The accessory genome of Pseudomonas aeruginosa

Microbiology and Molecular Biology Reviews

Volumn 74, Issue 4, 2010, Pages 621-641

  Kung, Vanderlene L ^a   Ozer, Egon A ^a   Hauser, Alan R ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSORY GENOME; BACTERIAL GENOME; BACTERIOPHAGE; ENHANCER REGION; GENE INSERTION SEQUENCE; GENE REPLICATION; GENOMIC ISLAND; HUMAN; INTEGRATIVE AND CONJUGATIVE ELEMENT; INTEGRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDOMONAS AERUGINOSA; REPLICON; RETROPOSON; REVIEW; TRANSPOSON;

DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; GENOMIC ISLANDS; PROPHAGES; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS;

PSEUDOMONAS AERUGINOSA;

EID: 78650103372     PISSN: 10922172     EISSN: 10985557     Source Type: Journal    
DOI: 10.1128/MMBR.00027-10     Document Type: Review

References (239)

1. Aas, F. E., M. Wolfgang, S. Frye, S. Dunham, C. Lovold, and M. Koomey. 2002. Competence for natural transformation in Neisseria gonorrhoeae: components of DNA binding and uptake linked to type IV pilus expression. Mol. Microbiol. 46:749-760.
2. Abd, H., B. Wretlind, A. Saeed, E. Idsund, K. Hultenby, and G. Sandstrom. 2008. Pseudomonas aeruginosa utilises its type III secretion system to kill the free-living amoeba Acanthamoeba castellanii. J. Eukaryot. Microbiol. 55:235-243.
3. Aguilar-Barajas, E., M. I. Ramírez-Díaz, H. Riveros-Rosas, and C. Cervantes. 2010. Heavy metal resistance in pseudomonads, p. 255-282. In J. L. Ramos and A. Filloux (ed.), Pseudomonas: molecular microbiology, infection and biodiversity, vol. 6. Springer, New York, NY.
4. Akhverdian, V. Z., E. A. Khrenova, V. G. Bogush, T. V. Gerasimova, and N. B. Kirsanov. 1984. Wide distribution of transposable phages in natural Pseudomonas aeruginosa populations. Genetika 20:1612-1619.
5. Andersen, S. R., G. Bjune, J. Lyngby, K. Bryn, and E. Jantzen. 1995. Short-chain lipopolysaccharide mutants of serogroup B Neisseria meningitidis of potential value for production of outer membrane vesicle vaccines. Microb. Pathog. 19:159-168.
6. Arnold, D. L., R. W. Jackson, N. R. Waterfield, and J. W. Mansfield. 2007. Evolution of microbial virulence: the benefits of stress. Trends Genet. 23:293-300.
7. Arora, S. K., M. Bangera, S. Lory, and R. Ramphal. 2001. A genomic island in Pseudomonas aeruginosa carries the determinants of flagellin glycosylation. Proc. Natl. Acad. Sci. U. S. A. 98:9342-9347.
8. Arora, S. K., A. N. Neely, B. Blair, S. Lory, and R. Ramphal. 2005. Role of motility and flagellin glycosylation in the pathogenesis of Pseudomonas aeruginosa burn wound infections. Infect. Immun. 73:4395-4398.
9. Arora, S. K., M. C. Wolfgang, S. Lory, and R. Ramphal. 2004. Sequence polymorphism in the glycosylation island and flagellins of Pseudomonas aeruginosa. J. Bacteriol. 186:2115-2122.
10. Aubert, D., T. Naas, and P. Nordmann. 2003. IS1999 increases expression of the extended-spectrum beta-lactamase VEB-1 in Pseudomonas aeruginosa. J. Bacteriol. 185:5314-5319.
11. Babalova, M., J. Blahova, M. Lesicka-Hupkova, K. Kralikova, V. Krcmery, and V. Schaefer. 1995. A bi-modal transfer of antibiotic resistance by conjugation and transduction from an imipenem-resistant strain of Pseudomonas aeruginosa. Zentralbl. Bakteriol. 283:61-68.
12. Baltch, A. L., R. P. Smith, M. Franke, W. Ritz, P. Michelsen, L. Bopp, and F. Lutz. 1994. Pseudomonas aeruginosa cytotoxin as a pathogenicity factor in a systemic infection of leukopenic mice. Toxicon 32:27-34.
13. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712.
14. Battle, S. E., F. Meyer, J. Rello, V. L. Kung, and A. R. Hauser. 2008. Hybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals. J. Bacteriol. 190:7130-7140.
15. Battle, S. E., J. Rello, and A. R. Hauser. 2009. Genomic islands of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 290:70-78.
16. Baysse, C., J. M. Meyer, P. Plesiat, V. Geoffroy, Y. Michel-Briand, and P. Cornelis. 1999. Uptake of pyocin S3 occurs through the outer membrane ferripyoverdine type II receptor of Pseudomonas aeruginosa. J. Bacteriol. 181:3849-3851. (Pubitemid 29283818)
17. Bennett, P. M. 2004. Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement. Methods Mol. Biol. 266: 71-113.
18. Bennett, P. M. 1999. Integrons and gene cassettes: a genetic construction kit for bacteria. J. Antimicrob. Chemother. 43:1-4.
19. Blazquez, J., J. M. Gomez-Gomez, A. Oliver, C. Juan, V. Kapur, and S. Martin. 2006. PBP3 inhibition elicits adaptive responses in Pseudomonas aeruginosa. Mol. Microbiol. 62:84-99.
20. Bodey, G. P., R. Bolivar, V. Fainstein, and L. Jadeja. 1983. Infections caused by Pseudomonas aeruginosa. Rev. Infect. Dis. 5:279-313.
21. Bodilis, J., B. Ghysels, J. Osayande, S. Matthijs, J. P. Pirnay, S. Denayer, D. De Vos, and P. Cornelis. 2009. Distribution and evolution of ferripyoverdine receptors in Pseudomonas aeruginosa. Environ. Microbiol. 11:2123-2135.
22. Bouffartigues, E., M. Buckle, C. Badaut, A. Travers, and S. Rimsky. 2007. H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat. Struct. Mol. Biol. 14:441-448.
23. Bradley, D. E. 1973. A pilus-dependent Pseudomonas aeruginosa bacteriophage with a long noncontractile tail. Virology 51:489-492.
24. Braid, M. D., J. L. Silhavy, C. L. Kitts, R. J. Cano, and M. M. Howe. 2004. Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa. J. Bacteriol. 186:6560-6574.
25. Brazas, M. D., and R. E. Hancock. 2005. Ciprofloxacin induction of a susceptibility determinant in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 49:3222-3227.
26. Budzik, J. M., W. A. Rosche, A. Rietsch, and G. A. O'Toole. 2004. Isolation and characterization of a generalized transducing phage for Pseudomonas aeruginosa strains PAO1 and PA14. J. Bacteriol. 186:3270-3273.
27. Burland, V., Y. Shao, N. T. Perna, G. Plunkett, H. J. Sofia, and F. R. Blattner. 1998. The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res. 26:4196-4204.
28. Burrus, V., G. Pavlovic, B. Decaris, and G. Guedon. 2002. Conjugative transposons: the tip of the iceberg. Mol. Microbiol. 46:601-610.
