Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genetic and Genomic Data Acquisition
2.2. Computational Analyses of Intergenic Regions
2.3. Calculation of Mutation Features
2.4. Repressor and Resistance Target Analyses
2.5. Typing and Phylogenomic Studies
3. Results
3.1. Identification of Expression Elements in Core MDR/Biocide Efflux Pumps of P. aeruginosa
3.2. Most P. aeruginosa Isolates Carry Mutations in Repeat Sequences Compared with the PAO1 Strain
3.3. Repeat Mutations Show Diverse Genetic Properties
3.4. Repeat Mutations Involve Relevant Pumps in High-Risk Clones
3.5. Several Non-High-Risk ST Isolates Harbor Five or More Efflux Pump Repeat Mutations
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Mutation | Number of Isolates | Change Type | Switch in the Number of H-Bonds | Position Palindromicity | Adjacency to Non-Palindromic Bases | Nucleotide Repeat Positioning | Repeat Order | Promoter Overlapping | DNA Bending Shift |
---|---|---|---|---|---|---|---|---|---|
emrE_R1’_A3C | 10838 | Transversion | Yes | No | Yes | Central | Downstream | No (upstream) | 1.783 |
mexM_R1’_T11C | 10774 | Transition | Yes | Yes | No | Terminal | Downstream | No (downstream) | −0.412 |
muxA_R2’_T5C | 9082 | Transition | Yes | No | Yes | Central | Downstream | No (box spacer) | 1.096 |
mexV_R1’_C6T | 9018 | Transition | Yes | Yes | Yes | Central | Downstream | No (box spacer) | 0.534 |
mexP_R1_G9A | 6264 | Transition | Yes | Yes | Yes | Central | Upstream | No (box spacer) | 1.684 |
mexM_R1’_T11G | 2686 | Transversion | Yes | Yes | No | Terminal | Downstream | No (downstream) | 0.522 |
mexP_R1’_C10T | 2438 | Transition | Yes | Yes | Yes | Terminal | Downstream | No (box spacer) | −1.561 |
mexA_R3_A9G | 656 | Transition | Yes | Yes | No | Central | Upstream | No (downstream) | −0.306 |
pmpM_R1’_G4C | 593 | Transversion | No | Yes | Yes | Central | Downstream | No (downstream) | −0.531 |
mexE_R1_T4C | 475 | Transition | Yes | Yes | Yes | Central | Upstream | No (downstream) | 1.025 |
mexX_R1’_T4C | 213 | Transition | Yes | No | No | Central | Downstream | No (box spacer) | 0.846 |
muxA_R2’_C1T | 200 | Transition | Yes | Yes | No | Terminal | Downstream | No (box spacer) | −1.571 |
mexV_R2’_A3C | 180 | Transversion | Yes | Yes | No | Central | Downstream | No (downstream) | −2.192 |
emrE_R1’_G10A | 94 | Transition | Yes | Yes | No | Terminal | Downstream | No (upstream) | 0.205 |
mexC_R1’_A5G | 51 | Transition | Yes | Yes | No | Terminal | Downstream | No (downstream) | 0.758 |
mexX_R1_A6G | 49 | Transition | Yes | Yes | Yes | Central | Upstream | No (box spacer) | −0.794 |
mexX_R1_C7T | 46 | Transition | Yes | No | No | Central | Upstream | No (box spacer) | 1.549 |
mexP_R1’_G2A | 42 | Transition | Yes | Yes | Yes | Terminal | Downstream | No (box spacer) | −0.48 |
mexC_R1_G3T | 33 | Transversion | Yes | Yes | No | Central | Upstream | No (box spacer) | −0.838 |
mexC_R1_T1C | 32 | Transition | Yes | Yes | No | Terminal | Upstream | No (box spacer) | −0.256 |
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Pérez-Vázquez, M.; López-Causapé, C.; Corral-Lugo, A.; McConnell, M.J.; Oteo-Iglesias, J.; Oliver, A.; Martín-Galiano, A.J. Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes. Microorganisms 2023, 11, 2486. https://doi.org/10.3390/microorganisms11102486
Pérez-Vázquez M, López-Causapé C, Corral-Lugo A, McConnell MJ, Oteo-Iglesias J, Oliver A, Martín-Galiano AJ. Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes. Microorganisms. 2023; 11(10):2486. https://doi.org/10.3390/microorganisms11102486
Chicago/Turabian StylePérez-Vázquez, María, Carla López-Causapé, Andrés Corral-Lugo, Michael J. McConnell, Jesús Oteo-Iglesias, Antonio Oliver, and Antonio J. Martín-Galiano. 2023. "Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes" Microorganisms 11, no. 10: 2486. https://doi.org/10.3390/microorganisms11102486
APA StylePérez-Vázquez, M., López-Causapé, C., Corral-Lugo, A., McConnell, M. J., Oteo-Iglesias, J., Oliver, A., & Martín-Galiano, A. J. (2023). Mutation Analysis in Regulator DNA-Binding Regions for Antimicrobial Efflux Pumps in 17,000 Pseudomonas aeruginosa Genomes. Microorganisms, 11(10), 2486. https://doi.org/10.3390/microorganisms11102486