Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India
Abstract
:1. Introduction
2. Results
2.1. Antibiotic Susceptibility
2.2. General Features of the Genomes
2.3. Acquired Resistance Genes
2.4. Possession of exoU and Mutations in the DNA Mismatch Repair System
2.5. Sequence Type Analysis and Phylogenetics
3. Discussion
4. Materials and Methods
4.1. P. aeruginosa Strains and Susceptibility Testing
4.2. Genomic Sequencing
4.3. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Strain Number | Fluoroquinolones * | Aminoglycosides | β-Lactams | Poly-Peptide | ||||
---|---|---|---|---|---|---|---|---|
2nd Generation | 3rd Generation | Penicillin 4th Generation | Carba-Penem | Cephalosporin 3rd Generation | ||||
Cipro µg/mL ≤1, 2, ≥4 # |
Levo µg/mL ≤2, 4, ≥8 |
Genta µg/mL ≤4, 8, ≥16 |
Tobra µg/mL ≤4, 8, ≥16 |
Pipera µg/mL ≤16 |
Imi µg/mL ≤2, 4, ≥8 |
Ceftaz µg/mL ≤8, 16, ≥32 |
PMB µg/mL ≤2, 4, ≥8 | |
MIC/ MBC | MIC/ MBC | MIC/ MBC | MIC/ MBC | MIC/ MBC | MIC/ MBC | MIC/ MBC | MIC/ MBC | |
123 | 1/1 | 1/1 | 0.25/0.5 | 4/4 | 8/16 | 4(I)/8 | 2/2 | 1280(R)/1280 |
126 | 0.5/1 | 0.5/1 | 0.5/1 | 0.25/0.5 | 8/16 | 8(R)/16 | 128(R)/256 | 1/1 |
127 | 1/2 | 0.25/1 | 2/4 | 32(R)/128 | 4/16 | 4(I)/8 | 128(R)/256 | 0.5/1 |
162 | 0.5/1 | 0.5/1 | 0.25/0.5 | 0.25/1 | 8/8 | 4(I)/4 | 2/4 | 0.25/0.5 |
169 | 2(I)/4 | 0.25/0.5 | 0.25/0.5 | 0.25/0.5 | 4/8 | 2/4 | 1/2 | 0.25/0.25 |
176 | 0.5/1 | 0.25/0.5 | 0.25/0.5 | 0.25/0.5 | 4/8 | 2/8 | 2/4 | 0.25/0.5 |
181 | 1/4 | 0.25/0.5 | 0.25/0.5 | 0.25/0.5 | 32(R)/64 | 4(I)/8 | 16(I)/32 | 0.5/1 |
182 | 1/2 | 0.25/0.5 | 0.25/0.5 | 0.25/0.5 | 4/8 | 8(R)/16 | 1/2 | 0.25/0.5 |
223 | 64(R)/128 | 1/2 | 0.5/1 | 0.5/1 | 160(R)/320 | 1/2 | 16(I)/32 | 2/4 |
224 | 16(R)/32 | 1/2 | 0.25/0.5 | 0.25/0.5 | 8/16 | 64(R)/128 | 16(I)/32 | 1/2 |
225 | 64(R)/128 | 16(R)/32 | 0.5/2 | 1/2 | 16/32 | 64(R)/128 | 8/16 | 0.25/0.5 |
227 | 64(R)/128 | 64(R)/128 | 0.5/1 | 0.25/1 | 16/32 | 16(R)/32 | 16(I)/32 | 0.25/0.5 |
233 | 8(R)/16 | 1/2 | 1/2 | 105/1 | 16/32 | 4(I)/8 | 160(I)/320 | 0.5/1 |
235 | 16(R)/32 | 0.5/1 | 2/4 | 0.5/1 | 64(R)/128 | 4(I)/8 | 64(I)/128 | 0.25 |
188 | 2(I)/4 | 1/2 | 0.5/1 | 32(R)/64 | 16/65 | 0.5/1 | 4/8 | 2/4 |
189 | 0.25/1 | 1/2 | 0.25/0.5 | 16(R)/32 | 4/8 | 2/1 | 8/16 | 2/4 |
193 | 1/1 | 0.25/1 | 0.25/0.25 | 0.25/0.5 | 4/8 | 2/4 | 2/2 | 0.5/1 |
