Developing an international Pseudomonas aeruginosa reference panel

MicrobiologyOpen

Volumn 2, Issue 6, 2013, Pages 1010-1023

  De Soyza, Anthony ^a   Hall, Amanda J ^b   Mahenthiralingam, Eshwar ^c   Drevinek, Pavel ^d   Kaca, Wieslaw ^e   Drulis Kawa, Zuzanna ^f   Stoitsova, Stoyanka R ^g   Toth, Veronika ^h   Coenye, Tom ⁱ   Zlosnik, James E A ^j   Burns, Jane L ^k   Sá Correia, Isabel ^l   De Vos, Daniel ^m   Pirnay, Jean Paul ^m   J Kidd, Timothy ⁿ   Reid, David ^o   Manos, Jim ^p   Klockgether, Jens ^q   Wiehlmann, Lutz ^q   Tümmler, Burkhard ^q   Mcclean, Siobhán ^r   Winstanley, Craig ^b   more..

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d UNIVERSITY HOSPITAL MOTOL   (Czech Republic)

^e JAN KOCHANOWSKI UNIVERSITY   (Poland)

^f UNIVERSITY OF WROC AW   (Poland)

^g INSTITUTE OF MICROBIOLOGY   (Bulgaria)

^h SEMMELWEIS UNIVERSITY   (Hungary)

ⁱ GHENT UNIVERSITY   (Belgium)

^j UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^k SEATTLE CHILDREN S HOSPITAL   (United States)

^l INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^m QUEEN ASTRID MILITARY HOSPITAL   (Belgium)

ⁿ UNIVERSITY OF QUEENSLAND   (Australia)

^o THE PRINCE CHARLES HOSPITAL   (Australia)

^p UNIVERSITY OF SYDNEY   (Australia)

^q HANNOVER MEDICAL SCHOOL   (Germany)

^r DUBLIN INSTITUTE OF TECHNOLOGY   (Ireland)

more..

Author keywords

Cystic fibrosis; Genotype; Pathogen; Pseudomonas aeruginosa

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BIODIVERSITY; CYSTIC FIBROSIS; GENOTYPE; MICROBIAL DIVERSITY; MICROBIOLOGICAL PARAMETERS; MORBIDITY; MORTALITY; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; REFERENCE PANEL STRAIN; SEROTYPE;

CYSTIC FIBROSIS; GENOTYPE; PATHOGEN; PSEUDOMONAS AERUGINOSA;

BIOMEDICAL RESEARCH; CYSTIC FIBROSIS; HUMANS; INTERNATIONAL COOPERATION; MICROBIOLOGY; PNEUMONIA, BACTERIAL; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS; REFERENCE STANDARDS;

EID: 84889642167     PISSN: None     EISSN: 20458827     Source Type: Journal    
DOI: 10.1002/mbo3.141     Document Type: Article

References (92)

