16S rDNA sequencing analysis of upper respiratory tract flora in patients with influenza H1N1 virus infection

Background

We analyzed respiratory tract bacterial flora in patients with influenza H1N1 virus infection, and investigated the role of H1N1 virus in secondary bacterial infection.

Method

A total of 12,766 operational taxonomic units (OTUs) were obtained, of which, 12,127 were identified to phylum level and 10,494 to genus level. We used next-generation sequencing technology to evaluate bacterial abundance in swab specimens from patients infected with influenza H1N1 virus or Non-H1N1 influenza and from healthy controls. Data analysis was carried out by using alpha analysis (Shannon-Wiener index and Rarefaction-Curve), beta analysis [UniFrac(abundance) and Metastats analysis], and Community-and-Phylogenesis analysis.

Results

At phylum level, Proteobacteria in patients with H1N1 virus infection (99.928 ± 0.008%) and common cold (89.019 ± 1.845%) were significantly higher than in healthy controls (26.103 ± 2.495%) (p < 0.01). In contrast, proportions of Firmicutes, Bacteroidetes, Actinobacteria, Candidate division TM7, Fusobacteria and SR1 were down-regulated (p < 0.01) in patients with H1N1 virus infection. At genus level, Pseudomonas increased >500-fold in patients with H1N1 virus infection compared with healthy controls. Ochrobactrum, Brevundimonas, Caulobacter, Aquabacterium and Serratia also increased significantly in H1N1 virus infection, while Neisseria, Prevotella, Veillonella, Actinomyces, Porphyromonas, Streptococcus, Haemophilus and Acinetobacter decreased.

Conclusion

Our data indicated that microbial abundance of the upper respiratory tract decreased in patients with H1N1 virus infection. Pseudomonas was the dominant genus among the upper respiratory tract bacterial flora in H1N1-infected patients. The changes in upper respiratory tract flora probably be closely related to the occurrence and progression of secondary bacterial infection.