198 | 1280(R)/2560 | 320(R)/1280 | 2560(R)/5120 | 16(R)/16 | 8/8 | 1/2 | 8/8 | 4(I)/4 |
202 | 640(R)/1280 | 320(R)/640 | 8(I)/32 | 320(R)/640 | 16/64 | 8(R)/32 | 8/32 | 0.25/0.25 |
206 | 1/1 | 0.5/0.5 | 1/1 | 0.25/0.5 | 8/8 | 2/4 | 2/4 | 0.25/0.5 |
216 | 64(R)/128 | 4 (I)/8 | 1/2 | 0.5/2 | 160(R)/320 | 16(R)/32 | 64(R)/128 | 64(R)/128 |
217 | 64(R)/128 | 32(R)/64 | 1/2 | 1/2 | 64(R)/128 | 8(R)/16 | 32(R)/64 | 0.25/1 |
218 | 8(R)/16 | 1/2 | 0.5/1 | 0.5/1 | 160(R)/320 | 8(R)/16 | 64(R)/128 | 1/4 |
219 | ≥5120(R)/≥5120 | 640(R)/1280 | ≥5120(R)/≥5120 | 1280(R)/2560 | 2560(R)/5120 | 40(R)/80 | 16(I)/32 | 0.25/1 |
220 | 2(I)/4 | 0.25/0.5 | 0.5/1 | 0.5/1 | 0.25/0.5 | 8(R)/16 | 160(R)/320 | 8(R)/16 |
221 | 2560(R)/5120 | 2560(R)/5120 | 2560(R)/5120 | 2560(R)/5120 | 64(R)/128 | 16(R)/32 | 32(R)/64 | 0.25/1 |
Genes | Australian Isolates | Indian Isolates | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123 | 126 | 127 | 162 | 169 | 176 | 181 | 182 | 223 | 224 | 225 | 227 | 233 | 235 | 188 | 189 | 193 | 198 | 202 | 206 | 216 | 217 | 218 | 219 | 220 | 221 | |
Aminoglycoside resistance genes | ||||||||||||||||||||||||||
aph(3’)-IIb | ||||||||||||||||||||||||||
aph(6)-Id | l; | |||||||||||||||||||||||||
rmtD2 | ||||||||||||||||||||||||||
rmtB | ||||||||||||||||||||||||||
aph(3’)-VI | ||||||||||||||||||||||||||
aph(3’)-lIb | ||||||||||||||||||||||||||
aph(3’’)-Ib | ||||||||||||||||||||||||||
aac(6’)-Ib3 | ||||||||||||||||||||||||||
aac(3)-IId | ||||||||||||||||||||||||||
aadA1 | ||||||||||||||||||||||||||
aac(6’)-Ib-cr | ||||||||||||||||||||||||||
Fluoroquinolone resistance genes | ||||||||||||||||||||||||||
crpP | ||||||||||||||||||||||||||
qnrVC1 | ||||||||||||||||||||||||||
Beta-lactamase resistance genes | ||||||||||||||||||||||||||
blaPAO | ||||||||||||||||||||||||||
blaLCR-1 | ||||||||||||||||||||||||||
blaOXA-485 | ||||||||||||||||||||||||||
blaOXA-486 | ||||||||||||||||||||||||||
blaOXA-488 | ||||||||||||||||||||||||||
blaOXA-396 | ||||||||||||||||||||||||||
blaOXA-395 | ||||||||||||||||||||||||||
blaOXA-50 | ||||||||||||||||||||||||||
blaOXA-10 | ||||||||||||||||||||||||||
blaTEM-1B | ||||||||||||||||||||||||||
blaVIM-2 | ||||||||||||||||||||||||||
blaPME-1 | ||||||||||||||||||||||||||
blaPAU-1 | ||||||||||||||||||||||||||
Sulphonamide, tetracycline, macrolide, fosfomycin, and chloramphenicol resistance genes | ||||||||||||||||||||||||||