29. Burrus, V., and M. K. Waldor. 2003. Control of SXT integration and excision. J. Bacteriol. 185:5045-5054.
30. Burrus, V., and M. K. Waldor. 2004. Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 155:376-386.
31. Bush, K. 2001. New beta-lactamases in gram-negative bacteria: diversity and impact on the selection of antimicrobial therapy. Clin. Infect. Dis. 32:1085-1089.
32. Byrne, M., and A. M. Kropinski. 2005. The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. Gene 346:187-194.
33. Campos-García, J. 2010. Metabolism of acyclic terpenes by Pseudomonas, p. 235-254. In J. L. Ramos and A. Filloux (ed.), Pseudomonas: molecular microbiology, infection and biodiversity, vol. 6. Springer, New York, NY.
34. Carmeli, Y., N. Troillet, A. W. Karchmer, and M. H. Samore. 1999. Health and economic outcomes of antibiotic resistance in Pseudomonas aeruginosa. Arch. Intern. Med. 159:1127-1132.
35. Carter, M. Q., J. Chen, and S. Lory. 2010. The Pseudomonas aeruginosa pathogenicity island PAPI-1 is transferred via a novel type IV pilus. J. Bacteriol. 192:3249-3258.
36. Carvalho, A. P., R. M. Albano, D. N. de Oliveira, D. A. Cidade, L. M. Teixeira, and A. Marques Ede. 2006. Characterization of an epidemic carbapenem-resistant Pseudomonas aeruginosa producing SPM-1 metallo-beta- lactamase in a hospital located in Rio de Janeiro, Brazil. Microb. Drug Resist. 12:103-108.
37. Castang, S., H. R. McManus, K. H. Turner, and S. L. Dove. 2008. H-NS family members function coordinately in an opportunistic pathogen. Proc. Natl. Acad. Sci. U. S. A. 105:18947-18952.
38. Castric, P. 1995. pilO, a gene required for glycosylation of Pseudomonas aeruginosa 1244 pilin. Microbiology 141:1247-1254.
39. Chanawong, A., F. H. M'Zali, J. Heritage, A. Lulitanond, and P. M. Hawkey. 2001. SHV-12, SHV-5, SHV-2a and VEB-1 extended-spectrum beta-lactamases in Gram-negative bacteria isolated in a university hospital in Thailand. J. Antimicrob. Chemother. 48:839-852.
40. Chandler, M., and J. Mahillon. 2002. Insertion sequences revisited, p. 305-366. In N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, DC.
41. Chang, W., D. A. Small, F. Toghrol, and W. E. Bentley. 2005. Microarray analysis of Pseudomonas aeruginosa reveals induction of pyocin genes in response to hydrogen peroxide. BMC Genomics 6:115.
42. Chibeu, A., P. J. Ceyssens, K. Hertveldt, G. Volckaert, P. Cornelis, S. Matthijs, and R. Lavigne. 2009. The adsorption of Pseudomonas aeruginosa bacteriophage phiKMV is dependent on expression regulation of type IV pili genes. FEMS Microbiol. Lett. 296:210-218.
43. Comolli, J. C., A. R. Hauser, L. Waite, C. B. Whitchurch, J. S. Mattick, and J. N. Engel. 1999. Pseudomonas aeruginosa gene products PilT and PilU are required for cytotoxicity in vitro and virulence in a mouse model of acute pneumonia. Infect. Immun. 67:3625-3630.
44. Corvec, S., L. Poirel, E. Espaze, C. Giraudeau, H. Drugeon, and P. Nordmann. 2008. Long-term evolution of a nosocomial outbreak of Pseudomonas aeruginosa producing VIM-2 metallo-enzyme. J. Hosp. Infect. 68:73-82.
45. Costas, A. M., A. K. White, and W. W. Metcalf. 2001. Purification and characterization of a novel phosphorus-oxidizing enzyme from Pseudomonas stutzeri WM88. J. Biol. Chem. 276:17429-17436.
46. Coyne, S., P. Courvalin, and M. Galimand. 2010. Acquisition of multidrug resistance transposon Tn6061 and IS6100-mediated large chromosomal inversions in Pseudomonas aeruginosa clinical isolates. Microbiology 156: 1448-1458.
47. Croft, L., S. A. Beatson, C. B. Whitchurch, B. Huang, R. L. Blakeley, and J. S. Mattick. 2000. An interactive web-based Pseudomonas aeruginosa genome database: discovery of new genes, pathways and structures. Microbiology 146:2351-2364.
48. Cryz, S. J., Jr., T. L. Pitt, E. Furer, and R. Germanier. 1984. Role of lipopolysaccharide in virulence of Pseudomonas aeruginosa. Infect. Immun. 44:508-513.
49. Dahlberg, C., and L. Chao. 2003. Amelioration of the cost of conjugative plasmid carriage in Escherichia coli K12. Genetics 165:1641-1649. (Pubitemid 38040259)
50. Dantas, G., M. O. Sommer, R. D. Oluwasegun, and G. M. Church. 2008. Bacteria subsisting on antibiotics. Science 320:100-103.
51. Dasgupta, T., T. R. de Kievit, H. Masoud, E. Altman, J. C. Richards, I. Sadovskaya, D. P. Speert, and J. S. Lam. 1994. Characterization of lipopolysaccharide- deficient mutants of Pseudomonas aeruginosa derived from serotypes O3, O5, and O6. Infect. Immun. 62:809-817. (Pubitemid 24065559)
52. Daubin, V., and H. Ochman. 2004. Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14:1036-1042. (Pubitemid 38811539)
53. Dean, C. R., C. V. Franklund, J. D. Retief, M. J. Coyne, Jr., K. Hatano, D. J. Evans, G. B. Pier, and J. B. Goldberg. 1999. Characterization of the serogroup O11 O-antigen locus of Pseudomonas aeruginosa PA103. J. Bacteriol. 181:4275-4284.
54. Dobrindt, U., B. Hochhut, U. Hentschel, and J. Hacker. 2004. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2:414-424.
55. Dorn, E., M. Hellwig, W. Reineke, and H. J. Knackmuss. 1974. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch. Microbiol. 99:61-70.
56. Drenkard, E., and F. M. Ausubel. 2002. Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature 416: 740-743.
57. Dubois, V., C. Arpin, P. Noury, C. Andre, L. Coulange, and C. Quentin. 2005. Prolonged outbreak of infection due to TEM-21-producing strains of Pseudomonas aeruginosa and enterobacteria in a nursing home. J. Clin. Microbiol. 43:4129-4138.
58. Dubois, V., C. Arpin, P. Noury, and C. Quentin. 2002. Clinical strain of Pseudomonas aeruginosa carrying a bla(TEM-21) gene located on a chromosomal interrupted TnA type transposon. Antimicrob. Agents Chemother. 46:3624-3626.
59. Eberl, L., and B. Tummler. 2004. Pseudomonas aeruginosa and Burkholderia cepacia in cystic fibrosis: genome evolution, interactions and adaptation. Int. J. Med. Microbiol. 294:123-131.
60. Empel, J., K. Filczak, A. Mrowka, W. Hryniewicz, D. M. Livermore, and M. Gniadkowski. 2007. Outbreak of Pseudomonas aeruginosa infections with PER-1 extended-spectrum beta-lactamase in Warsaw, Poland: further evidence for an international clonal complex. J. Clin. Microbiol. 45:2829-2834.
