author":"Rowther","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"8576494","DOI":"10.1155\/ijm\/8576494","article-title":"Validation of CRownLab Pneumoplex for the Detection of Klebsiella pneumoniae and Acinetobacter baumannii Using RT-PCR in Patients with Sepsis at a Tertiary Hospital in Indonesia","volume":"2026","author":"Fadrian","year":"2026","journal-title":"Int. J. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"493","DOI":"10.24953\/turkjped.2019.04.004","article-title":"The potential utility of real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal sepsis","volume":"61","author":"Istanbullu","year":"2019","journal-title":"Turk. J. Pediatr."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1001\/jama.2016.0288","article-title":"Assessment of clinical criteria for sepsis: For the third international consensus definitions for sepsis and septic shock (Sepsis-3)","volume":"315","author":"Seymour","year":"2016","journal-title":"JAMA"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1186\/s13054-021-03787-z","article-title":"Timing of antibiotic therapy in the ICU","volume":"25","author":"Kollef","year":"2021","journal-title":"Crit. Care"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1001\/jama.2016.0287","article-title":"The third international consensus definitions for sepsis and septic shock (Sepsis-3)","volume":"315","author":"Singer","year":"2016","journal-title":"JAMA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1128\/CMR.00062-05","article-title":"Updated review of blood culture contamination","volume":"19","author":"Hall","year":"2006","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_26","unstructured":"European Committee on Antimicrobial Susceptibility Testing (EUCAST) (2026, June 26). Breakpoint Tables for Interpretation of MICs and Zone Diameters. Available online: www.eucast.org."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7669\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T08:05:22Z","timestamp":1787817922000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7669"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,27]]},"references-count":26,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177669"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177669","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,27]]}}}