An observational study in Pneumonia, Next-generation Sequencing and Microbiome, sponsored by Shanghai General Hospital, China. Recruiting at 1 site in China. Per ClinicalTrials.gov, last updated 2026-04-23.
Sponsored by Shanghai General Hospital, China · Observational
Monitoring of antimicrobial resistance (AMR) based on metagenomics analyses in pneumonia patients is critical for optimizing clinical diagnosis and treatment and improving clinical prognosis. This study is designed to ask the following key questions:
This is a historical prospective obsevational study. Patients diagnosed with severe and mild pneumonia are recruited continously from four hospitals (Shanghai General Hospital, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuhan Union Hospital, and Huanggang Central Hospital) in China during March, 2019 to March, 2025.
Next-generation sequencing: Metagenomics and metatranscriptomic libraries undergo next-generation sequencing using the Illumina Novaseq 6000 platform.
Microbiome analysis: using KneadData (v0.10.0) reference from the human genome (GRCH38 reference database) to filter out the quality control of illumina sequencing data in Virosaurus download virus genome data sets for reference, bowtie2 (v2.3.4.1) (genome coverage >30%, depth >1X) was used to locate and analyze the post-host sequence, and then the "samtools idxstats" command was used to calculate the classification and relative abundance of viruses. Meanwhile, in order to obtain the annotation information of bacteria at the species level, PhyloFlash (v3.4) was used to calculate read counts for 16S rRNA genes in the SILVA database, selecting similarity greater than or equal to 98% as a threshold. Using eukaryotic pathogen genome database EUPATHDB46 as reference, bowtie2 and samtools were used for qualitative and quantitative analysis of fungal pathogens.
The criteria for determining the cause of respiratory infection are: (1) existing species known to be associated with human disease (ICD-10), (2) previously unidentified potential novel pathogens (only DNA and RNA viruses whose genera or families have previously been shown to infect mammals), and (3) possible symbiotic bacteria not included.
Analysis of AMR: by comparing the sequence similarity between the sequencing fragments and known drug resistance genes, the detection content can determine whether drug resistance genes exist, and suggest drug resistance caused by modification, inactivation, repression and other drug resistance genes.
Drug resistance genes detection: genes related to drug resistance recorded in CARD (Comprehensive Antibiotic Resistance Database) and ARG-ANNOT database. In this assay, only functional genes with drug resistance activities such as modification, inactivation, and repression, as well as pathway and target changes caused by some point mutations, were reported.
Genetic diversity was computed as the mean pairwise genetic distance within a group. Maximum likelihood phylogenetic trees were constructed using RaxML with a general time-reversible nucleotide substitution model and 1000 bootstraps. The genetic distance between sequences was calculated using MEGAX, with a bootstrap method for variance estimation.
1,564 studies on the registry are indexed under Pneumonia; 265 are open to participants now.
This study's planned enrollment of 800 is above the median of 252 across 535 observational studies indexed under Pneumonia.
Browse Pneumonia studies →Shanghai General Hospital, China is the lead sponsor of 8 studies on the registry; 7 are open to participants now.
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Pneumonia patients from four centers in China during 2022-2025.
Go through the criteria one by one — yes, no or not sure — and take the list to your doctor or the study team. Kept in this browser only.
Exclusion Criteria:
Patients clinically diagnosed as severe pneumonia are diagnosed according to the Guidelines for the diagnosis and Treatment of community-acquired pneumonia in Adults (2019 edition) formulated by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA), who meet 1 of the following major criteria or ≥3 minor criteria can be diagnosed. The diagnostic criteria for severe pneumonia in children were adopted by the British Thoracic Society (BTS) in 2011.
Patients clinically diagnosed as severe pneumonia and mild pneumonia are diagnosed according to the Guidelines for the diagnosis and Treatment of community-acquired pneumonia in Adults (2019 edition) formulated by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). The diagnostic criteria for severe and mild pneumonia in children were adopted by the British Thoracic Society (BTS) in 2011
Microbiome composition
a collection of microbial communities detected in the biospecimen
Time frame: during the study period, 2019-2025
Alpha diversity
the diversity within a particular area or ecosystem
Time frame: during the study period, 2019-2025
Prevalence of bacterial resistance genes
the number of bacterial resistance genes divided by the number of biospecimen
Time frame: during the study period, 2019-2025
Beta diversity
a comparison of of diversity between ecosystems, usually measured as the amount of species change between the ecosystems
Time frame: during the study period, 2019-2025
Plan to share: Undecided — The datasets used in this study are available upon request to the principle investigator.
Ran from Aug 2024 to primary completion in Apr 2026, 20 months.
Of 210 non-industry observational studies under Pneumonia, half reached primary completion within 27 months of starting (the median), counting those still running; a quarter within 14 and three quarters within 57. This study's 20 months is below that.
Counting every sponsor, half of 223 studies reached it within 27 months; a quarter within 13 and three quarters within 53.
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Shanghai General Hospital, China