Aetiology of severe community acquired pneumonia in adults identified by combined detection methods: a multi-centre prospective study in China

Abstract

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 .

Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study

“…78 patients including 21 patients with PTB, eight patients with newly diagnosed LC, and 49 patients with CAP admitted to our hospital between February 2021 and December 2021 were enrolled. All these patients were diagnosed via case history, chest radiography, and blood markers examinations following Chinese clinical guidelines ( Commission, N.H., 2020 ; He et al., 2021 ; Qu et al., 2022 ). We also collected the demographic data and medical history of all study participants using a set of questionnaires, such as age, gender, ethnicity, body mass index (BMI), smoking history, smoking amount, comorbidities, lifestyle, eating habits and so on.…”

A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

“…Given the lack of standard threshold criteria for interpreting mNGS results, we used the criteria derived and revised from previous studies. [36][37][38][39][40] The mNGS results were considered as positive if one of the following thresholds were met, and a literature evidence of its pulmonary pathogenicity is available: (i) culture/PCR and mNGS identified the same microbe;…”

Identification ofMycoplasma pneumoniae-associated pneumonia cases among hospitalized patients using CLART® microarray technology

“…4,9 Among these microbes, M. pneumoniae accounts for a fairly high percentage of CAP cases in adult and pediatric populations, and nearly half of the affected individuals require hospitalization. 4,10–14 Although M. pneumoniae is an important etiological agent of CAP, there are challenges associated with its diagnosis mainly because of its fastidious nature, seroprevalence, and possible transient asymptomatic carriage. Therefore, it is important to explore and develop efficient techniques for the detection of M. pneumoniae as an atypical pathogen of CAP.…”