Genomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients

Journal of Bacteriology

Volumn 194, Issue 18, 2012, Pages 4857-4866

  Chung, Jade C S ^a   Becq, Jennifer ^d   Fraser, Louise ^d   Schulz Trieglaff, Ole ^d   Bond, Nicholas J ^a   Foweraker, Juliet ^b   Bruce, Kenneth D ^c   Smith, Geoffrey P ^d   Welch, Martin ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b PAPWORTH HOSPITAL   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

^d Illumina Cambridge Limited   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CYSTIC FIBROSIS; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; INDEL MUTATION; NONHUMAN; PRIORITY JOURNAL; PROPHAGE; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHRONIC DISEASE; CYSTIC FIBROSIS; DNA, BACTERIAL; GENETIC VARIATION; HUMANS; INDEL MUTATION; POINT MUTATION; PROPHAGES; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS; SEQUENCE ANALYSIS, DNA; SPUTUM;

PSEUDOMONAS AERUGINOSA;

EID: 84866380002     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01050-12     Document Type: Article

References (47)

1. Battle SE, Rello J, Hauser AR. 2009. Genomic islands of Pseudomonas aeruginosa. FEMS Microbiol. Lett. 290:70-78.
2. Ciofu O, Mandsberg LF, Wang H, Høiby N. 2012. Phenotypes selected during chronic lung infection in cystic fibrosis patients: implications for the treatment of Pseudomonas aeruginosa biofilm infections. FEMS Immunol. Med. Microbiol. doi:10.1111/j.1574-695X.2012.00983.x.
3. Cramer N, et al. 2011. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ. Microbiol. 3:1690-1704.
4. D'Argenio DA, et al. 2007. Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol. Microbiol. 64:512-533.
5. Dekimpe V, Déziel E. 2009. Revisiting the quorum-sensing hierarchy in Pseudomonas aeruginosa: the transcriptional regulator RhlR regulates LasR-specific factors. Microbiology 155:712-723.
6. Deretic V, Konyecsni WM. 1990. A procaryotic regulatory factor with a histone H1-like carboxy-terminal domain: clonal variation of repeats within algP, a gene involved in regulation of mucoidy in Pseudomonas aeruginosa. J. Bacteriol. 172:5544-5554.
7. Diaz MR, King JM, Yahr TL. 2011. Intrinsic and extrinsic regulation of type III secretion gene expression in Pseudomonas aeruginosa. Front. Microbiol. 2:89. doi:10.3389/fmicb.2011.00089.
8. Diggle SP, et al. 2003. The Pseudomonas aeruginosa quinolone signal molecule overcomes the cell density-dependency of the quorum sensing hierarchy, regulates rhl-dependent genes at the onset of stationary phase and can be produced in the absence of LasR. Mol. Microbiol. 50:29-43.
9. Foweraker J. 2009. Recent advances in the microbiology of respiratory tract infection in cystic fibrosis. Br. Med. Bull. 89:93-110.
10. Foweraker JE, Laughton CR, Brown DF, Bilton D. 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.
11. Govan JR, Deretic V. 1996. Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol. Rev. 60:539-574.
12. Heurlier K, et al. 2005. Quorum-sensing-negative (lasR) mutants of Pseudomonas aeruginosa avoid cell lysis and death. J. Bacteriol. 187:4875-4883.
13. Hoffman LR, et al. 2009. Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression. J. Cyst. Fibros. 8:66-70.
14. Jalal S, Ciofu O, Hoiby N, Gotoh N, Wretlind B. 2000. Molecular mechanisms of fluoroquinolone resistance in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Antimicrob. Agents Chemother. 44: 710-712.
15. Jones AK, et al. 2010. Activation of the Pseudomonas aeruginosa AlgU regulon through mucA mutation inhibits cyclic AMP/Vfr signaling. J. Bacteriol. 192:5709-5717.
16. Kong KF, Aguila A, Schneper L, Mathee K. 2010. Pseudomonas aeruginosa -lactamase induction requires two permeases, AmpG and AmpP. BMC Microbiol. 10:328. doi:10.1186/1471-2180-10-328.
17. Leong PM, Hsia HC, Miller JH. 1986. Analysis of spontaneous base substitutions generated in mismatch-repair-deficient strains of Escherichia coli. J. Bacteriol. 168:412-416.
18. Macvanin M, et al. 2003. Fusidic acid-resistant mutants of Salmonella enterica serovar Typhimurium with low fitness in vivo are defective in RpoS induction. Antimicrob. Agents Chemother. 47:3743-3749.