61. Ernst, R. K., D. A. D'Argenio, J. K. Ichikawa, M. G. Bangera, S. Selgrade, J. L. Burns, P. Hiatt, K. McCoy, M. Brittnacher, A. Kas, D. H. Spencer, M. V. Olson, B. W. Ramsey, S. Lory, and S. I. Miller. 2003. Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis. Environ. Microbiol. 5:1341-1349.
62. Fagon, J. Y., J. Chastre, Y. Domart, J. L. Trouillet, J. Pierre, C. Carne, and C. Gibert. 1989. Nosocomial pneumonia in patients receiving continuous mechanical ventilation. Am. Rev. Respir. Dis. 139:877-884.
63. Feldman, M., R. Bryan, S. Rajan, L. Scheffler, S. Brunnert, H. Tang, and A. Prince. 1998. Role of flagella in pathogenesis of Pseudomonas aeruginosa pulmonary infection. Infect. Immun. 66:43-51.
64. Feltman, H., G. Schulert, S. Khan, M. Jain, L. Peterson, and A. R. Hauser. 2001. Prevalence of type III secretion genes in clinical and environmental isolates of Pseudomonas aeruginosa. Microbiology 147:2659-2669.
65. Filiatrault, M. J., R. S. Munson, Jr., and A. A. Campagnari. 2001. Genetic analysis of a pyocin-resistant lipooligosaccharide (LOS) mutant of Haemophilus ducreyi: restoration of full-length LOS restores pyocin sensitivity. J. Bacteriol. 183:5756-5761.
66. Finck-Barbançon, V., J. Goranson, L. Zhu, T. Sawa, J. P. Wiener-Kronish, S. M. J. Fleiszig, C. Wu, L. Mende-Mueller, and D. Frank. 1997. ExoU expression by Pseudomonas aeruginosa correlates with acute cytotoxicity and epithelial injury. Mol. Microbiol. 25:547-557.
67. Fischer, D., and D. Eisenberg. 1999. Finding families for genomic ORFans. Bioinformatics 15:759-762.
68. Fothergill, J. L., E. Mowat, M. J. Ledson, M. J. Walshaw, and C. Winstanley. 2010. Fluctuations in phenotypes and genotypes within populations of Pseudomonas aeruginosa in the cystic fibrosis lung during pulmonary exacerbations. J. Med. Microbiol. 59:472-481.
69. Fyfe, J. A., G. Harris, and J. R. Govan. 1984. Revised pyocin typing method for Pseudomonas aeruginosa. J. Clin. Microbiol. 20:47-50.
70. Gaillard, M., N. Pernet, C. Vogne, O. Hagenbuchle, and J. R. van der Meer. 2008. Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1. Proc. Natl. Acad. Sci. U. S. A. 105:7058-7063.
71. Gaillard, M., T. Vallaeys, F. J. Vorholter, M. Minoia, C. Werlen, V. Sentchilo, A. Puhler, and J. R. van der Meer. 2006. The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J. Bacteriol. 188:1999-2013. (Pubitemid 43346880)
72. Geiben-Lynn, R., K. Sauber, and F. Lutz. 2001. Flagellin inhibits Myoviridae phage phiCTX infection of Pseudomonas aeruginosa strain GuA18: purification and mapping of binding site. Arch. Microbiol. 176:339-346.
73. Ghosh, D., K. Roy, K. E. Williamson, S. Srinivasiah, K. E. Wommack, and M. Radosevich. 2009. Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl. Environ. Microbiol. 75:7142-7152.
74. Gibb, A. P., C. Tribuddharat, R. A. Moore, T. J. Louie, W. Krulicki, D. M. Livermore, M. F. Palepou, and N. Woodford. 2002. Nosocomial outbreak of carbapenem-resistant Pseudomonas aeruginosa with a new bla(IMP) allele, bla(IMP-7). Antimicrob. Agents Chemother. 46:255-258.
75. Glonti, T., N. Chanishvili, and P. W. Taylor. 2010. Bacteriophage-derived enzyme that depolymerizes the alginic acid capsule associated with cystic fibrosis isolates of Pseudomonas aeruginosa. J. Appl. Microbiol. 108:695-702.
76. Govan, J. R. 1974. Studies on the pyocins of Pseudomonas aeruginosa: morphology and mode of action of contractile pyocins. J. Gen. Microbiol. 80:1-15.
77. Graupner, S., V. Frey, R. Hashemi, M. G. Lorenz, G. Brandes, and W. Wackernagel. 2000. Type IV pilus genes pilA and pilC of Pseudomonas stutzeri are required for natural genetic transformation, and pilA can be replaced by corresponding genes from nontransformable species. J. Bacteriol. 182:2184-2190.
78. Grinsted, J., F. de la Cruz, and R. Schmitt. 1990. The Tn21 subgroup of bacterial transposable elements. Plasmid 24:163-189.
79. Hahn, H. P. 1997. The type-4 pilus is the major virulence-associated adhesin of Pseudomonas aeruginosa. Gene 192:99-108.
80. Hanlon, G. W., S. P. Denyer, C. J. Olliff, and L. J. Ibrahim. 2001. Reduction in exopolysaccharide viscosity as an aid to bacteriophage penetration through Pseudomonas aeruginosa biofilms. Appl. Environ. Microbiol. 67: 2746-2753.
81. Harris, A., C. Torres-Viera, L. Venkataraman, P. DeGirolami, M. Samore, and Y. Carmeli. 1999. Epidemiology and clinical outcomes of patients with multiresistant Pseudomonas aeruginosa. Clin. Infect. Dis. 28:1128-1133.
82. Harrison, E. M., M. E. Carter, S. Luck, H. Y. Ou, X. He, Z. Deng, C. O'Callaghan, A. Kadioglu, and K. Rajakumar. 2010. Pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to the virulence of Pseudomonas aeruginosa strain PA14. Infect. Immun. 78:1437-1446.
83. Hauser, A. R. 2009. The type III secretion system of Pseudomonas aeruginosa: infection by injection. Nat. Rev. Microbiol. 7:654-665.
84. Hauser, A. R., E. Cobb, M. Bodí, D. Mariscal, J. Vallés, J. N. Engel, and J. Rello. 2002. Type III protein secretion is associated with poor clinical outcomes in patients with ventilator-associated pneumonia caused by Pseudomonas aeruginosa. Crit. Care Med. 30:521-528.
85. Hauser, A. R., P. J. Kang, and J. Engel. 1998. PepA, a novel secreted protein of Pseudomonas aeruginosa, is necessary for cytotoxicity and virulence. Mol. Microbiol. 27:807-818.
86. Hayden, H. S., W. Gillett, C. Saenphimmachak, R. Lim, Y. Zhou, M. A. Jacobs, J. Chang, L. Rohmer, D. A. D'Argenio, A. Palmieri, R. Levy, E. Haugen, G. K. Wong, M. J. Brittnacher, J. L. Burns, S. I. Miller, M. V. Olson, and R. Kaul. 2008. Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients. Genomics 91:530-537.
