Journal
EMERGING MICROBES & INFECTIONS
Volume 11, Issue 1, Pages 556-566Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/22221751.2022.2035194
Keywords
Severe community acquired pneumonia; mNGS; combined detection; multi-centre study; Chlamydia Psittaci
Categories
Funding
- Severe Pneumonia Cohort and Biological Sample Data Repository [SHDC2020CR5010]
- Cultivation Project of Shanghai Major Infectious Disease Research Base [20dz2210500]
- Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai [20dz2261100]
- National Innovative Research Team of High-level Local Universities in Shanghai
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This prospective study in China evaluated the use of multiple pathogen detection methods in patients with severe community acquired pneumonia (SCAP) and assessed their impact on clinical outcomes. The results showed that early combined detection improved the identification rate of pathogens and may have benefited survival. Influenza virus, S pneumoniae, and Enterobacteriaceae were identified as the leading causes of SCAP in China.
Severe Community Acquired Pneumonia (SCAP) challenges public health globally. Considerable improvements in molecular pathogen testing emerged in the last few years. Our prospective study combinedly used traditional culture, antigen tests, PCR and mNGS in SCAP pathogen identification with clinical outcomes. From June 2018 to December 2019, we conducted a multi-centre prospective study in 17 hospitals of SCAP patients within 48 hours of emergency room stay or hospitalization in China. All clinical data were uploaded into an online database. Blood, urine and respiratory specimens were collected for routine culture, antigen detection, PCR and mNGS as designed appropriately. Aetiology confirmation was made by the local attending physician group and scientific committee according to microbiological results, clinical features, and response to the treatment. Two hundred seventy-five patients were included for final analysis. Combined detection methods made identification rate up to 74.2% (222/299), while 14.4% (43/299) when only using routine cultures and 40.8% (122/299) when not using mNGS. Influenza virus (23.2%, 46/198), S. pneumoniae (19.6%, 39/198), Enterobacteriaceae (14.6%, 29/198), Legionella pneumophila (12.6%, 25/198), Mycoplasma pneumoniae (11.1%, 22/198) were the top five common pathogens. The in-hospital mortality of patients with pathogen identified and unidentified was 21.7% (43/198) and 25.9% (20/77), respectively. In conclusion, early combined detection increased the pathogen identification rate and possibly benefitted survival. Influenza virus, S. pneumoniae, Enterobacteriaceae was the leading cause of SCAP in China, and there was a clear seasonal distribution pattern of influenza viruses. Physicians should be aware of the emergence of uncommon pathogens, including Chlamydia Psittaci and Leptospira.
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