nankaiwolf/pcptocap

Microbiome analysis of PCP, comparing to CAP.

Metagenomic Analysis of Lower Respiratory Tract of Pneumocystic Pneumonia Patients

Dexun Zhou1, Yu Xu1,2, Wen Xi1, Ying Shang1, Zhengwu Yang1, Ran Li1, Zhancheng Gao1

Affiliations:

1. Department of Respiratory and Critical Care Medicine, Peking University People's Hospital
2. Department of Respiratory and Critical Care Medicine, Beijing Jishuitan Hospital

Abstract: Background: To analysis the metagenomic characteristics of lower respiratory tract of pneumocystic pneumonia (PCP) patients. Methods: We recruited 6 PCP patients confirmed by PCR and microscopic examination as PCP group, and 6 community acquired pneumonia (CAP) patients as CAP group in critical care unit, from November, 2019, to April, 2021. We extracted DNA from the bronchoalveolar lavage fluid (BALF) of the two groups, and applied the next generation sequencing and bioinformatic analysis. Results: 6 patients in PCP group (5 males) had the age of 68(9.0) year-old, while 6 patients in CAP group (4 males) had the age of 67(26.3) year-old, and the differences had no statistically significance (P＞0.05). All patients in PCP group had long-time corticosteroid use for underlying diseases (prednisone ≥20 mg/day, ≥2 months), including dermatomyositis, idiopathic pulmonary fibrosis, Evans Syndrome, radiation pneumonia (for radiotherapy of esophageal cancer), ANCA associated vasculitis, and lymphoma. Shannon index of PCP and CAP groups were 4.1(0.53) versus 3.6(1.35) (P = 0.18), and Pielou index were 0.55(0.052) versus 0.47(0.165) (P = 0.48), and the differences had no statistically significance. The PCoA demonstrated no statistically significant difference between these groups (P = 0.22). The dominant phylum in both PCP and CAP groups was Proteobacteria, but there was no difference between two groups (53.5(22.90)% versus 43.4(45.14)%, P = 0.5887 > 0.05). Alphaproteobacteria (P＝0.010), Crenarchaeota (P＝0.009), Thermoprotei (P＝0.009), Sulfolobales (P＝0.009), Caulobacterales (P＝0.037), Rhodospirillales (P＝0.016), Selenomonadales (P＝0.036), Legionellales (P＝0.037), Haloferacales (P＝0.020), Chloroflexi (P＝0.009), and Cardiobacteriales (P＝0.022) were enriched in PCP group by LEfSe analysis. The expression of K03257, K02937, K02951 were increased in PCP (P-values were 0.044, 0.044, and 0.024, respectively) in ontology analysis, while the expression of K03283, K04282, K09441, K08517, K12877, K07949, and K03462 were decreased (P values were 0.029, 0.034, 0.046, 0.048, 0.006, 0.018, and 0.046, respectively). Conclusion: The dominant phylum of lower respiratory tract of PCP was Proteobacteria, and there were also multiple enriched classes and orders. However, the diversities between PCP and CAP had no significant differences. The ontology expressions may suggest some potential mechanisms of PCP pathogenesis. Keywords: Pneumocystic Pneumonia, metagenome, next generation sequencing, microbiome