87. He, J., R. L. Baldini, E. Deziel, M. Saucier, Q. Zhang, N. T. Liberati, D. Lee, J. Urbach, H. M. Goodman, and L. G. Rahme. 2004. The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc. Natl. Acad. Sci. U. S. A. 101:2530-2535.
88. Hentschel, U., and J. Hacker. 2001. Pathogenicity islands: the tip of the iceberg. Microbes Infect. 3:545-548.
89. Hertveldt, K., and R. Lavigne. 2008. Bacteriophages of Pseudomonas, p. 255-263. In B. H. A. Rehm (ed.), Pseudomonas: model organism, pathogen, cell factory. Wiley-VCH, Weinheim, Germany.
90. Hill, C. W. 1999. Large genomic sequence repetitions in bacteria: lessons from rRNA operons and Rhs elements. Res. Microbiol. 150:665-674.
91. Hill, C. W., C. H. Sandt, and D. A. Vlazny. 1994. Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein. Mol. Microbiol. 12:865-871.
92. Hill, D. F., N. J. Short, R. N. Perham, and G. B. Petersen. 1991. DNA sequence of the filamentous bacteriophage Pf1. J. Mol. Biol. 218:349-364.
93. Holloway, B. W. 1955. Genetic recombination in Pseudomonas aeruginosa. J. Gen. Microbiol. 13:572-581.
94. Holloway, B. W., J. B. Egan, and M. Monk. 1960. Lysogeny in Pseudomonas aeruginosa. Aust. J. Exp. Biol. Med. Sci. 38:321-329.
95. Holmes, A. J., M. R. Gillings, B. S. Nield, B. C. Mabbutt, K. M. Nevalainen, and H. W. Stokes. 2003. The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ. Microbiol. 5:383-394.
96. Hou, Y. M. 1999. Transfer RNAs and pathogenicity islands. Trends Biochem. Sci. 24:295-298.
97. Hupkova, M., J. Blahova, and V. Krcmery. 1994. Transfer, by conjugation and transduction, of resistance to ceftazidime and cefotaxime from the same clinical isolate of Pseudomonas aeruginosa. Zentralbl. Bakteriol. 281: 196-200.
98. Inon de Iannino, N., G. Briones, M. Tolmasky, and R. A. Ugalde. 1998. Molecular cloning and characterization of cgs, the Brucella abortus cyclic beta(1-2) glucan synthetase gene: genetic complementation of Rhizobium meliloti ndvB and Agrobacterium tumefaciens chvB mutants. J. Bacteriol. 180:4392-4400.
99. Jackson, A. P., G. H. Thomas, J. Parkhill, and N. R. Thomson. 2009. Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics 10:584.
100. Jacob, F. 1954. Induced biosynthesis and mode of action of a pyocine, antibiotic produced by Pseudomonas aeruginosa. Ann. Inst. Pasteur (Paris) 86:149-160.
101. Jarvis, W. R. 2003. Epidemiology and control of Pseudomonas aeruginosa infections in the intensive care unit, p. 153-168. In A. R. Hauser and J. Rello (ed.), Severe infections caused by Pseudomonas aeruginosa. Kluwer Academic Publishers, Boston, MA.
102. Jeong, J. H., K. S. Shin, J. W. Lee, E. J. Park, and S. Y. Son. 2009. Analysis of a novel class 1 integron containing metallo-beta-lactamase gene VIM-2 in Pseudomonas aeruginosa. J. Microbiol. 47:753-759.
103. Juhas, M., D. W. Crook, I. D. Dimopoulou, G. Lunter, R. M. Harding, D. J. Ferguson, and D. W. Hood. 2007. Novel type IV secretion system involved in propagation of genomic islands. J. Bacteriol. 189:761-771.
104. Juhas, M., J. R. van der Meer, M. Gaillard, R. M. Harding, D. W. Hood, and D. W. Crook. 2009. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33:376-393.
105. Kageyama, M., and F. Egami. 1962. On the purification and some properties of a pyocin, a bacteriocin produced by Pseudomonas aeruginosa. Life Sci. 1:471-476.
106. Kiewitz, C., K. Larbig, J. Klockgether, C. Weinel, and B. Tummler. 2000. Monitoring genome evolution ex vivo: reversible chromosomal integration of a 106 kb plasmid at two tRNA(Lys) gene loci in sequential Pseudomonas aeruginosa airway isolates. Microbiology 146:2365-2373.
107. Kiewitz, C., and B. Tummler. 2000. Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution. J. Bacteriol. 182:3125-3135.
108. Klockgether, J., O. Reva, K. Larbig, and B. Tummler. 2004. Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C. J. Bacteriol. 186:518-534.
109. Klockgether, J., D. Wurdemann, O. Reva, L. Wiehlmann, and B. Tummler. 2007. Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J. Bacteriol. 189:2443-2459. (Pubitemid 46411359)
110. Klockgether, J., D. Wurdemann, L. Wiehlmann, and B. Tummler. 2008. Transcript profiling of the Pseudomonas aeruginosa genomic islands PAGI-2 and pKLC102. Microbiology 154:1599-1604.
111. Kouda, S., M. Ohara, M. Onodera, Y. Fujiue, M. Sasaki, T. Kohara, S. Kashiyama, S. Hayashida, T. Harino, T. Tsuji, H. Itaha, N. Gotoh, A. Matsubara, T. Usui, and M. Sugai. 2009. Increased prevalence and clonal dissemination of multidrug-resistant Pseudomonas aeruginosa with the blaIMP-1 gene cassette in Hiroshima. J. Antimicrob. Chemother. 64:46-51.
112. Kropinski, A. M. 2000. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J. Bacteriol. 182: 6066-6074.
113. Kulasekara, B. R., H. D. Kulasekara, M. C. Wolfgang, L. Stevens, D. W. Frank, and S. Lory. 2006. Acquisition and evolution of the exoU locus in Pseudomonas aeruginosa. J. Bacteriol. 188:4037-4050.
114. Kurahashi, K., O. Kajikawa, T. Sawa, M. Ohara, M. A. Gropper, D. W. Frank, T. R. Martin, and J. P. Wiener-Kronish. 1999. Pathogenesis of septic shock in Pseudomonas aeruginosa pneumonia. J. Clin. Invest. 104: 743-750.
115. Kus, J. V., J. Kelly, L. Tessier, H. Harvey, D. G. Cvitkovitch, and L. L. Burrows. 2008. Modification of Pseudomonas aeruginosa Pa5196 type IV pilins at multiple sites with D-Araf by a novel GT-C family arabinosyltransferase, TfpW. J. Bacteriol. 190:7464-7478.
116. Kus, J. V., E. Tullis, D. G. Cvitkovitch, and L. L. Burrows. 2004. Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients. Microbiology 150:1315-1326.
117. Kuzio, J., and A. M. Kropinski. 1983. O-antigen conversion in Pseudomonas aeruginosa PAO1 by bacteriophage D3. J. Bacteriol. 155:203-212.
118. Kwan, T., J. Liu, M. Dubow, P. Gros, and J. Pelletier. 2006. Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J. Bacteriol. 188:1184-1187.
119. Larbig, K. D., A. Christmann, A. Johann, J. Klockgether, T. Hartsch, R. Merkl, L. Wiehlmann, H. J. Fritz, and B. Tummler. 2002. Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J. Bacteriol. 184:6665-6680.
120. Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
121. Lee, D. G., J. M. Urbach, G. Wu, N. T. Liberati, R. L. Feinbaum, S. Miyata, L. T. Diggins, J. He, M. Saucier, E. Deziel, L. Friedman, L. Li, G. Grills, K. Montgomery, R. Kucherlapati, L. G. Rahme, and F. M. Ausubel. 2006. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol. 7:R90.
122. Lee, S. W., and G. Edlin. 1985. Expression of tetracycline resistance in pBR322 derivatives reduces the reproductive fitness of plasmid-containing Escherichia coli. Gene 39:173-180.
123. Lee, V. T., R. S. Smith, B. Tummler, and S. Lory. 2005. Activities of Pseudomonas aeruginosa effectors secreted by the type III secretion system in vitro and during infection. Infect. Immun. 73:1695-1705.
124. Lesic, B., S. Bach, J. M. Ghigo, U. Dobrindt, J. Hacker, and E. Carniel. 2004. Excision of the high-pathogenicity island of Yersinia pseudotuberculosis requires the combined actions of its cognate integrase and Hef, a new recombination directionality factor. Mol. Microbiol. 52:1337-1348.
125. Levin, J. C., and D. C. Stein. 1996. Cloning, complementation, and characterization of an rfaE homolog from Neisseria gonorrhoeae. J. Bacteriol. 178:4571-4575.
126. Li, C., H. Wally, S. J. Miller, and C. D. Lu. 2009. The multifaceted proteins MvaT and MvaU, members of the H-NS family, control arginine metabolism, pyocyanin synthesis, and prophage activation in Pseudomonas aeruginosa PAO1. J. Bacteriol. 191:6211-6218.
127. Li, H., M. A. Toleman, P. M. Bennett, R. N. Jones, and T. R. Walsh. 2008. Complete sequence of p07-406, a 24,179-base-pair plasmid harboring the blaVIM-7 metallo-beta-lactamase gene in a Pseudomonas aeruginosa isolate from the United States. Antimicrob. Agents Chemother. 52:3099-3105.
128. Liang, X., X. Q. Pham, M. V. Olson, and S. Lory. 2001. Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa. J. Bacteriol. 183:843-853.
129. Libisch, B., L. Poirel, Z. Lepsanovic, V. Mirovic, B. Balogh, J. Paszti, Z. Hunyadi, A. Dobak, M. Fuzi, and P. Nordmann. 2008. Identification of PER-1 extended-spectrum beta-lactamase producing Pseudomonas aeruginosa clinical isolates of the international clonal complex CC11 from Hungary and Serbia. FEMS Immunol. Med. Microbiol. 54:330-338.
130. Liebert, C. A., R. M. Hall, and A. O. Summers. 1999. Transposon Tn21, flagship of the floating genome. Microbiol. Mol. Biol. Rev. 63:507-522.
131. Lin, R. J., M. Capage, and C. W. Hill. 1984. A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome. J. Mol. Biol. 177:1-18.
132. Lister, P. D., D. J. Wolter, and N. D. Hanson. 2009. Antibacterial- resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms. Clin. Microbiol. Rev. 22:582-610.
133. Liu, P. V., and S. Wang. 1990. Three new major somatic antigens of Pseudomonas aeruginosa. J. Clin. Microbiol. 28:922-925.
134. Livermore, D. M., and N. Woodford. 2000. Carbapenemases: a problem in waiting? Curr. Opin. Microbiol. 3:489-495.
135. Lolans, K., A. M. Queenan, K. Bush, A. Sahud, and J. P. Quinn. 2005. First nosocomial outbreak of Pseudomonas aeruginosa producing an integron-borne metallo-beta-lactamase (VIM-2) in the United States. Antimicrob. Agents Chemother. 49:3538-3540.
136. Lucchini, S., G. Rowley, M. D. Goldberg, D. Hurd, M. Harrison, and J. C. Hinton. 2006. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2:e81.
137. Lyras, D., A. W. Chan, J. McFarlane, and V. A. Stanisich. 1994. The surface exclusion system of RP1: investigation of the roles of trbJ and trbK in the surface exclusion, transfer, and slow-growth phenotypes. Plasmid 32:254-261.
138. Mahillon, J., C. Leonard, and M. Chandler. 1999. IS elements as constituents of bacterial genomes. Res. Microbiol. 150:675-687.
139. Marraffini, L. A., and E. J. Sontheimer. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-1845.
140. Mathee, K., G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish, M. Koehrsen, A. Rokas, C. N. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R. S. Smith, P. Montgomery, J. R. White, P. A. Godfrey, C. Kodira, B. Birren, J. E. Galagan, and S. Lory. 2008. Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. U. S. A. 105:3100-3105.
141. Matz, C., A. M. Moreno, M. Alhede, M. Manefield, A. R. Hauser, M. Givskov, and S. Kjelleberg. 2008. Pseudomonas aeruginosa uses type III secretion system to kill biofilm-associated amoebae. ISME J. 2:843-852.
142. Mazel, D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4:608-620.
143. McNulty, C., J. Thompson, B. Barrett, L. Lord, C. Andersen, and I. S. Roberts. 2006. The cell surface expression of group 2 capsular polysaccharides in Escherichia coli: the role of KpsD, RhsA and a multi-protein complex at the pole of the cell. Mol. Microbiol. 59:907-922.
144. Mesaros, N., P. Nordmann, P. Plesiat, M. Roussel-Delvallez, J. Van Eldere, Y. Glupczynski, Y. Van Laethem, F. Jacobs, P. Lebecque, A. Malfroot, P. M. Tulkens, and F. Van Bambeke. 2007. Pseudomonas aeruginosa: resistance and therapeutic options at the turn of the new millennium. Clin. Microbiol. Infect. 13:560-578.
145. Metcalf, W. W., and R. S. Wolfe. 1998. Molecular genetic analysis of phosphite and hypophosphite oxidation by Pseudomonas stutzeri WM88. J. Bacteriol. 180:5547-5558.
146. Meyer, J. M. 2000. Pyoverdines: pigments, siderophores and potential taxonomic markers of fluorescent Pseudomonas species. Arch. Microbiol. 174: 135-142.
147. Meyer, J. M., V. A. Geoffroy, C. Baysse, P. Cornelis, I. Barelmann, K. Taraz, and H. Budzikiewicz. 2002. Siderophore-mediated iron uptake in fluorescent Pseudomonas: characterization of the pyoverdine-receptor binding site of three cross-reacting pyoverdines. Arch. Biochem. Biophys. 397:179-183.
148. Michael, C. A., M. R. Gillings, A. J. Holmes, L. Hughes, N. R. Andrew, M. P. Holley, and H. W. Stokes. 2004. Mobile gene cassettes: a fundamental resource for bacterial evolution. Am. Nat. 164:1-12.
149. Mohd-Zain, Z., S. L. Turner, A. M. Cerdeno-Tarraga, A. K. Lilley, T. J. Inzana, A. J. Duncan, R. M. Harding, D. W. Hood, T. E. Peto, and D. W. Crook. 2004. Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands. J. Bacteriol. 186:8114-8122.
