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Identification of pathogens by comprehensive real-time PCR versus conventional methods in community-acquired
Yutaka Yoshii1, Kenichiro Shimizu1, Miyuki Morozumi2
1a Division of Respiratory Diseases, Department of Internal Medicine , The Jikei University School of Medicine , Tokyo , Japan ;
Background:
Community-acquired pneumonia (CAP) has high morbidity and mortality. Unfortunately, the pathogen detection rate using conventional culture methods is relatively low. We compared comprehensive real-time polymerase chain reaction (real-time PCR) analysis of nasopharyngeal swab specimens (NPS) and sputum samples against conventional methods for ability to detect causative pathogens of CAP.
Methods:
We prospectively enrolled adult CAP patients, including those with prior antibiotic use, from December 2012 to May 2014. For each patient, causative pathogens were investigated conventionally and by real-time PCR that can identify 6 bacterial and 11 viral pathogens.
Results:
Patients numbered 92 (mean age, 63 years; 59 male), including 30 (33%) with prior antibiotic use. Considering all patients, identification of causative pathogens by real-time PCR was significantly more frequent than by conventional methods in all patients (72% vs. 57%, p = 0.018). In patients with prior antibiotic use, identification rates also differed significantly (PCR, 77%; conventional, 50%; p = 0.027). Mixed infections were more frequent according to real-time PCR than conventional methods (26% vs. 4%, p < 0.001). By the real-time PCR, Streptococcus pneumoniae was most frequently identified (38%) as a causative pathogen, followed by Haemophilus influenzae (37%) and Mycoplasma pneumoniae (5%). PCR also identified viral pathogens (21%), with sensitivity enhanced by simultaneous examination of both NPS and sputum samples rather than only NPS samples.
Conclusions:
Real-time PCR of NPS and sputum samples could better identify bacterial and viral pathogens in CAP than conventional methods, both overall and in patients with prior antibiotic treatment.
Insights
Real-time PCR significantly improves pathogen detection for community-acquired pneumonia (CAP) compared to conventional methods. This advanced technique is especially beneficial for identifying bacteria and viruses in patients with prior antibiotic use.
Area of Science:
- Infectious Diseases
- Molecular Diagnostics
- Respiratory Medicine
Background:
- Community-acquired pneumonia (CAP) presents a significant global health challenge with high morbidity and mortality rates.
- Conventional diagnostic methods for CAP often yield low pathogen detection rates, hindering effective treatment.
- Accurate and timely identification of causative pathogens is crucial for managing CAP effectively.
Purpose of the Study:
- To compare the diagnostic yield of comprehensive real-time polymerase chain reaction (real-time PCR) with conventional methods for detecting CAP pathogens.
- To evaluate the effectiveness of real-time PCR in identifying both bacterial and viral pathogens in CAP patients.
- To assess the performance of real-time PCR in patients with and without prior antibiotic exposure.
Main Methods:
- A prospective study enrolled 92 adult CAP patients between December 2012 and May 2014.
- Causative pathogens were investigated using both conventional methods and real-time PCR, which targets 6 bacterial and 11 viral pathogens.
- Nasopharyngeal swab specimens (NPS) and sputum samples were analyzed.
Main Results:
- Real-time PCR demonstrated significantly higher pathogen identification rates (72%) than conventional methods (57%) in all CAP patients (p=0.018).
- This improvement was also observed in patients with prior antibiotic use (PCR 77% vs. conventional 50%; p=0.027).
- Real-time PCR identified mixed infections more frequently (26% vs. 4%) and detected bacterial pathogens like Streptococcus pneumoniae (38%) and Haemophilus influenzae (37%), as well as viral pathogens (21%).
Conclusions:
- Real-time PCR analysis of NPS and sputum samples offers superior pathogen detection for CAP compared to conventional techniques.
- The enhanced sensitivity of real-time PCR is valuable for both overall CAP diagnosis and in cases with prior antibiotic treatment.
- Simultaneous examination of NPS and sputum samples improves the detection of viral pathogens in CAP.
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