Mixed microbial detection by sputum multiplex PCR in severe community-acquired pneumonia in Vietnam

Severe community-acquired pneumonia (CAP) remains difficult to manage when empirical treatment must be started before conventional microbiology yields results. This cross-sectional study characterized microorganisms detected by sputum multiplex real-time PCR in adults with severe CAP at Can Tho Central General Hospital, Vietnam, and explored selected associated factors. Adults admitted between December 2024 and May 2025 who met ATS/IDSA severe CAP criteria were enrolled by convenience sampling. Only Gram-screened sputum specimens considered reliable (≥ 25 polymorphonuclear leukocytes and ≤ 10 squamous epithelial cells per field) underwent nucleic acid extraction and testing using a 75-target multiplex real-time PCR panel. General pathogens were considered positive at ≥ 100,000 copies/mL, while viruses and atypical bacteria were considered positive at ≥ 5000 copies/mL. Among 51 patients, 47 (92.2%) had at least one detected microorganism. Bacterial detection occurred in 35 (68.6%), viral detection in 45 (88.2%), and fungal detection in 26 (51.0%). All monomicrobial detections were viral (8/51, 15.7%), while 23/51 (45.1%) showed concurrent bacterial, viral, and fungal detections. The leading bacterial detections were Klebsiella pneumoniae (23.5%), Acinetobacter baumannii (21.6%), Streptococcus pneumoniae (19.6%), Escherichia coli (17.6%), and Haemophilus influenzae (11.8%). The most frequent viral detections were Epstein–Barr virus (62.7%), cytomegalovirus (33.3%), SARS-CoV-2 (11.8%), and rhinovirus (9.8%). Candida albicans was the dominant fungal detection (51.0%). In exploratory analyses, viral detection was more frequent in patients with radiographic lung abnormalities than in those without documented abnormalities (93.5% vs 40.0%; OR 21.5, 95% CI 2.5–182.4; p = 0.009); no other factor reached statistical significance. Severe CAP in this tertiary Vietnamese cohort showed extensive mixed microbial detection, including frequent Gram-negative signals and occasional unexpected pathogens such as Mycobacterium tuberculosis and Pneumocystis jirovecii. Sputum multiplex PCR may support early diagnostic orientation, isolation, and targeted diagnostic reassessment, but without susceptibility data it should complement – not replace - culture-based stewardship. Detections - particularly K. pneumoniae , A. baumannii , E. coli , EBV, CMV, and Candida spp. - require careful clinical adjudication in sputum.