Background
Methods
Collection of samples and bacterial identification
Biofilm detection
Visualization of biofilm by scanning-electron microscopy (SEM) and confocal laser scanning microscope (CLSM)
Antibiotic susceptibility of ocular E. coli
S. no |
E. coli strain | Ocular sample | Patient diagnosis | Resistance to antibiotics (µg/disc) | Biofilm production by TCP method ± |
---|---|---|---|---|---|
1 | L-1339/2013 | Conjunctival swab | Conjunctivitis | Ce, Cef, Ci, Ga, Ge, Mo, Of | − |
2 | L-1216/2010 | Vitreous | Endophthalmitis | Ci | + |
3 | L-2561/2013 | Vitreous | Endophthalmitis | None | + |
4 | L-1920/2011 | Corneal scraping | Keratitis | Am, Ce, Cef, Ch, Ci, Ga, Ge, Mo, Of | + |
5 | L-3781/2010 | Vitreous | Endophthalmitis | Ce | + |
6 | L-3484/2010 | Vitreous | Endophthalmitis | None | − |
7 | L-1573/2013 | Vitreous | Endophthalmitis | Ci, Mo, Of | + |
8 | L-494/2011 | Vitreous | Endophthalmitis | Am, Ce, Cef, Ci, Ga, Ge, Mo, Of | + |
9 | L-223/2014 | Corneal scraping | Keratitis | Ce, Cef, Ci, Ga, Mo, Of | + |
10 | L-304/2014 | Corneal scraping | Keratitis | Ce, Cef | + |
11 | L-811/2014 | Lacrimal sac | Dacryocystitis | Ce, Cef, Ci, Ga, Ge, Mo, Of | + |
12 | L-823/2014 | Corneal scraping | Keratitis | Cef | + |
DNA microarray analysis
Annotation of the genes
Validation of microarray data by real time PCR (RT-PCR)
Results
Ocular isolates of E. coli and antibiotic susceptibility
Biofilm potential of ocular isolates of E. coli
E. coli strain | Sample | Amikacin | Ceftazidime | Cefuroxime | Chloramphenicol | Ciprofloxacin | Gentamicin | Streptomycin | Cefotaxime |
---|---|---|---|---|---|---|---|---|---|
Antibiotics MIC (µg/ml) | |||||||||
L-1339/2013 | Conjunctival swab | 12 | 24 | 48 | 16 | 12 | 32 | 24 | 32 |
L-1216/2013 | Vitreous | 16 | 12 | 28 | 20 | 12 | 12 | 16 | 16 |
L-2561/2013 | Vitreous | 6 | 2 | 4 | 4 | 0.5 | 2 | 12 | 1 |
L-1920/2011 | Corneal scraping | 64 | 16 | 32 | 32 | 12 | 16 | 8 | 12 |
L-3781/2010 | Vitreous | 12 | 16 | 8 | 6 | 0.5 | 2 | 16 | 16 |
L-3484/2010 | Vitreous | 12 | 2 | 4 | 6 | 1 | 2 | 8 | 2 |
L-1573/2010 | Vitreous | 6 | 4 | 8 | 4 | 4 | 4 | 8 | 1 |
L-494/2011 | Vitreous | 64 | 16 | 32 | 6 | 8 | 16 | 12 | 12 |
L-223/2014 | Corneal scraping | 12 | 24 | 48 | 8 | 4 | 4 | 16 | 32 |
L-304/2014 | Corneal scraping | 6 | 24 | 32 | 6 | 0.5 | 2 | 8 | 1 |
L-811/2014 | Lacrimal sac | 6 | 16 | 32 | 4 | 4 | 32 | 12 | 32 |
L-823/2014 | Corneal scraping | 6 | 2 | 24 | 2 | 0.5 | 4 | 6 | 1 |
Expression of genes in E. coli biofilm forming cells
Functional annotation of differentially expressed genes in E. coli biofilm forming cells
Functional group classification based on COG | Beloin et al. [40] | Domka et al. [42] | Hancock et al. [43] | This study | ||||
---|---|---|---|---|---|---|---|---|
E. coli strain |
E. coli K-12 |
E. coli K-12 | ABU E. coli
| Ocular E. coli
| ||||
Regulation | Up | Down | Up | Down | Up | Down | Up | Down |
Cellular processes and signaling | ||||||||
M. Cell wall/membrane/envelope biogenesis | 19 | 9 | 9 | 8 | 4 | 25 | 14 | 14 |
D. Cell cycle control, mitosis and meiosis | 2 | 1 | 0 | 0 | 3 | 6 | 14 | 14 |
N. Cell motility | NA | NA | 32 | 1 | 1 | 0 | 7 | 19 |
O. Post-translational modification, protein turnover, and chaperones | 13 | 13 | 13 | 7 | 25 | 56 | 8 | 11 |
T. Signal transduction mechanisms | 5 | 0 | 11 | 3 | 12 | 2 | 7 | 5 |
U. Intracellular trafficking, secretion, and vesicular transport | NA | NA | 28 | 1 | 2 | 17 | 8 | 19 |
V. Defense mechanisms | NA | NA | 4 | 0 | 1 | 0 | 1 | 0 |
Sub-total | 39 | 23 | 97 | 20 | 48 | 106 | 59 | 82 |
Information storage and processing | ||||||||
A. Transcription, RNA processing and modification | 11 | 5 | 17 | 7 | 44 | 8 | 12 | 6 |
L. Replication, recombination and repair | 10 | 7 | 5 | 1 | 17 | 14 | 16 | 10 |
Sub-total | 21 | 12 | 22 | 8 | 61 | 22 | 28 | 16 |
Metabolism | ||||||||
C. Energy production and conversation | 23 | 9 | 23 | 16 | 12 | 34 | 12 | 18 |
E. Amino acid transport and metabolism | 9 | 22 | 20 | 15 | 5 | 36 | 20 | 17 |
F. Nucleotide transport and metabolism | 0 | 3 | 8 | 1 | 6 | 8 | 5 | 5 |
G. Carbohydrate transport and metabolism | 16 | 22 | 27 | 5 | 13 | 23 | 26 | 12 |
H. Coenzyme transport and metabolism | 3 | 5 | 6 | 1 | 9 | 14 | 5 | 7 |
I. Lipid transport and metabolism | 7 | 0 | 5 | 3 | 3 | 8 | 2 | 5 |
P. Inorganic ion transport and metabolism | 12 | 6 | 24 | 9 | 14 | 7 | 4 | 8 |
Q. Secondary metabolites biosynthesis, transport and catabolism | 2 | 1 | 5 | 0 | 2 | 7 | 5 | 2 |
Sub-total | 72 | 68 | 118 | 50 | 64 | 137 | 79 | 74 |
Unknown and general prediction only | 121 | 86 | 53 | 6 | 57 | 23 | 24 | 29 |
Total | 253 | 189 | 290 | 84 | 230 | 288 | 190 | 201 |