Journal Article
Diagnosis of pneumococcal pneumonia using quantitative PCR targeting lytA and piaB in adult patients with community-acquired pneumonia
Nienke Paternotte; Willem R. Miellet; Tessa Nieuwenhuijsen; Rob Mariman; Wil A. van der Reijden; Wouter Rozemeijer; Elisabeth A.M. Sanders; Dominic Snijders; Cornelis H. van Werkhoven; Marc J.M. Bonten; Krzysztof Trzciński; Wim G. Boersma
European Journal of Clinical Microbiology & Infectious Diseases · 2026
Abstract
Purpose Accurate diagnosis of pneumococcal pneumonia remains challenging due to suboptimal sensitivity of conventional microbiological methods. Molecular techniques may improve Streptococcus pneumoniae detection, but their clinical utility remains uncertain. Methods In this prospective observational study, we compared conventional diagnostics with qPCR-based detection of lytA and piaB genes in nasopharyngeal, oropharyngeal, saliva, and sputum samples collected from adults with community-acquired pneumonia (CAP) and three control groups without acute respiratory symptoms. Stringent sample-specific cut-offs ( low Cq), defined by the lowest cycle threshold (Cq) values observed among controls, were applied to reduce classification of background carriage as pneumococcal CAP. Results S. pneumoniae was detected by conventional methods in 53 (21.1%) of 251 CAP patients. Overall pneumococcal detection by qPCR was higher in CAP patients than in 564 individuals without CAP (35.9% vs. 10.3%, p < 0.001), but pneumococcal density showed substantial overlap between CAP patients and controls and across aetiological groups within the CAP cohort. Using the low Cq criteria, 63 (25.1%) CAP patients met the study definition of pneumococcal CAP (PCAP), including ten (4.0%) identified by qPCR alone. Detection rates and pneumococcal density were highest in sputum and lower in patients pretreated with antibiotics. Conclusions qPCR targeting lytA and piaB increased pneumococcal detection in CAP patients, but substantial overlap in pneumococcal density limited its added diagnostic value for PCAP. Using stringent lowCq criteria, qPCR identified only a small number of additional PCAP cases beyond conventional diagnostics. Our findings do not support routine use of qPCR as a stand-alone diagnostic test for PCAP. Nevertheless, sputum-based molecular detection may contribute to future surveillance studies when combined with serotype-specific analyses.