150. Naas, T., G. Cuzon, M. V. Villegas, M. F. Lartigue, J. P. Quinn, and P. Nordmann. 2008. Genetic structures at the origin of acquisition of the beta-lactamase blaKPC gene. Antimicrob. Agents Chemother. 52:1257-1263.
151. Naas, T., L. Philippon, L. Poirel, E. Ronco, and P. Nordmann. 1999. An SHV-derived extended-spectrum beta-lactamase in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 43:1281-1284.
152. Naas, T., L. Poirel, A. Karim, and P. Nordmann. 1999. Molecular characterization of In50, a class 1 integron encoding the gene for the extended-spectrum beta-lactamase VEB-1 in Pseudomonas aeruginosa. FEMS Microbiol. Lett. 176:411-419.
153. Nakayama, K., S. Kanaya, M. Ohnishi, Y. Terawaki, and T. Hayashi. 1999. The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol. Microbiol. 31:399-419.
154. Nakayama, K., K. Takashima, H. Ishihara, T. Shinomiya, M. Kageyama, S. Kanaya, M. Ohnishi, T. Murata, H. Mori, and T. Hayashi. 2000. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol. Microbiol. 38:213-231.
155. Newton, G. J., C. Daniels, L. L. Burrows, A. M. Kropinski, A. J. Clarke, and J. S. Lam. 2001. Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Mol. Microbiol. 39:1237-1247.
156. Nguyen, T. N., Q. G. Phan, L. P. Duong, K. P. Bertrand, and R. E. Lenski. 1989. Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12. Mol. Biol. Evol. 6:213-225.
157. Nicas, T., and B. H. Iglewski. 1985. The contribution of exoproducts to virulence of Pseudomonas aeruginosa. Can. J. Microbiol. 31:387-392.
158. Nordmann, P., G. Cuzon, and T. Naas. 2009. The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect. Dis. 9:228-236.
159. Nordmann, P., and L. Poirel. 2002. Emerging carbapenemases in Gramnegative aerobes. Clin. Microbiol. Infect. 8:321-331.
160. Obritsch, M. D., D. N. Fish, R. MacLaren, and R. Jung. 2004. National surveillance of antimicrobial resistance in Pseudomonas aeruginosa isolates obtained from intensive care unit patients from 1993 to 2002. Antimicrob. Agents Chemother. 48:4606-4610.
161. O'Callaghan, R. J., L. S. Engel, J. A. Hobden, M. C. Callegan, L. C. Green, and J. M. Hill. 1996. Pseudomonas keratitis. The role of an uncharacterized exoprotein, protease IV, in corneal virulence. Invest. Ophthalmol. Vis. Sci. 37:534-543.
162. Ou, H. Y., X. He, E. M. Harrison, B. R. Kulasekara, A. B. Thani, A. Kadioglu, S. Lory, J. C. Hinton, M. R. Barer, Z. Deng, and K. Rajakumar. 2007. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res. 35:W97-W104.
163. Pagani, L., C. Colinon, R. Migliavacca, M. Labonia, J. D. Docquier, E. Nucleo, M. Spalla, M. Li Bergoli, and G. M. Rossolini. 2005. Nosocomial outbreak caused by multidrug-resistant Pseudomonas aeruginosa producing IMP-13 metallo-beta-lactamase. J. Clin. Microbiol. 43:3824-3828.
164. Pena, C., C. Suarez, F. Tubau, C. Juan, B. Moya, M. A. Dominguez, A. Oliver, M. Pujol, and J. Ariza. 2009. Nosocomial outbreak of a non-cefepime- susceptible ceftazidime-susceptible Pseudomonas aeruginosa strain overexpressing MexXY-OprM and producing an integron-borne PSE-1 beta-lactamase. J. Clin. Microbiol. 47:2381-2387.
165. Peters, J. E., and N. L. Craig. 2001. Tn7: smarter than we thought. Nat. Rev. Mol. Cell. Biol. 2:806-814.
166. Petrovski, S., and V. A. Stanisich. 2010. Tn502 and Tn512 are res site hunters that provide evidence of resolvase-independent transposition to random sites. J. Bacteriol. 192:1865-1874.
167. Phillips, N. J., C. M. John, L. G. Reinders, B. W. Gibson, M. A. Apicella, and J. M. Griffiss. 1990. Structural models for the cell surface lipooligosaccharides of Neisseria gonorrhoeae and Haemophilus influenzae. Biomed. Environ. Mass Spectrom. 19:731-745.
168. Pier, G. B. 2007. Pseudomonas aeruginosa lipopolysaccharide: a major virulence factor, initiator of inflammation and target for effective immunity. Int. J. Med. Microbiol. 297:277-295.
169. Pier, G. B., and R. Ramphal. 2005. Pseudomonas aeruginosa, p. 2587-2615. In G. Mandell, J. Bennett, and R. Dolin (ed.), Principles and practice of infectious diseases. Elsevier Churchill Livingstone, Philadelphia, PA.
170. Pirnay, J. P., F. Bilocq, B. Pot, P. Cornelis, M. Zizi, J. Van Eldere, P. Deschaght, M. Vaneechoutte, S. Jennes, T. Pitt, and D. De Vos. 2009. Pseudomonas aeruginosa population structure revisited. PLoS One 4:e7740.
171. Pirnay, J. P., S. Matthijs, H. Colak, P. Chablain, F. Bilocq, J. Van Eldere, D. De Vos, M. Zizi, L. Triest, and P. Cornelis. 2005. Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river. Environ. Microbiol. 7:969-980.
172. Pitout, J. D., G. Revathi, B. L. Chow, B. Kabera, S. Kariuki, P. Nordmann, and L. Poirel. 2008. Metallo-beta-lactamase-producing Pseudomonas aeruginosa isolated from a large tertiary centre in Kenya. Clin. Microbiol. Infect. 14:755-759.
173. Poirel, L., L. Brinas, A. Verlinde, L. Ide, and P. Nordmann. 2005. BEL-1, a novel clavulanic acid-inhibited extended-spectrum beta-lactamase, and the class 1 integron In120 in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 49:3743-3748.
174. Poirel, L., L. Cabanne, H. Vahaboglu, and P. Nordmann. 2005. Genetic environment and expression of the extended-spectrum beta-lactamase blaPER-1 gene in Gram-negative bacteria. Antimicrob. Agents Chemother. 49:1708-1713.
175. Poirel, L., E. Lebessi, M. Castro, C. Fevre, M. Foustoukou, and P. Nordmann. 2004. Nosocomial outbreak of extended-spectrum beta-lactamase SHV-5-producing isolates of Pseudomonas aeruginosa in Athens, Greece. Antimicrob. Agents Chemother. 48:2277-2279.
176. Prince, A. 2006. Flagellar activation of epithelial signaling. Am. J. Respir. Cell Mol. Biol. 34:548-551.
177. Qiu, X., A. U. Gurkar, and S. Lory. 2006. Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 103:19830-19835.
178. Qiu, X., B. R. Kulasekara, and S. Lory. 2009. Role of horizontal gene transfer in the evolution of Pseudomonas aeruginosa virulence. Genome Dyn. 6:126-139.
179. Rakhimova, E., L. Wiehlmann, A. L. Brauer, S. Sethi, T. F. Murphy, and B. Tummler. 2009. Pseudomonas aeruginosa population biology in chronic obstructive pulmonary disease. J. Infect. Dis. 200:1928-1935.