1. Aaron, S. D., K. L. Vandemheen, K. Ramotar, T. Giesbrecht-Lewis, E. Tullis, A. Freitag, et al. 2010. Infection with transmissible strains of Pseudomonas aeruginosa and clinical outcomes in adults with cystic fibrosis. JAMA 304:2145-2153.
2. Ader, F., R. le Berre, K. Faure, P. Gosset, O. Epaulard, B. Toussaint, et al. 2005. Alveolar response to Pseudomonas aeruginosa: role of the type III secretion system. Infect. Immun. 73:4263-4271.
3. Al-Aloul, M., J. Crawley, C. Winstanley, C. A. Hart, M. J. Ledson, and M. J. Walshaw. 2004. Increased morbidity associated with chronic infection by an epidemic Pseudomonas aeruginosa strain in CF patients. Thorax 59:334-336.
4. Armstrong, D. S., G. M. Nixon, R. Carzino, A. Bigham, J. B. Carlin, R. M. Robins-Browne, et al. 2002. Detection of a widespread clone of Pseudomonas aeruginosa in a pediatric cystic fibrosis clinic. Am. J. Respir. Crit. Care Med. 166: 983-987.
5. Armstrong, D., S. Bell, M. Robinson, P. Bye, B. Rose, C. Harbour, et al. 2003. Evidence for spread of a clonal strain of Pseudomonas aeruginosa among cystic fibrosis clinics. J. Clin. Microbiol. 41:2266-2267.
6. 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. USA 98:9342-9347.
7. Ashish, A., M. Shaw, C. Winstanley, M. J. Ledson, and M. J. Walshaw. 2012. Increasing resistance of the Liverpool Epidemic Strain (LES) of Pseudomonas aeruginosa (Psa) to antibiotics in cystic fibrosis (CF)-a cause for concern? J. Cyst. Fibros. 11:173-179.
8. Bezuidt, O. K., J. Klockgether, S. Elsen, I. Attree, C. F. Davenport, and B. Tummler. 2013. Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB. BMC Genomics 14:416.
9. Blainey, P. C., C. E. Milla, D. N. Cornfield, and S. R. Quake. 2012. Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Sci. Transl. Med. 4:153ra130.
10. Bohn, Y.-S. T., G. Brandes, E. Rakhimova, S. Horatzek, P. Salunkhe, A. Munder, et al. 2009. Multiple roles of Pseudomonas aeruginosa TBCF10839 PilY1 in motility, transport and infection. Mol. Microbiol. 71:730-747.
11. Bradbury, R., A. Champion, and D. W. Reid. 2008. Poor clinical outcomes associated with a multi-drug resistant clonal strain of Pseudomonas aeruginosa in the Tasmanian cystic fibrosis population. Respirology 13:886-892.
12. Bragonzi, A., L. Wiehlmann, J. Klockgether, N. Cramer, D. Worlitzsch, G. Doring, et al. 2006. Sequence diversity of the mucABD locus in Pseudomonas aeruginosa isolates from patients with cystic fibrosis. Microbiology 152:3261-3269.
13. Bragonzi, A., M. Paroni, A. Nonis, N. Cramer, S. Montanari, J. Rejman, et al. 2009. Pseudomonas aeruginosa microevolution during cystic fibrosis lung infection establishes clones with adapted virulence. Am. J. Respir. Crit. Care Med. 180:138-145.
14. Brencic, A., and S. Lory. 2009. Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA. Mol. Microbiol. 72:612-632.
15. Callaghan, M., and S. McClean. 2012. Bacterial host interactions in cystic fibrosis. Curr. Opin. Microbiol. 15:71-77.
16. Carter, M. E., J. L. Fothergill, M. J. Walshaw, K. Rajakumar, A. Kadioglu, and C. Winstanley. 2010. A subtype of a Pseudomonas aeruginosa cystic fibrosis epidemic strain exhibits enhanced virulence in a murine model of acute respiratory infection. J. Infect. Dis. 202:935-942.
17. Cheng, K., R. L. Smyth, J. R. Govan, C. Doherty, C. Winstanley, N. Denning, et al. 1996. Spread of beta-lactam-resistant Pseudomonas aeruginosa in a cystic fibrosis clinic. Lancet 348:639-642.
18. de Chial, M., B. Ghysels, S. A. Beatson, V. Geoffroy, J. M. Meyer, T. Pattery, et al. 2003. Identification of type II and type III pyoverdine receptors from Pseudomonas aeruginosa. Microbiology 149:821-831.
