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Enhancing pathogen description and antibiotic regimen selection in community-acquired pneumonia through RT-qPCR
Na Zhao1, Hongyu Ren1, Yingmiao Zhang2
1National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Background:
Adults with community-acquired pneumonia (CAP) in China suffer high morbidity. CAP is caused by a multitude of pathogens; however, pathogen-directed clinical symptoms are often lacking. Therefore, patients lacking an accurate microbiological diagnosis are administered with empirical antimicrobials.
Methods:
We collected bronchoalveolar lavage fluid, as well as clinical and laboratory data from 650 adult patients with CAP admitted to three hospitals in Hubei, Sichuan, and Zhejiang provinces in China. Specimens were cultured and tested using real-time reverse transcription qPCR (RT-qPCR) assays for the presence of 42 respiratory bacteria and viruses. CAP was investigated with respect to regions, genders, and age and patterns of infections or co-infections. Employing clinical guidelines adapted for diagnosis, we assessed retrospectively the appropriate pathogen-directed therapy and compared it with the initial empirical therapies.
Results:
Our study identified that 21.38% (139/650) of the patients were classified as having Severe CAP (S-CAP), with a higher prevalence among males, older adults, and during the warm season. Bacterial pathogens were detected in 35.53% (231/650) of cases. K. pneumoniae, H. influenzae, and S. aureus were the most prevalent bacteria across different demographics and regions. Viral pathogens were found in 48.76% (317/650) of patients Epstein-Barr, Human rhinovirus, and Cytomegalovirus were the most common viruses. Co-infections were present in 24.31% (158/650) of cases, with viral-bacterial co-infections being the most frequent. The RT-qPCR demonstrated significantly higher detection rates for key pathogens compared to standard culture methods. It showed potential in optimizing antimicrobial prescriptions by allowing for de-escalation in 18.30% (95/518) of patients, among which reducing the number of excessive antibiotics mainly comprised decreasing the use of 2nd or 3rd generation cephalosporins (5.79%, 30/518) and β-lactamase inhibitor combinations.
Conclusion:
The study highlights the significant burden of S-CAP, particularly among specific demographics and seasons. The prevalence of bacterial and viral pathogens, along with the high rate of co-infections, emphasizes the need for comprehensive diagnostic approaches. The RT-qPCR assays emerge as a superior diagnostic tool, offering enhanced pathogen detection capabilities and facilitating more precise antimicrobial therapy. This could lead to improved patient outcomes and contribute to the rational use of antimicrobials, addressing the growing concern of antibiotic resistance.
Insights
Community-acquired pneumonia (CAP) in China affects many adults, with severe cases more common in males and older individuals. Advanced RT-qPCR testing improves pathogen detection and antimicrobial therapy, aiding antibiotic stewardship.
Area of Science:
- Infectious Diseases
- Microbiology
- Clinical Medicine
Background:
- Community-acquired pneumonia (CAP) presents a significant health challenge in China, characterized by high morbidity.
- The etiological diagnosis of CAP is often difficult due to a lack of specific clinical symptoms, leading to empirical antimicrobial treatment.
Purpose of the Study:
- To investigate the prevalence of various bacterial and viral pathogens in adult CAP patients in China.
- To compare the efficacy of real-time reverse transcription quantitative PCR (RT-qPCR) with standard culture methods for pathogen detection.
- To assess the impact of RT-qPCR on antimicrobial therapy prescription and de-escalation.
Main Methods:
- Bronchoalveolar lavage fluid and clinical data were collected from 650 adult CAP patients across three Chinese provinces.
- Real-time reverse transcription quantitative PCR (RT-qPCR) assays were used to detect 42 respiratory bacteria and viruses.
- Pathogen-directed therapy was retrospectively compared with initial empirical treatments.
Main Results:
- Severe CAP (S-CAP) was identified in 21.38% of patients, with higher rates in males, older adults, and during warmer seasons.
- Bacterial pathogens (e.g., *K. pneumoniae*, *H. influenzae*, *S. aureus*) were found in 35.53%, and viral pathogens (e.g., Epstein-Barr virus, Human rhinovirus) in 48.76%.
- Co-infections occurred in 24.31% of cases. RT-qPCR showed higher detection rates than culture and facilitated antimicrobial de-escalation in 18.30% of patients.
Conclusions:
- The study underscores the substantial burden of S-CAP and the commonality of bacterial, viral, and co-infections in China.
- RT-qPCR is a valuable diagnostic tool for enhanced pathogen detection in CAP, surpassing traditional culture methods.
- Improved diagnostics through RT-qPCR can optimize antimicrobial prescriptions, support de-escalation, and promote rational antibiotic use, crucial for combating antimicrobial resistance.
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