180. Ramsay, J. P., J. T. Sullivan, G. S. Stuart, I. L. Lamont, and C. W. Ronson. 2006. Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol. Microbiol. 62:723-734.
181. Ravatn, R., S. Studer, D. Springael, A. J. Zehnder, and J. R. van der Meer. 1998. Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J. Bacteriol. 180:4360-4369. (Pubitemid 28405556)
182. Ravatn, R., S. Studer, A. J. Zehnder, and J. R. van der Meer. 1998. Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. strain B13. J. Bacteriol. 180:5505-5514. (Pubitemid 28489839)
183. Ravatn, R., A. J. Zehnder, and J. R. van der Meer. 1998. Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms. Appl. Environ. Microbiol. 64:2126-2132.
184. Raymond, C. K., E. H. Sims, A. Kas, D. H. Spencer, T. V. Kutyavin, R. G. Ivey, Y. Zhou, R. Kaul, J. B. Clendenning, and M. V. Olson. 2002. Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa. J. Bacteriol. 184:3614-3622.
185. Recchia, G. D., and R. M. Hall. 1995. Gene cassettes: a new class of mobile element. Microbiology 141:3015-3027.
186. Riccio, M. L., L. Pallecchi, J. D. Docquier, S. Cresti, M. R. Catania, L. Pagani, C. Lagatolla, G. Cornaglia, R. Fontana, and G. M. Rossolini. 2005. Clonal relatedness and conserved integron structures in epidemiologically unrelated Pseudomonas aeruginosa strains producing the VIM-1 metallobeta- lactamase from different Italian hospitals. Antimicrob. Agents Chemother. 49:104-110.
187. Rice, S. A., C. H. Tan, P. J. Mikkelsen, V. Kung, J. Woo, M. Tay, A. Hauser, D. McDougald, J. S. Webb, and S. Kjelleberg. 2009. The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage. ISME J. 3:271-282.
188. Roncero, C., A. Darzins, and M. J. Casadaban. 1990. Pseudomonas aeruginosa transposable bacteriophages D3112 and B3 require pili and surface growth for adsorption. J. Bacteriol. 172:1899-1904.
189. Roy, P. H., S. G. Tetu, A. Larouche, L. Elbourne, S. Tremblay, Q. Ren, R. Dodson, D. Harkins, R. Shay, K. Watkins, Y. Mahamoud, and I. T. Paulsen. 2010. Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7. PLoS One 5:e8842.
190. Roy-Burman, A., R. H. Savel, S. Racine, B. L. Swanson, N. S. Revadigar, J. Fujimoto, T. Sawa, D. W. Frank, and J. P. Wiener-Kronish. 2001. Type III protein secretion is associated with death in lower respiratory and systemic Pseudomonas aeruginosa infections. J. Infect. Dis. 183:1767-1774.
191. Schirm, M., S. K. Arora, A. Verma, E. Vinogradov, P. Thibault, R. Ramphal, and S. M. Logan. 2004. Structural and genetic characterization of glycosylation of type a flagellin in Pseudomonas aeruginosa. J. Bacteriol. 186:2523-2531.
192. Schulert, G. S., H. Feltman, S. D. P. Rabin, C. G. Martin, S. E. Battle, J. Rello, and A. R. Hauser. 2003. Secretion of the toxin ExoU is a marker for highly virulent Pseudomonas aeruginosa isolates obtained from patients with hospital-acquired pneumonia. J. Infect. Dis. 188:1695-1706.
193. Sekiguchi, J., T. Asagi, T. Miyoshi-Akiyama, T. Fujino, I. Kobayashi, K. Morita, Y. Kikuchi, T. Kuratsuji, and T. Kirikae. 2005. Multidrug-resistant Pseudomonas aeruginosa strain that caused an outbreak in a neurosurgery ward and its aac(6′)-Iae gene cassette encoding a novel aminoglycoside acetyltransferase. Antimicrob. Agents Chemother. 49:3734-3742.
194. Sentchilo, V., R. Ravatn, C. Werlen, A. J. Zehnder, and J. R. van der Meer. 2003. Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13. J. Bacteriol. 185:4530-4538. (Pubitemid 36890500)
195. Sentchilo, V., A. J. Zehnder, and J. R. van der Meer. 2003. Characterization of two alternative promoters for integrase expression in the clc genomic island of Pseudomonas sp. strain B13. Mol. Microbiol. 49:93-104.
196. Shaver, C. M., and A. R. Hauser. 2004. Relative contributions of Pseudomonas aeruginosa ExoU, ExoS, and ExoT to virulence in the lung. Infect. Immun. 72:6969-6977.
197. Sherratt, D. 1989. Tn3 and other related transposable elements: site-specific recombination and transposition, p. 163-184. In D. E. Berg and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, DC.
198. Siarkou, V. I., D. Vitti, E. Protonotariou, A. Ikonomidis, and D. Sofianou. 2009. Molecular epidemiology of outbreak-related Pseudomonas aeruginosa strains carrying the novel variant blaVIM-17 metallo-beta-lactamase gene. Antimicrob. Agents Chemother. 53:1325-1330.
199. Sisto, A., M. G. Cipriani, M. Morea, S. L. Lonigro, F. Valerio, and P. Lavermicocca. 2010. An Rhs-like genetic element is involved in bacteriocin production by Pseudomonas savastanoi pv. savastanoi. Antonie Van Leeuwenhoek 98:505-517.
200. Smedley, J. G., III, E. Jewell, J. Roguskie, J. Horzempa, A. Syboldt, D. B. Stolz, and P. Castric. 2005. Influence of pilin glycosylation on Pseudomonas aeruginosa 1244 pilus function. Infect. Immun. 73:7922-7931.
201. Smith, E. E., E. H. Sims, D. H. Spencer, R. Kaul, and M. V. Olson. 2005. Evidence for diversifying selection at the pyoverdine locus of Pseudomonas aeruginosa. J. Bacteriol. 187:2138-2147.
202. Sorensen, S. J., M. Bailey, L. H. Hansen, N. Kroer, and S. Wuertz. 2005. Studying plasmid horizontal transfer in situ: a critical review. Nat. Rev. Microbiol. 3:700-710.
203. Spangenberg, C., R. Fislage, W. Sierralta, B. Tummler, and U. Romling. 1995. Comparison of type IV-pilin genes of Pseudomonas aeruginosa of various habitats has uncovered a novel unusual sequence. FEMS Microbiol. Lett. 127:158.
204. Spencer, D. H., A. Kas, E. E. Smith, C. K. Raymond, E. H. Sims, M. Hastings, J. L. Burns, R. Kaul, and M. V. Olson. 2003. Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa. J. Bacteriol. 185:1316-1325.
205. Springael, D., K. Peys, A. Ryngaert, S. Van Roy, L. Hooyberghs, R. Ravatn, M. Heyndrickx, J. R. van der Meer, C. Vandecasteele, M. Mergeay, and L. Diels. 2002. Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Environ. Microbiol. 4:70-80.
206. Sriramulu, D. D., H. Lunsdorf, J. S. Lam, and U. Romling. 2005. Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J. Med. Microbiol. 54:667-676.