19. Cigana, C., L. Curcuru, M. R. Leone, T. Ierano, N. I. Lore, I. Bianconi, et al. 2009. Pseudomonas aeruginosa exploits lipid A and muropeptides modification as a strategy to lower innate immunity during cystic fibrosis lung infection. PLoS ONE 4:e8439.
20. Coenye, T., P. Vandamme, J. J. Lipuma, J. R. Govan, and E. Mahenthiralingam. 2003. Updated version of the Burkholderia cepacia complex experimental strain panel. J. Clin. Microbiol. 41:2797-2798.
21. Cramer, N., J. Klockgether, K. Wrasman, M. Schmidt, C. F. Davenport, and B. Tummler. 2011. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ. Microbiol. 13: 1690-1704.
22. Cramer, N., L. Wiehlmann, O. Ciofu, S. Tamm, N. Hoiby, and B. Tummler. 2012. Molecular epidemiology of chronic Pseudomonas aeruginosa airway infections in cystic fibrosis. PLoS ONE 7:e50731.
23. Dacheux, D., B. Toussaint, M. Richard, G. Brochier, J. Croize, and I. Attree. 2000. Pseudomonas aeruginosa cystic fibrosis isolates induce rapid, type III secretion-dependent, but ExoU-independent, oncosis of macrophages and polymorphonuclear neutrophils. Infect. Immun. 68: 2916-2924.
24. D'Argenio, D. A., M. Wu, L. R. Hoffman, H. D. Kulasekara, E. Deziel, E. E. Smith, et al. 2007. Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol. Microbiol. 64:512-533.
25. Davies, J. C., and B. K. Rubin. 2007. Emerging and unusual gram-negative infections in cystic fibrosis. Semin. Respir. Crit. Care Med. 28:312-321.
26. Ernst, R. K., S. M. Moskowitz, J. C. Emerson, G. M. Kraig, K. N. Adams, M. D. Harvey, et al. 2007. Unique lipid a modifications in Pseudomonas aeruginosa isolated from the airways of patients with cystic fibrosis. J. Infect. Dis. 196:1088-1092.
27. Feil, E. J., B. C. Li, D. M. Aanensen, W. P. Hanage, and B. G. Spratt. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186:1518-1530.
28. Fodor, A. A., E. R. Klem, D. F. Gilpin, J. S. Elborn, R. C. Boucher, M. M. Tunney, et al. 2012. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS ONE 7:e45001.
29. Fothergill, J. L., M. J. Walshaw, and C. Winstanley. 2012a. Transmissible strains of Pseudomonas aeruginosa in Cystic Fibrosis lung infections. Eur. Respir. J. 40:227-238.
30. Fothergill, J. L., C. Winstanley, and C. E. James. 2012b. Novel therapeutic strategies to counter Pseudomonas aeruginosa infections. Expert Rev. Anti Infect Ther. 10:219-235.
31. Foweraker, J. E., C. R. Laughton, D. F. Brown, and D. Bilton. 2005. Phenotypic variability of Pseudomonas aeruginosa in sputa from patients with acute infective exacerbation of cystic fibrosis and its impact on the validity of antimicrobial susceptibility testing. J. Antimicrob. Chemother. 55:921-927.
32. Francis, H. C., C. O. Prys-Picard, D. Fishwick, C. Stenton, P. S. Burge, L. M. Bradshaw, et al. 2007. Defining and investigating occupational asthma: a consensus approach. Occup. Environ. Med. 64:361-365.
33. Govan, J. R., and V. Deretic. 1996. Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol. Rev. 60:539-574.
34. Hajjar, A. M., R. K. Ernst, J. H. Tsai, C. B. Wilson, and S. I. Miller. 2002. Human Toll-like receptor 4 recognizes host-specific LPS modifications. Nat. Immunol. 3:354-359.
35. Hall, A. J., J. L. Fothergill, S. B. Kaye, T. J. Neal, P. S. McNamara, K. W. Southern, et al. 2013. Intraclonal genetic diversity amongst cystic fibrosis and keratitis isolates of Pseudomonas aeruginosa. J. Med. Microbiol. 62:208-216.
36. He, J., R. L. Baldini, E. Deziel, M. Saucier, Q. Zhang, N. T. Liberati, et al. 2004. The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc. Natl Acad. Sci. USA 101:2530-2535.
