Mutational basis of Meropenem resistance in Pseudomonas aeruginosa

About authors

Pirogov Russian National Research Medical University, Moscow, Russia

Ostrovityanova, 1, Moscow, 117997, Russia: Correspondence should be addressed: Igor V. Chebotar

About paper

Funding: the study was supported by the Russian Science Foundation (project No. 20-15-00235).

Acknowledgements: the authors thank the Center of Precision Genome Editing and Genetic Technologies for Biomedicine of the Pirogov Russian National Research Medical University for their advice on the research methods.

Author contribution: Chebotar IV — concept, manuscript writing; Bocharova YuA — methods, formal analysis; Chaplin AV — formal analysis of sequencing data; Savinova TA — formal analysis of sequencing data; Vasiliadis YuA — methods, sequencing; Mayansky NA — concept, manuscript editing.

Compliance with ethical standards: the study was performed in full compliance with the principles of the Declaration of Helsinki and the standards for handling opportunistic pathogens.

Received: 2022-11-25 Accepted: 2022-12-11 Published online: 2022-12-28
  1. Lazareva AV, Chebotar IV, Kryzhanovskaya OA, Chebotar VI, Mayanskiy NA. Pseudomonas aeruginosa: patogennost', patogenez i patologiya. Klin Mikrobiol Antimikrob Ximioter. 2015; 17 (3): 170– 86. Russian.
  2. WHO priority list for research and development of new antibiotics for antibiotic-resistant bacteria. Geneva: World Health Organization, 2017. Available from: https://www.who.int/news/ item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed (accessed September 1, 2012).
  3. Oliver A, Mulet X, López-Causapé C, Juan C. The increasing threat of Pseudomonas aeruginosa high-risk clones. Drug Resistance Updates. 2015; 21: 41–59. Available from: https:// doi.org/10.1016/j.drup.2015.08.002.
  4. López-Causapé C, Sommer LM, Cabot G, Rubio R, Ocampo- Sosa AA, Johansen H et al. Evolution of the Pseudomonas aeruginosa mutational resistome in an international cystic fibrosis clone. Sci Rep. 2017; 7: 5555. Available from: https://doi. org/10.1038/s41598-017-05621-5.
  5. Barbosa C, Trebosc V, Kemmer C, Rosenstiel P, Beardmore R, Schulenburg H, et al. Alternative evolutionary paths to bacterial antibiotic resistance cause distinct collateral effects. Mol Biol Evol. 2017; 34 (9): 2229–44. Available from: https://doi.org/10.1093/ molbev/msx158.
  6. Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016; 353 (6304): 1147–51. Available from: https://doi. org/10.1126/science.aag0822.
  7. Savinova TA, Bocharova YA, Chaplin AV, Korostin DO, Shamina OV, Mayanskiy NA, et al. Meropenem-induced reduction in colistin susceptibility in Pseudomonas aeruginosa strain ATCC 27853. Bulletin of RSMU. 2022; 1: 30–4. Available from: https://doi. org/10.24075/brsmu.2022.001.
  8. European Committee for Antimicrobial Susceptibility Testing (EUCAST) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Determination of minimum inhibitory concentrations (MICs) of antibacterial agents by agar dilution. Clin Microbiol Infect. 2000; 6 (9): 509–15. Available from: https://doi.org/10.1046/j.1469-0691.2000.00142.x.
  9. Kazanova AM, Stepanova ES, Makarenkova LM, Chistyakov VV, Zyryanov SK, Senchenko SP. Razrabotka i validaciya metodiki kolichestvennogo opredeleniya meropenema v plazme krovi dlya terapevticheskogo lekarstvennogo monitoringa. Ximiko-farmacevticheskij zhurnal. 2020; 54 (4): 56–60. Available from: https://doi.org/10.30906/0023-1134-2020-54-4-56-60. Russian.
  10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19: 455–77. Available from: https://doi.org/10.1089/cmb.2012.0021.
  11. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29 (8): 1072–5. Available from: https://doi.org/10.1093/ bioinformatics/btt086.
  12. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014; 42: D206–14. Available from: https://doi.org/10.1093/nar/gkt1226.
  13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30 (14): 2068–9. Available from: https://doi. org/10.1093/bioinformatics/btu153.
  14. Seemann T. 2015. Snippy: fast bacterial variant calling from NGS reads. GitHub. Available at: https://github.com/tseemann/snippy (accessed November 2022).
  15. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012; 6 (2): 80–92. Available from: https://doi.org/10.4161/fly.19695.
  16. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018; 46 (W1): W537–44. Available from: https://doi.org/10.1093/nar/gky379 .
  17. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020; 75 (12): 3491–500. Available from: https://doi.org/10.1093/jac/dkaa345.
  18. Li H, Luo YF, Williams BJ, Blackwell TS, Xie CM. Structure and function of OprD protein in Pseudomonas aeruginosa: from antibiotic resistance to novel therapies. Int J Med Microbiol. 2012; 302 (2): 63–8. Available from: https://doi.org/10.1016/j. ijmm.2011.10.001.
  19. Lister PD, Wolter DJ, Hanson ND. Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clin Microbiol Rev. 2009; 22 (4): 582–610. Available from: https://doi. org/10.1128/CMR.00040-09.
  20. Srikumar R, Kon T, Gotoh N, Poole K. Expression of Pseudomonas aeruginosa multidrug efflux pumps MexA-MexB-OprM and MexC-MexD-OprJ in a multidrug-sensitive Escherichia coli strain. Antimicrob Agents Chemother. 1998; 42 (1): 65–71. Available from: https://doi.org/10.1128/AAC.42.1.65.
  21. Glen KA, Lamont IL. β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects. Pathogens. 2021; 10 (12): 1638. Available from: https://doi.org/10.3390/ pathogens10121638.