Syndromic molecular testing in mechanically ventilated patients with severe pneumonia : a supportive diagnostic approach

Uršič, Tina (author), Erzar, Kaja (author), Seme, Katja (author), Jereb, Matjaž (author), Strle, Franc (author), Petrovec, Miroslav (author)

Rapid identification of pathogens is critical in severe pneumonia patients for timely therapy in mechanically ventilated intensive care unit patients. Conventional diagnostics are time-consuming. The Allplex Respiratory Panels 1-4 detect 16 viruses and seven bacteria and provide faster results; however, because this molecular assay does not yield viable organisms, antimicrobial susceptibility testing cannot be performed. We compared conventional diagnostics with commercial panels to evaluate diagnostic performance and clinical utility. In this prospective study, a total of 30 bronchoalveolar lavage fluids and 80 tracheal aspirates were obtained from 110 unique ICU patients with severe pneumonia (January 2014 and April 2016). Conventional diagnostics were performed during illness, whereas testing of these specimens by commercial panels was performed retrospectively. Pathogen detection rates and co-detections were analyzed by pneumonia type (community-acquired, hospital-acquired, and ventilator-associated). Conventional diagnostics detected pathogens in 87 of 110 patients (79.1%) versus 70 of 110 (63.6%) detected by the commercial approach (P = 0.016). Detection of viruses was most frequent, predominantly influenza A and human rhinoviruses; common bacterial detections included Haemophilus influenzae, Legionella pneumophila, and Streptococcus pneumoniae. Co-detections occurred in 12.7% patients by the commercial approach and in 21.8% by the conventional approach, including virus-bacterium co-detections in 10.9% and 14.5% of cases, respectively. The commercial approach missed eight bacterial and four fungal detections identified by conventional methods. Conventional diagnostics showed higher yield in hospital-acquired pneumonia (82.5% vs 50.0%; P = 0.004), whereas both approaches were comparable in community-acquired cases (75% vs 73.4%). Conventional diagnostics (including culture-based methods) provide broader detection and offer the ability for phenotypic antimicrobial susceptibility testing to be performed, whereas commercial panels offer speed; together, they may optimize pathogen detection and therapy in critically ill patients.IMPORTANCESevere pneumonia in critically ill patients remains a major clinical challenge due to its diverse etiology, rapid progression, and the need for timely, targeted therapy. This study demonstrates that conventional diagnostic approaches-combining culture and molecular tests-identify the etiology more effectively than a commercial multiplex PCR-based syndromic panel in ICU patients. While the molecular approach offers faster results, it lacks the breadth of bacterial and fungal targets and does not provide the opportunity for antimicrobial susceptibility testing. Importantly, viral pathogens-particularly influenza A and rhinoviruses-were frequently detected, underscoring their role in severe pneumonia and the relevance of viral-bacterial co-infections. This work highlights that syndromic molecular diagnostics may be valuable for rapid screening or in community-acquired pneumonia but are insufficient for hospital- or ventilator-associated pneumonia. Our findings support a complementary diagnostic strategy to optimize pneumonia management in ICU settings, improve antimicrobial stewardship, and ultimately impact clinical outcomes for patients with life-threatening respiratory infections.

• Language: English
• Keywords: bacteria, fungi, intensive care unit, molecular methods, severe pneumonia, viruses
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2026
• Number of pages: 16 stra.
• Numbering: Vol. 14, iss. 1, art. e0215525
• PID: 20.500.12556/RUL-177860
• UDC: 616.9:579
• ISSN on article: 2165-0497
• DOI: 10.1128/spectrum.02155-25
• COBISS.SI-ID: 260338435
• Publication date in RUL: 13.01.2026

Record is a part of a journal

• Title: Microbiology spectrum
• Shortened title: Microbiol. spectr.
• Publisher: American society for Microbiology
• ISSN: 2165-0497
• COBISS.SI-ID: 4526968

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: bakterije, glive, enota intenzivne nege, molekularne metode, huda pljučnica, virusi

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P3-0083
• Name: Odnosi parazitskega obstajanja