37. Hoffmann, N., T. B. Rasmussen, P. O. Jensen, C. Stub, M. Hentzer, S. Molin, et al. 2005. Novel mouse model of chronic Pseudomonas aeruginosa lung infection mimicking cystic fibrosis. Infect. Immun. 73:2504-2514.
38. Jones, A. M., M. E. Dodd, C. J. Doherty, J. R. Govan, and A. K. Webb. 2002. Increased treatment requirements of patients with cystic fibrosis who harbour a highly transmissible strain of Pseudomonas aeruginosa. Thorax 57:924-925.
39. Jones, A. M., M. E. Dodd, J. Morris, C. Doherty, J. R. Govan, and A. K. Webb. 2010. Clinical outcome for cystic fibrosis patients infected with transmissible pseudomonas aeruginosa: an 8-year prospective study. Chest 137:1405-1409.
40. Kidd, T. J., S. R. Ritchie, K. A. Ramsay, K. Grimwood, S. C. Bell, and P. B. Rainey. 2012. Pseudomonas aeruginosa Exhibits Frequent Recombination, but Only a Limited Association between Genotype and Ecological Setting. PLoS ONE 7:e44199.
41. Kidd, T. J., K. A. Ramsay, H. Hu, G. B. Marks, C. E. Wainwright, P. T. Bye, et al. 2013. Shared Pseudomonas aeruginosa genotypes are common in Australian cystic fibrosis centres. Eur. Respir. J. 41: 1091-1100.
42. 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.
43. Klockgether, J., A. Munder, J. Neugebauer, C. F. Davenport, F. Stanke, K. D. Larbig, et al. 2010. Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J. Bacteriol. 192:1113-1121.
44. Klockgether, J., N. Miethke, P. Kubesch, Y. S. Bohn, I. Brockhausen, N. Cramer, et al. 2013. Intraclonal diversity of the Pseudomonas aeruginosa cystic fibrosis airway isolates TBCF10839 and TBCF121838: distinct signatures of transcriptome, proteome, metabolome, adherence and pathogenicity despite an almost identical genome sequence. Environ. Microbiol. 15:191-210.
45. Kohler, T., A. Buckling, and C. van Delden. 2009. Cooperation and virulence of clinical Pseudomonas aeruginosa populations. Proc. Natl Acad. Sci. USA 106:6339-6344.
46. Kukavica-Ibrulj, I., A. Bragonzi, M. Paroni, C. Winstanley, F. Sanschagrin, G. A. O'toole, et al. 2008. In vivo growth of Pseudomonas aeruginosa strains PAO1 and PA14 and the hypervirulent strain LESB58 in a rat model of chronic lung infection. J. Bacteriol. 190:2804-2813.
47. Larbig, K. D., A. Christmann, A. Johann, J. Klockgether, T. Hartsch, R. Merkl, et al. 2002. Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J. Bacteriol. 184:6665-6680.
48. Lee, D. G., J. M. Urbach, G. Wu, N. T. Liberati, R. L. Feinbaum, S. Miyata, et al. 2006. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol. 7:R90.
49. Leitao, J. H., T. Alvim, and I. Sa-Correia. 1996. Ribotyping of Pseudomonas aeruginosa isolates from patients and water springs and genome fingerprinting of variants concerning mucoidy. FEMS Immunol. Med. Microbiol. 13:287-292.
50. 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.
51. Lipuma, J. J. 2010. The changing microbial epidemiology in cystic fibrosis. Clin. Microbiol. Rev. 23:299-323.
52. Lore, N. I., C. Cigana, I. de Fino, C. Riva, M. Juhas, S. Schwager, et al. 2012. Cystic fibrosis-niche adaptation of Pseudomonas aeruginosa reduces virulence in multiple infection hosts. PLoS ONE 7:e35648.
53. Mahenthiralingam, E., T. Coenye, J. W. Chung, D. P. Speert, J. R. Govan, P. Taylor, et al. 2000. Diagnostically and experimentally useful panel of strains from the Burkholderia cepacia complex. J. Clin. Microbiol. 38:910-913.
54. Manos, J., J. Arthur, B. Rose, P. Tingpej, C. Fung, M. Curtis, et al. 2008. Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung. J. Med. Microbiol. 57:1454-1465.
55. Martin, K., B. Baddal, N. Mustafa, C. Perry, A. Underwood, C. Constantidou, et al. 2013. Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the United Kingdom. J. Med. Microbiol. 62(Pt.7): 988-1000.
