Differentially Expressed Genes of Pseudomonas aeruginosa Isolates from Eyes with Keratitis and Healthy Conjunctival Sacs

Figures & data

Table 1 Characteristics of the Four Patients with Keratitis and Three Healthy Individuals

Number	Age (Years)	Sex	Clinical Status	Onset Time (Days)	Isolates
1	46	Male	Keratitis	6	P. aeruginosa
2	51	Male	Keratitis	12	P. aeruginosa
3	48	Female	Keratitis	11	P. aeruginosa
4	58	Male	Keratitis	8	P. aeruginosa
5	62	Male	–	–	P. aeruginosa
6	54	Female	–	–	P. aeruginosa
7	57	Male	–	–	P. aeruginosa

Table 2 Genes Validated by Quantitative RT-PCR

Number	log2 Fold Change	p value	Description
Q010_02058	−2.005947844	2.54E-11	Pyoverdine non-ribosomal peptide synthase/polyketide synthase Pvd L
Q010_02099	−3.203126088	9.38E-21	Acyl-homoserine lactone acylase Pvd Q
Q010_06256	12.08248173	0.009316769	Type II secretion system protein Gsp H
Q010_06248	4.012695607	3.58E-10	Type II secretion system protein Gsp E
Q010_03784	9.014665152	4.60E-104	Type 4b pilus Flp major pilin
Q010_01891	13.25174128	6.65E-10	Type 1 fimbrial protein
Q010_02816	2.997495685	0.000126626	Translocation protein in type III secretion
Q010_02805	2.453935282	2.00E-07	CesD/SycD/LcrH family type III secretion system chaperone
Q010_02806	2.274800987	1.48E-06	Type III secretion protein
Q010_03570	18.56935871	4.56E-94	Type III secretion system effector cytotoxin Exo U
Q010_02802	2.272453438	9.77E-17	Exo S synthesis protein C

Figure 1 DEGs in the P. aeruginosa isolates from keratitis and healthy conjunctival sacs. Scatter plot (A) and volcano plot (B) of the upregulated and downregulated DEGs were shown. Genes with a corrected p value of less than 0.05 found with DEseq were assigned as differentially expressed.

Figure 2 GO enrichment analysis of DEGs in the keratitis group compared with the healthy conjunctival sacs group. The top 30 enriched GO terms were shown. Enriched GO terms with a corrected p value of less than 0.05 were considered significantly enriched.

Figure 3 KEGG pathways of DEGs in the keratitis group compared with the healthy conjunctival sacs group. The top 30 upregulated (A) and the top 29 downregulated (B) KEGG pathways of the DEGs were shown. Enriched pathways with an adjusted p value of less than 0.05 were considered significantly enriched.

Figure 4 Validation of DEGs using real-time PCR. A total of 11 genes (log2 fold change >2 and adjusted p <0.05) from the significantly enriched KEGG pathway were chosen to be validated. The mRNA expression of pyoverdine metabolism-related genes (A), T2SS- and pili-related genes (B), and T3SS-related genes (C) were shown. Each genes were validated in all the P. aeruginosa isolates and the results showed as mean ± standard deviation of all P. aeruginosa isolates from keratitis or the healthy conjunctival sac group. (*p<0.05, **p<0.01, ***p<0.001, n = 3). (Control: healthy conjunctival sac).

Figure 5 Changes of the DEGs of P. aeruginosa isolates from eye with healthy conjunctival sac to keratitis. Representative slit lamp microscopy images at 24, 48, 72 h (A), clinical scores (B), and bacterial load (C) at 24 and 72 h after bacterial inoculation (1, 2, 3: healthy conjunctival sac number), and qRT-PCR results of DEGs of P. aeruginosa from murine infectious keratitis at 48 h after bacterial inoculation and healthy conjunctival sac (D) are shown (*p < 0.05, **p < 0.01, ***p < 0.001, n = 5). (Control: healthy conjunctival sac).