sul1 | ||||||||||||||||||||||||||
tet(G) | ||||||||||||||||||||||||||
mph(E) | ||||||||||||||||||||||||||
mph(A) | ||||||||||||||||||||||||||
msr(E)* | ||||||||||||||||||||||||||
fosA | ||||||||||||||||||||||||||
catB |
P. aeruginosa Isolates | Total Variants | Variant Complex | Variants Insertions | Variants Deletions | Variants MNP | Variant SNP |
---|---|---|---|---|---|---|
123 | 28,279 | 1593 | 187 | 163 | 398 | 25,938 |
126 | 26,258 | 1416 | 164 | 159 | 355 | 24,164 |
127 | 25,760 | 1362 | 163 | 176 | 391 | 23,668 |
162 | 50,999 | 3481 | 281 | 257 | 951 | 46,029 |
169 | 50,283 | 3359 | 269 | 245 | 922 | 45,488 |
176 | 26,065 | 1372 | 168 | 161 | 342 | 24,022 |
181 | 22,536 | 1063 | 162 | 133 | 283 | 20,895 |
182 | 25,684 | 1359 | 172 | 180 | 368 | 23,605 |
223 | 25,672 | 1358 | 167 | 176 | 402 | 23,568 |
224 | 26,376 | 1435 | 163 | 165 | 353 | 24,260 |
225 | 28,070 | 1566 | 167 | 156 | 385 | 25,796 |
227 | 28,000 | 1560 | 162 | 154 | 370 | 25,754 |
233 | 52,392 | 3590 | 285 | 263 | 956 | 47,298 |
235 | 24,919 | 1349 | 162 | 171 | 354 | 22,883 |
188 | 25,833 | 1435 | 164 | 154 | 351 | 23,729 |
189 | 25,910 | 1458 | 165 | 155 | 365 | 23,767 |
193 | 26,567 | 1445 | 180 | 147 | 389 | 24,406 |
198 | 50,631 | 3503 | 280 | 236 | 945 | 45,667 |
202 | 49,981 | 3461 | 257 | 236 | 902 | 45,125 |
206 | 76,180 | 6449 | 336 | 371 | 1653 | 67,271 |
216 | 28,166 | 1548 | 183 | 164 | 433 | 25,838 |
217 | 51,119 | 3575 | 290 | 226 | 944 | 46,084 |
218 | 29,161 | 1676 | 182 | 181 | 430 | 26,692 |
219 | 50,507 | 3484 | 273 | 237 | 925 | 45,588 |
220 | 50,180 | 3452 | 267 | 234 | 894 | 45,332 |
221 | 50,030 | 3477 | 260 | 237 | 906 | 45,150 |
P. aeruginosa Isolates | Type III Secretion System Genes | mutL | mutS | uvrD |
---|---|---|---|---|
123 | exoU | 1 SNP | 0 | 1 complex |
126 | exoU/exoS | 0 | 0 | 0 |
127 | exoU | 0 | 1 MNP | 1 MNP, 1 complex |
162 | exoU | 1 SNP | 0 | 2 SNP, 1 MNP, 2 complexes |
169 | exoU | 1 SNP | 1 complex | 2 SNP, 2 MNP, 1 complex |
176 | exoS | 1 SNP | 0 | 1 SNP |
181 | exoS | 0 | 0 | 0 |
182 | exoS | 0 | 0 | 1 MNP 1complex |
223 | exoS | 0 | 1 SNP | 1 MNP, 1 complex |
224 | exoS | 1 SNP | 0 | 1 MNP, 1 complex |
225 | exoS | 0 | 0 | 2 SNP, 2 MNP, 1 complex |
227 | exoS | 0 | 0 | 2 SNP, 2 MNP, 1 complex |
233 | exoU | 0 | 0 | 1 MNP, 1 complex |
235 | exoS | 0 | 0 | 0 |
188 | exoS | 0 | 0 | 1 MNP, 1 complex |
