Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain
Abstract
:1. Introduction
2. Materials and Methods
2.1. Pseudomonas aeruginosa Isolates and Antimicrobial Susceptibility
2.2. Sequence Analysis
2.3. Ciprofloxacin Resistance Determinants
2.4. Genetic Context of crpP Gene
2.5. Statistical Analysis
2.6. Accession Numbers
3. Results
3.1. Ciprofloxacin Resistance in STEP and SUPERIOR P. aeruginosa Isolates
3.2. P. aeruginosa Genome Analysis and Molecular Typing
3.3. Acquired Resistance Genes
3.4. Mutational Resistome
3.5. crpP-Encoding Genes
3.6. crpP-Carrying Pathogenicity Genomic Islands (PAGI)
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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CT-R | CT-S | p-Value | Odd Ratio (95%CI) | ||||
---|---|---|---|---|---|---|---|
Total No. | CIP-R No. (%) | CIP-S No. (%) | CIP-R No. (%) | CIP-S No. (%) | |||
STEP | 396 | 19 (90.5) | 2 (9.5) | 128 (34.1) | 247 (65.9) | <0.001 | 18.2 (4.3–163.5) |
SUPERIOR | 80 | 6 (85.7) | 1 (14.3) | 22 (30.1) | 51 (69.9) | 0.006 | 13.4 (1.5–649.5) |
Total (n = 55) | CIP a Susceptibility Profile * | p-Value | Odd Ratio (95%CI) | ||
---|---|---|---|---|---|
I [No. (%)] (n = 9) | R [No. (%)] (n = 46) | ||||
ARG b | 6 (10.9) | 0 | 6 (13) | 0.57 | 0 (0–4.55) |
qnrS2 | 2 (3.6) | 0 | 2 (4.3) | 0.57 | 0 (0–4.55) |
aac(6′)-Ib-cr | 6 (10.9) | 0 | 6 (13) | 1 | 0 (0–28.23) |
QRDR c | 47 (85.5) | 5 (55.6) | 42 (91.3) | 0.02 | 7.90 (1.12–59.46) |
GyrA | 42 (76.4) | 4 (44.4) | 38 (82.6) | 0.03 | 5.69 (0.99–35.95) |
GyrB | 1 (1.8) | 0 | 1 (2.2) | NA | NA |
ParC | 40 (72.7) | 3 (33.3) | 37 (80.4) | 0.01 | 7.81 (1.37–57.90) |
ParE | 26 (47.3) | 4 (44.4) | 22 (47.8) | 1 | 1.14 (0.21–6.54) |
CrpP d | 36 (65.5) | 8 (88.9) | 28 (60.9) | 0.14 | 0.20 (0.01–1.70) |
CrpP1 | 23 (41.8) | 2 (22.2) | 21 (45.6) | 0.27 | 2.89 (0.48–31.41) |
CrpP2 | 4 (7.2) | 3 (33.3) | 1 (2.2) | 0.01 | 0.05 (0.001–0.72) |
CrpP3 | 4 (7.2) | 0 | 4 (8.7) | NA | NA |
CrpP4 | 3 (5.4) | 1 (11.1) | 2 (4.3) | 0.07 | 11.89 (0.55–769.73) |
CrpP5 | 1 (1.8) | 1 (11.1) | 0 | NA | NA |
CrpP6 | 1 (1.8) | 0 | 1 (2.2) | NA | NA |
nalCe | 48 (87.3) | 6 (66.7) | 42 (91.3) | 0.08 | 0.20 (0.03–1.70) |
nfxBe | 4 (7.3) | 2 (22.2) | 2 (4.3) | 0.12 | 5.97 (0.38–95.35) |
Enzyme (No. of Isolates) | Gene (No. of Isolates) | Mutations (nt) * | Missense Mutations (aa) * | Clonal Complex (No. of Isolates) | CIP-MIC Interpretation (No. of Isolates) |
---|---|---|---|---|---|
CrpP1 (23) | crpP1.1 (20) | 20(A-G), 192(C-T) | G7D | CC175 (10), CC348 (5), CC253 (3), CC179 (1), CC308 (1) | I (2), R (18) |
crpP1.2 (2) | 20(A-G), 66(C-T) | CC554 (2) | R (2) | ||
crpP1.3 (1) | 1 (T-C), 20(A-G), 192(C-T) | CC235 (1) | R (1) | ||
CrpP2 (4) | crpP2 (4) | 19(CA-GG), 39(G-A), 45(T-C), 76(C-A), 81(C-T), 123(T-C), 183(A-G), 192(C-T) | G7H, I26L | CC244 (4) | I (3), R (1) |
CrpP3 (4) | crpP3 (4) | 19(CA-GG), 39(G-A), 45(T-C), 47(A-T), 76(C-A), 81(C-T), 123(T-C), 183(A-G), 192(C-T) | G7H, F16Y, I26L | CC244 (3), CC313 (1) | I (1), R (3) |
CrpP4 (3) | crpP4.1 (1) | 11(A-G), 20(A-G), 138(A-G) | K4R, G7D | CC27 (1) | I (1) |
crpP4.2 (1) | 11(A-G), 20(A-G), 192(C-T) | CC446 (1) | R (1) | ||
crpP4.3 (1) | 11(A-G), 18(T-C), 20(A-G), 174(A-G), 183 (A-G) | CC179 (1) | R (1) | ||
CrpP5 (1) | crpP5 (1) | 19(CA-GG), 39(G-A), 45(CT-TC), 76(C-A), 81(C-T), 123(T-C), 162(A-G), 183(A-G), 192(C-T) | G7H, F16L, I26L | CC971 (1) | I (1) |
CrpP6 (1) | crpP6 (1) | 33(A-G), 73(insGCTTACGG) | I26fs | CC499 (1) | R (1) |
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Hernández-García, M.; García-Castillo, M.; García-Fernández, S.; López-Mendoza, D.; Díaz-Regañón, J.; Romano, J.; Pássaro, L.; Paixão, L.; Cantón, R. Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain. Microorganisms 2021, 9, 388. https://doi.org/10.3390/microorganisms9020388
Hernández-García M, García-Castillo M, García-Fernández S, López-Mendoza D, Díaz-Regañón J, Romano J, Pássaro L, Paixão L, Cantón R. Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain. Microorganisms. 2021; 9(2):388. https://doi.org/10.3390/microorganisms9020388
Chicago/Turabian StyleHernández-García, Marta, María García-Castillo, Sergio García-Fernández, Diego López-Mendoza, Jazmín Díaz-Regañón, João Romano, Leonor Pássaro, Laura Paixão, and Rafael Cantón. 2021. "Presence of Chromosomal crpP-like Genes Is Not Always Associated with Ciprofloxacin Resistance in Pseudomonas aeruginosa Clinical Isolates Recovered in ICU Patients from Portugal and Spain" Microorganisms 9, no. 2: 388. https://doi.org/10.3390/microorganisms9020388