56. Mathee, K., G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish, M. Koehrsen, et al. 2008. Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl Acad. Sci. USA 105:3100-3105.
57. McCallum, S. J., M. J. Gallagher, J. E. Corkill, C. A. Hart, M. J. Ledson, and M. J. Walshaw. 2002. Spread of an epidemic Pseudomonas aeruginosa strain from a patient with cystic fibrosis (CF) to non-CF relatives. Thorax 57:559-560.
58. Miller, W. L., M. J. Matewish, D. J. McNally, N. Ishiyama, E. M. Anderson, D. Brewer, et al. 2008. Flagellin glycosylation in Pseudomonas aeruginosa PAK requires the O-antigen biosynthesis enzyme WbpO. J. Biol. Chem. 283:3507-3518.
59. Moskowitz, S. M., and R. K. Ernst. 2010. The role of Pseudomonas lipopolysaccharide in cystic fibrosis airway infection. Subcell. Biochem. 53:241-253.
60. Mowat, E., S. Paterson, J. L. Fothergill, E. A. Wright, M. J. Ledson, M. J. Walshaw, et al. 2011. Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. Am. J. Respir. Crit. Care Med. 183:1674-1679.
61. Mulcahy, L. R., J. L. Burns, S. Lory, and K. Lewis. 2010. Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. J. Bacteriol. 192:6191-6199.
62. Naughton, S., D. Parker, T. Seemann, T. Thomas, L. Turnbull, B. Rose, et al. 2011. Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung. PLoS ONE 6:e24526.
63. O'Carroll, M. R., M. W. Syrmis, C. E. Wainwright, R. M. Greer, P. Mitchell, C. Coulter, et al. 2004. Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. Eur. Respir. J. 24:101-106.
64. Oliver, A., R. Canton, P. Campo, F. Baquero, and J. Blazquez. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288:1251-1254.
65. Parkins, M. D., J. C. Rendall, and J. S. Elborn. 2012. Incidence and risk factors for pulmonary exacerbation treatment failures in patients with cystic fibrosis chronically infected with Pseudomonas aeruginosa. Chest 141:485-493.
66. Pirnay, J. P., D. De Vos, C. Cochez, F. Bilocq, A. Vanderkelen, M. Zizi, et al. 2002. Pseudomonas aeruginosa displays an epidemic population structure. Environ. Microbiol. 4:898-911.
67. Pirnay, J. P., F. Bilocq, B. Pot, P. Cornelis, M. Zizi, J. van Eldere, et al. 2009. Pseudomonas aeruginosa population structure revisited. PLoS ONE 4:e7740.
68. Rahme, L. G., E. J. Stevens, S. F. Wolfort, J. Shao, R. G. Tompkins, and F. M. Ausubel. 1995. Common virulence factors for bacterial pathogenicity in plants and animals. Science 268:1899-1902.
69. 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.
70. Romling, U., A. Kader, D. D. Sriramulu, R. Simm, and G. Kronvall. 2005. Worldwide distribution of Pseudomonas aeruginosa clone C strains in the aquatic environment and cystic fibrosis patients. Environ. Microbiol. 7:1029-1038.
71. Salunkhe, P., C. H. Smart, J. A. Morgan, S. Panagea, M. J. Walshaw, C. A. Hart, et al. 2005. A cystic fibrosis epidemic strain of Pseudomonas aeruginosa displays enhanced virulence and antimicrobial resistance. J. Bacteriol. 187:4908-4920.
72. Scott, F. W., and T. L. Pitt. 2004. Identification and characterization of transmissible Pseudomonas aeruginosa strains in cystic fibrosis patients in England and Wales. J. Med. Microbiol. 53:609-615.
73. Semblat, J. P., and C. Doerig. 2012. PAK in pathogen-host interactions. Cell Logist. 2:126-131.
74. Shankar, J., H. Sueke, L. Wiehlmann, M. J. Horsburgh, S. Tuft, T. J. Neal, et al. 2012. Genotypic analysis of UK keratitis-associated Pseudomonas aeruginosa suggests adaptation to environmental water as a key component in the development of eye infections. FEMS Microbiol. Lett. 334:79-86.