189 | exoS | 1 SNP | 0 | 1 MNP, 1 complex |
193 | exoS | 0 | 0 | 0 |
198 | exoU | 2 SNP | 0 | 1 SNP, 3 complexes |
202 | exoU | 1 SNP | 1 complex | 1 SNP, 2 MNP, 2 complexes |
206 | exoS | 1 MNP | 1 complex | 0 |
216 | exoS | 0 | 0 | 0 |
217 | exoU | 2 SNP | 1 complex | 1 SNP, 2 MNP, 1 complex |
218 | exoS | 0 | 0 | 0 |
219 | exoU | 2 SNP | 0 | 1 SNP, 1 MNP, 2 complexes |
220 | exoU | 1 SNP | 1 complex | 1 SNP, 2 MNP, 2 complexes |
221 | exoU | 1 SNP | 1 complex | 1 SNP, 2 MNP, 2 complexes |
P. aeruginosa Isolates | Sequence Types | Core Genes | Shell Genes | Pan/Total Genes |
---|---|---|---|---|
123 | ST218 | 5496 | 508 | 6004 |
126 | ST2726 | 5483 | 712 | 6195 |
127 | ST845 | 5483 | 938 | 6421 |
162 | ST298 | 5439 | 905 | 6344 |
169 | ST1027 | 5456 | 694 | 6150 |
176 | ST709 | 5547 | 1112 | 6659 |
181 | ST244 | 5588 | 1047 | 6662 |
182 | ST27 | 5486 | 1096 | 6582 |
223 | ST17 | 5471 | 1232 | 6703 |
224 | ST168 | 5483 | 607 | 6090 |
225 ¤ | ST233 | 5515 | 1338 | 6853 |
227 ¤ | ST233 | 5493 | 1304 | 6797 |
233 | NEWST | 5440 | 624 | 6064 |
235 | ST262 | 5470 | 540 | 6010 |
188 * | ST491 | 5490 | 535 | 6025 |
189 * | ST491 | 5492 | 531 | 6023 |
193 | ST760 | 5490 | 594 | 6084 |
198 † | ST308 | 5454 | 1428 | 6882 |
202 # | ST316 | 5425 | 1505 | 6930 |
206 | NEWST | 5331 | 1084 | 6415 |
216 | ST1527 | 5480 | 1488 | 6968 |
217 | ST1047 | 5448 | 1173 | 6621 |
218 | ST3083 | 5513 | 488 | 6001 |
219 † | ST308 | 5451 | 1796 | 7247 |
220 # | ST316 | 5430 | 948 | 6378 |
221 # | ST316 | 5425 | 1511 | 6936 |
PA7 | ST1196 | 3599 | 4586 | 8185 |
PA14 | ST253 | 5436 | 790 | 6226 |
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Khan, M.; Stapleton, F.; Summers, S.; Rice, S.A.; Willcox, M.D.P. Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India. Antibiotics 2020, 9, 600. https://doi.org/10.3390/antibiotics9090600
Khan M, Stapleton F, Summers S, Rice SA, Willcox MDP. Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India. Antibiotics. 2020; 9(9):600. https://doi.org/10.3390/antibiotics9090600
Chicago/Turabian StyleKhan, Mahjabeen, Fiona Stapleton, Stephen Summers, Scott A. Rice, and Mark D. P. Willcox. 2020. "Antibiotic Resistance Characteristics of Pseudomonas aeruginosa Isolated from Keratitis in Australia and India" Antibiotics 9, no. 9: 600. https://doi.org/10.3390/antibiotics9090600