Abstract:

Objective

To investigate the metagenomics of gut microbiota in patients with severe pneumonia （SP） and the predictive value for the efficacy of antimicrobial agents.

Methods

Total of 126 patients with SP treated in Shijiazhuang People's Hospital from March 2022 to March 2024 were selected as the research objects， retrospectively.According to the efficacy of antibiotics， 126 cases were divided into effective group （84 cases） and ineffective group （42 cases）.Stool samples were collected from both groups for DNA extraction， followed by sequencing analysis of the V4 region of the 16S rRNA gene.The results of sequencing analysis were included in the metagenomics study.The abundance， microbial network and gene function of the patients were analyzed by independent sample t test， principal coordinate analysis（PCoA）， non-parametric analysis of covariance （PERMANOVA） and analysis of similarity （ANOSIM）.

Results

There were no significant differences in age， gender， BMI， drinking history， smoking history，complications， comorbidities and medication for underlying diseases between the two groups （all P ＞ 0.05）.The dilution curve and species accumulation curve showed that the sequencing amount of this system was sufficient and the sequencing depth was reasonable.The results of α diversity analysis showed that there were significant differences in Shannon index and Simpson index between the two groups （t = 3.958， P = 0.025；t = 6.583， P ＜ 0.001）.β diversity analysis showed that the two groups of samples were significantly separated（F = 6.665， P ＜ 0.001）.Total of 18 phyla were detected in the two groups of samples， mainly including Firmicutes， Proteobacteria， Bacteroidetes， Actinobacteria and Tenericutes.At the genus level， a total of 952 bacterial genera were detected， of which 8 genera had a relative abundance above 3%.The dominant species of the two groups were not consistent.The abundance comparison showed that： at the phylum level，the relative abundance of Firmicutes and Proteobacteria in the effective group was lower than that of the ineffective group （t = 14.889， P ＜ 0.001； t = 2.508， P = 0.013）， and the relative abundance of Bacteroidetes，Actinobacteria and Tenericutes in the effective group was higher than that in the ineffective group （t =17.776， P ＜ 0.001； t = 16.802， P ＜ 0.001； t = 1.997， P = 0.048）.At the genus level， the relative abundance of Enterococcus， Streptococcus， Klebsiella and Ruminococcus in the effective group was higher than that of the ineffective group （t = 16.663， P ＜ 0.001； t = 6.313， P ＜ 0.001； t = 9.826， P ＜ 0.001； t = 13.158， P ＜ 0.001）.The relative abundance of Bifidobacterium， Escherichia coli and Clostridium in effective group was lower than that of the ineffective group （t = 16.642， P ＜ 0.001； t = 18.814， P ＜ 0.001； t = 12.762， P ＜ 0.001）.Network analysis showed that the number of nodes and edges of the effective group was significantly higher than that of the ineffective group， and the structure of the microbial network was more complex than that of the ineffective group.Gene function enrichment analysis showed that the gene functions with higher relative abundance in the effective group were ATP binding， IMP biosynthesis process and chlorate biosynthesis process.The functions of genes with higher relative abundance in the ineffective group were cytoplasm and structural components of ribosomes.Pathway enrichment analysis showed that the signaling pathways with high relative abundance in the effective group were starch degradation， sucrose degradation and isoleucine biosynthesis.The signaling pathways with high relative abundance in the ineffective group were isoprene biosynthesis and methylerythritol phosphate pathway.

Conclusions

Enterococcus， Streptococcus and Klebsiella were the most abundant bacteria in samples of patients with SP effectively treated with antibiotics.Enterococcus， Escherichia coli and Bifidobacterium were the most abundant bacteria in samples of patients with SP ineffectively treated with antibiotics， and the metagenomics of intestinal microbial community has a certain predictive value for the efficacy of antibiotics.

Key words: Intestinal microorganisms, Severe pneumonia, Metagenomics, Antibiotic