207. Stanisich, V. A., R. Arwas, P. M. Bennett, and F. de la Cruz. 1989. Characterization of Pseudomonas mercury-resistance transposon Tn502, which has a preferred insertion site in RP1. J. Gen. Microbiol. 135:2909-2915.
208. Stoebel, D. M., A. Free, and C. J. Dorman. 2008. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154:2533-2545.
209. Stokes, H. W., A. J. Holmes, B. S. Nield, M. P. Holley, K. M. Nevalainen, B. C. Mabbutt, and M. R. Gillings. 2001. Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl. Environ. Microbiol. 67:5240-5246.
210. Stokes, H. W., D. B. O'Gorman, G. D. Recchia, M. Parsekhian, and R. M. Hall. 1997. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol. Microbiol. 26:731-745.
211. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. L. Brinkman, W. O. Hufnagle, D. J. Kowalk, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K.-S. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saler, R. E. W. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959-964.
212. Takeda, Y., and M. Kageyama. 1975. Subunit arrangement in the extended sheath of pyocin R. J. Biochem. 77:679-684.
213. Talbot, G. H., J. Bradley, J. E. Edwards, Jr., D. Gilbert, M. Scheld, and J. G. Bartlett. 2006. Bad bugs need drugs: an update on the development pipeline from the Antimicrobial Availability Task Force of the Infectious Diseases Society of America. Clin. Infect. Dis. 42:657-668.
214. Tang, H., M. Kays, and A. Prince. 1995. Role of Pseudomonas aeruginosa pili in acute pulmonary infection. Infect. Immun. 63:1278-1285.
215. Tsakris, A., A. Poulou, I. Kristo, T. Pittaras, N. Spanakis, S. Pournaras, and F. Markou. 2009. Large dissemination of VIM-2-metallo-beta- lactamase- producing Pseudomonas aeruginosa strains causing health care-associated community-onset infections. J. Clin. Microbiol. 47:3524-3529.
216. Tseng, S. P., J. C. Tsai, L. J. Teng, and P. R. Hsueh. 2009. Dissemination of transposon Tn6001 in carbapenem-non-susceptible and extensively drug-resistant Pseudomonas aeruginosa in Taiwan. J. Antimicrob. Chemother. 64:1170-1174.
217. Vaca-Pacheco, S., G. L. Paniagua-Contreras, O. Garcia-Gonzalez, and M. de la Garza. 1999. The clinically isolated FIZ15 bacteriophage causes lysogenic conversion in Pseudomonas aeruginosa PAO1. Curr. Microbiol. 38:239-243.
218. van der Meer, J. R., C. Werlen, S. F. Nishino, and J. C. Spain. 1998. Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Appl. Environ. Microbiol. 64: 4185-4193.
219. Verma, A., S. K. Arora, S. K. Kuravi, and R. Ramphal. 2005. Roles of specific amino acids in the N terminus of Pseudomonas aeruginosa flagellin and of flagellin glycosylation in the innate immune response. Infect. Immun. 73:8237-8246.
220. Verma, A., M. Schirm, S. K. Arora, P. Thibault, S. M. Logan, and R. Ramphal. 2006. Glycosylation of b-type flagellin of Pseudomonas aeruginosa: structural and genetic basis. J. Bacteriol. 188:4395-4403.
221. Voisin, S., J. V. Kus, S. Houliston, F. St. Michael, D. Watson, D. G. Cvitkovitch, J. Kelly, J. R. Brisson, and L. L. Burrows. 2007. Glycosylation of Pseudomonas aeruginosa strain Pa5196 type IV pilins with mycobacterium- like alpha-1,5-linked D-Araf oligosaccharides. J. Bacteriol. 189:151-159.
222. Walsh, T. R. 2005. The emergence and implications of metallo-beta- lactamases in Gram-negative bacteria. Clin. Microbiol. Infect. 11(Suppl. 6):2-9.
223. Walsh, T. R., M. A. Toleman, L. Poirel, and P. Nordmann. 2005. Metallobeta- lactamases: the quiet before the storm? Clin. Microbiol. Rev. 18:306-325.
224. Wang, P. W., L. Chu, and D. S. Guttman. 2004. Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J. Bacteriol. 186:400-410.
225. Waters, L. S., and G. Storz. 2009. Regulatory RNAs in bacteria. Cell 136:615-628.
226. Webb, J. S., M. Lau, and S. Kjelleberg. 2004. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J. Bacteriol. 186:8066-8073.
227. West, S. A., and A. Buckling. 2003. Cooperation, virulence and siderophore production in bacterial parasites. Proc. Biol. Sci. 270:37-44.
228. Whiteley, M., M. G. Bangera, R. E. Bumgarner, M. R. Parsek, G. M. Teitzel, S. Lory, and E. P. Greenberg. 2001. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860-864.
229. Wiehlmann, L., G. Wagner, N. Cramer, B. Siebert, P. Gudowius, G. Morales, T. Kohler, C. van Delden, C. Weinel, P. Slickers, and B. Tummler. 2007. Population structure of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 104:8101-8106.
230. Wilderman, P. J., A. I. Vasil, Z. Johnson, and M. L. Vasil. 2001. Genetic and biochemical analyses of a eukaryotic-like phospholipase D of Pseudomonas aeruginosa suggest horizontal acquisition and a role for persistence in a chronic pulmonary infection model. Mol. Microbiol. 39:291-303.
231. Williams, K. P. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res. 30:866-875.
232. Winstanley, C., M. G. Langille, J. L. Fothergill, I. Kukavica-Ibrulj, C. Paradis-Bleau, F. Sanschagrin, N. R. Thomson, G. L. Winsor, M. A. Quail, N. Lennard, A. Bignell, L. Clarke, K. Seeger, D. Saunders, D. Harris, J. Parkhill, R. E. Hancock, F. S. Brinkman, and R. C. Levesque. 2009. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool epidemic strain of Pseudomonas aeruginosa. Genome Res. 19:12-23.
233. Wolfgang, M. C., B. R. Kulasekara, X. Liang, D. Boyd, K. Wu, Q. Yang, C. G. Miyada, and S. Lory. 2003. Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 100:8484-8489.
234. Woods, D. E., S. J. Cruz, and R. L. Friedman. 1982. Contribution of toxin A and elastase to virulence of Pseudomonas aeruginosa in chronic lung infections of rats. Infect. Immun. 36:1223-1228.
235. Wurdemann, D., and B. Tummler. 2007. In silico comparison of pKLC102- like genomic islands of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 275:244-249.
236. Xu, Z., L. Li, M. E. Shirtliff, M. J. Alam, S. Yamasaki, and L. Shi. 2009. Occurrence and characteristics of class 1 and 2 integrons in Pseudomonas aeruginosa isolates from patients in southern China. J. Clin. Microbiol. 47:230-234.
237. Yahr, T. L., J. T. Barbieri, and D. W. Frank. 1996. Genetic relationship between the 53- and 49-kilodalton forms of exoenzyme S from Pseudomonas aeruginosa. J. Bacteriol. 178:1412-1419.
238. Zaneveld, J. R., D. R. Nemergut, and R. Knight. 2008. Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology 154:1-15.
239. Zegans, M. E., J. C. Wagner, K. C. Cady, D. M. Murphy, J. H. Hammond, and G. A. O'Toole. 2009. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J. Bacteriol. 191:210-219.