Baker S, Thomson N, Weill FX, Holt KE (2018) Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science 360(6390):733–738
Article CAS PubMed PubMed Central Google Scholar
Mathers AJ, Peirano G, Pitout JD (2015) The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 28(3):565–591
Article CAS PubMed PubMed Central Google Scholar
Pitout JD, Peirano G, DeVinney R (2023) The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 21(4):343–353
Article CAS PubMed Google Scholar
Woodford N, Turton JF, Livermore DM (2011) Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev 35(5):736–755
Article CAS PubMed Google Scholar
Oliver A, Mulet X, Lopez-Causape C, Juan C (2015) The increasing threat of Pseudomonas aeruginosa high-risk clones. Drug Resist Updat 21–22:41–59
Peirano G, Chen L, Kreiswirth BN, Pitout JDD (2020) Emerging Antimicrobial-Resistant High-Risk Klebsiella pneumoniae Clones ST307 and ST147. Antimicrob Agents Chemother 64:10
Del Barrio-Tofino E, Lopez-Causape C, Oliver A (2020) Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired beta-lactamases: 2020 update. Int J Antimicrob Agents 56(6):106196
Cabot G, Ocampo-Sosa AA, Dominguez MA, Gago JF, Juan C, Tubau F, Rodriguez C, Moya B, Pena C, Martinez-Martinez L, Oliver A, Spanish Network for Research in Infectious D (2012) Genetic markers of widespread extensively drug-resistant Pseudomonas aeruginosa high-risk clones. Antimicrob Agents Chemother 56(12):6349–6357
Article CAS PubMed PubMed Central Google Scholar
Peirano G, Matsumara Y, Nobrega D, Church D, Pitout JDD (2024) Population-based genomic surveillance of Pseudomonas aeruginosa causing bloodstream infections in a large Canadian health region. Eur J Clin Microbiol Infect Dis 43(3):501–510
Article CAS PubMed Google Scholar
Anbo M, Chichkova MAT, Gencay YE, Salazar A, Jeannot K, Jelsbak L (2023) Whole-Genome Sequencing of 11 High-Risk Clone ST111 Pseudomonas aeruginosa Isolates from French Hospitals. Microbiol Resour Announc 12(7):e0009123
Molina-Mora JA, Campos-Sanchez R, Rodriguez C, Shi L, Garcia F (2020) High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers. Sci Rep 10(1):1392
Article CAS PubMed PubMed Central Google Scholar
van der Zee A, Kraak WB, Burggraaf A, Goessens WHF, Pirovano W, Ossewaarde JM, Tommassen J (2018) Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa. Front Microbiol 9:2057
Article PubMed PubMed Central Google Scholar
Lowe M, Kock MM, Coetzee J, Hoosien E, Peirano G, Strydom KA, Ehlers MM, Mbelle NM, Shashkina E, Haslam DB, Dhawan P, Donnelly RJ, Chen L, Kreiswirth BN, Pitout JDD (2019) Klebsiella pneumoniae ST307 with blaOXA-181, South Africa, 2014–2016. Emerg Infect Dis 25(4):739–747
Article PubMed PubMed Central Google Scholar
Peirano G, Matsumura Y, Adams MD, Bradford P, Motyl M, Chen L, Kreiswirth BN, Pitout JDD (2018) Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008–2014. Emerg Infect Dis 24(6):1010–1019
Article PubMed PubMed Central Google Scholar
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6):e1005595
Article PubMed PubMed Central Google Scholar
Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W (2021) AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728
Article CAS PubMed PubMed Central Google Scholar
Thrane SW, Taylor VL, Lund O, Lam JS, Jelsbak L (2016) Application of Whole-Genome Sequencing Data for O-Specific Antigen Analysis and In Silico Serotyping of Pseudomonas aeruginosa Isolates. J Clin Microbiol 54(7):1782–1788
Article CAS PubMed PubMed Central Google Scholar
Jolley KA, Bray JE, Maiden MCJ (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:124
Article PubMed PubMed Central Google Scholar
Kos VN, Deraspe M, McLaughlin RE, Whiteaker JD, Roy PH, Alm RA, Corbeil J, Gardner H (2015) The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrob Agents Chemother 59(1):427–436
Thrane SW, Taylor VL, Freschi L, Kukavica-Ibrulj I, Boyle B, Laroche J, Pirnay JP, Levesque RC, Lam JS, Jelsbak L (2015) The Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters. mBio 6 (5):e01396–01315
Jung H, Pitout JDD, Mitton BC, Strydom KA, Kingsburgh C, Coetzee J, Ehlers MM, Kock M (2021) Evaluation of the rapid ResaPolymyxin Acinetobacter/Pseudomonas NP test for rapid colistin resistance detection in lactose non-fermenting Gram-negative bacteria. J Med Microbiol 70(6):001373
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313
Article CAS PubMed PubMed Central Google Scholar
Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR (2015) Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 43(3):e15
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44(W1):W16-21
Article CAS PubMed PubMed Central Google Scholar
Cheng L, Connor TR, Siren J, Aanensen DM, Corander J (2013) Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 30(5):1224–1228
Article CAS PubMed PubMed Central Google Scholar
Didelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ (2018) Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Res 46(22):e134
Article PubMed PubMed Central Google Scholar
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A, Heled J, Jones G, Kuhnert D, De Maio N, Matschiner M, Mendes FK, Muller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 15(4):e1006650
Article CAS PubMed PubMed Central Google Scholar
Molina-Mora JA, Chinchilla-Montero D, Garcia-Batan R, Garcia F (2021) Genomic context of the two integrons of ST-111 Pseudomonas aeruginosa AG1: A VIM-2-carrying old-acquaintance and a novel IMP-18-carrying integron. Infect Genet Evol 89:104740
Article CAS PubMed Google Scholar
Stanislavsky ES, Lam JS (1997) Pseudomonas aeruginosa antigens as potential vaccines. FEMS Microbiol Rev 21(3):243–277
Article CAS PubMed Google Scholar
Pitout JDD, Finn TJ (2020) The evolutionary puzzle of Escherichia coli ST131. Infect Genet Evol 81:104265
Comments (0)