19. Mathee K, et al. 2008. Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. U. S. A. 105:3100-3105.
20. Mena A, et al. 2008. Genetic adaptation of Pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation. J. Bacteriol. 190:7910-7917.
21. Mikkelsen H, Duck Z, Lilley KS, Welch M. 2007. Interrelationships between colonies, biofilms, and planktonic cells of Pseudomonas aeruginosa. J. Bacteriol. 189:2411-2416.
22. Mowat E, et al. 2011. Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. Am. J. Respir. Crit. Care Med. 183:1674-1679.
23. Oliver A, Cantón R, Campo P, Baquero F, Blázquez J. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288:1251-1254.
24. Pearson JP, Pesci EC, Iglewski BH. 1997. Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes. J. Bacteriol. 179:5756-5767.
25. Pesci EC, Pearson JP, Seed PC, Iglewski BH. 1997. Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa. J. Bacteriol. 179:3127-3132.
26. Rashid MH, Kornberg A. 2000. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 97:4885-4890.
27. Römling U, Wingender J, Muller H, Tummler B. 1994. A major Pseudomonas aeruginosa clone common to patients and aquatic habitats. Appl. Environ. Microbiol. 60:1734-1738.
28. Römling U, et al. 1994. Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis. J. Infect. Dis. 170:1616-1621.
29. Schaber JA, et al. 2004. Analysis of quorum sensing-deficient clinical isolates of Pseudomonas aeruginosa. J. Med. Microbiol. 53:841-853.
30. Schwyn B, Neilands JB. 1987. Universal chemical assay for the detection and determination of siderophores. Anal. Biochem. 160:47-56.
31. Sennhauser G, Bukowska MA, Briand C, Grütter MG. 2009. Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa. J. Mol. Biol. 389:134-145.
32. Siegmund I, Wagner F. 1991. New method for detecting rhamnolipids excreted by Pseudomonas species during growth on mineral agar. Biotechnol. Tech. 5:265-268.
33. Smith D, et al. 2006. Variations on a theme: diverse N-acyl homoserine lactone-mediated quorum sensing mechanisms in gram-negative bacteria. Sci. Prog. 89:167-211.
34. Smith EE, et al. 2006. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. U. S. A. 103: 8487-8492.
35. Stover CK, et al. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959-964.
36. Swift S, et al. 1997. Quorum sensing in Aeromonas hydrophila and Aeromonas salmonicida: identification of the LuxRI homologs AhyRI and AsaRI and their cognate N-acylhomoserine lactone signal molecules. J. Bacteriol. 179:5271-5281.
37. Tremblay J, Deziel E. 2008. Improving the reproducibility of Pseudomonas aeruginosa swarming motility assays. J. Basic Microbiol. 48: 509-515.
38. van Delden C, Comte R, Bally AM. 2001. Stringent response activates quorum sensing and modulates cell density-dependent gene expression in Pseudomonas aeruginosa. J. Bacteriol. 183:5376-5384.
39. Wiehlmann L, et al. 2007. Population structure of Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. U. S. A. 104:8101-8106.
40. Winson MK, et al. 1998. Construction and analysis of luxCDABE-based plasmid sensors for investigating N-acyl homoserine lactone-mediated quorum sensing. FEMS Microbiol. Lett. 163:185-192.
41. Winstanley C, Fothergill JL. 2009. The role of quorum sensing in chronic cystic fibrosis Pseudomonas aeruginosa infections. FEMS Microbiol. Lett. 290:1-9.
42. Winstanley C, 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.
43. Yang L, et al. 2011. Evolutionary dynamics of bacteria in a human host environment. Proc. Natl. Acad. Sci. U. S. A. 108:7481-7486.
44. Yonezawa M, Takahata M, Matsubara N, Watanabe Y, Narita H. 1995. DNA gyrase gyrA mutations in quinolone-resistant clinical isolates of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 39:1970-1972.
45. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
46. Zhang L, Mah TF. 2008. Involvement of a novel efflux system in biofilmspecific resistance to antibiotics. J. Bacteriol. 190:4447-4452.
47. Zhang S, McCormack FX, Levesque RC, O'Toole GA, Lau GW. 2007. The flagellum of Pseudomonas aeruginosa is required for resistance to clearance by surfactant protein A. PLoS One 2(6):e564. doi:10.1371/journal.pone.0000564.