75. Smith, E. E., D. G. Buckley, Z. Wu, C. Saenphimmachak, L. R. Hoffman, D. A. D'argenio, et al. 2006. From the Cover: genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl Acad. Sci. USA 103:8487-8492.
76. de Soyza, A., K. Morris, A. McDowell, C. Doherty, L. Archer, J. Perry, et al. 2004. Prevalence and clonality of Burkholderia cepacia complex genomovars in UK patients with cystic fibrosis referred for lung transplantation. Thorax 59:526-528.
77. Spencer, D. H., A. Kas, E. E. Smith, C. K. Raymond, E. H. Sims, M. Hastings, et al. 2003. Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa. J. Bacteriol. 185:1316-1325.
78. Spratt, B. G., W. P. Hanage, B. Li, D. M. Aanensen, and E. J. Feil. 2004. Displaying the relatedness among isolates of bacterial species - the eBURST approach. FEMS Microbiol. Lett. 241:129-134.
79. Stewart, R. M., L. Wiehlmann, K. E. Ashelford, S. J. Preston, E. Frimmersdorf, B. J. Campbell, et al. 2011. Genetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections. J. Clin. Microbiol. 49:993-1003.
80. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, et al. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
81. Syrmis, M. W., M. R. O'carroll, T. P. Sloots, C. Coulter, C. E. Wainwright, S. C. Bell, et al. 2004. Rapid genotyping of Pseudomonas aeruginosa isolates harboured by adult and paediatric patients with cystic fibrosis using repetitive-element-based PCR assays. J. Med. Microbiol. 53:1089-1096.
82. Tavares, I. M., J. H. Leitao, A. M. Fialho, and I. Sa-Correia. 1999. Pattern of changes in the activity of enzymes of GDP-D-mannuronic acid synthesis and in the level of transcription of algA, algC and algD genes accompanying the loss and emergence of mucoidy in Pseudomonas aeruginosa. Res. Microbiol. 150:105-116.
83. Totten, P. A., and S. Lory. 1990. Characterization of the type a flagellin gene from Pseudomonas aeruginosa PAK. J. Bacteriol. 172:7188-7199.
84. Toussaint, B., I. Delic-Attree, and P. M. Vignais. 1993. Pseudomonas aeruginosa contains an IHF-like protein that binds to the algD promoter. Biochem. Biophys. Res. Commun. 196:416-421.
85. Tummler, B., U. Koopmann, D. Grothues, H. Weissbrodt, G. Steinkamp, and H. von der Hardt. 1991. Nosocomial acquisition of Pseudomonas aeruginosa by cystic fibrosis patients. J. Clin. Microbiol. 29:1265-1267.
86. Vasseur, P., I. Vallet-Gely, C. Soscia, S. Genin, and A. Filloux. 2005. The pel genes of the Pseudomonas aeruginosa PAK strain are involved at early and late stages of biofilm formation. Microbiology 151:985-997.
87. Wiehlmann, L., G. Wagner, N. Cramer, B. Siebert, P. Gudowius, G. Morales, et al. 2007. Population structure of Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 104:8101-8106.
88. Winsor, G. L., D. K. Lam, L. Fleming, R. Lo, M. D. Whiteside, N. Y. Yu, et al. 2011. Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res. 39:D596-D600.
89. Winstanley, C., M. G. Langille, J. L. Fothergill, I. Kukavica-Ibrulj, C. Paradis-Bleau, F. Sanschagrin, et al. 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.
90. Yang, L., L. Jelsbak, R. L. Marvig, S. Damkiaer, C. T. Workman, M. H. Rau, et al. 2011a. Evolutionary dynamics of bacteria in a human host environment. Proc. Natl Acad. Sci. USA 108:7481-7486.
91. Yang, L., L. Jelsbak, R. L. Marvig, S. Damkiaer, C. T. Workman, M. H. Rau, et al. 2011b. Evolutionary dynamics of bacteria in a human host environment. Proc. Natl Acad. Sci. USA 108:7481-7486.
92. Zhao, J., P. D. Schloss, L. M. Kalikin, L. A. Carmody, B. K. Foster, J. F. Petrosino, et al. 2012. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc. Natl Acad. Sci. USA 109:5809-5814.