The DOI matches its Crossref record; 57 of the 57 references it cites were found in a registry or an index.
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
Open accessAbstract
Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children’s cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes.
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Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen
Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S. L., Hufnagle, W. O., Kowalik, D. J., Lagrou, M., et al. (2000) · Nature · doi:10.1038/35023079 · Cited by 4,573
Self-citationIdentifying bacterial genes and endosymbiont DNA with Glimmer
Delcher, A. L., Bratke, K. A., Powers, E. C., & Salzberg, S. L. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm009 · Cited by 3,134
Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506758102 · Cited by 2,631
de Lorenzo, V, Herrero, M., Jakubzik, U., & Timmis, K. N. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.11.6568-6572.1990 · Cited by 1,444
Gardy, J. L., Laird, M. R., Chen, F., Rey, S., Walsh, C. J., Ester, M., & Brinkman, F. S. L. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti057 · Cited by 718
Self-citationCDD: a database of conserved domain alignments with links to domain three-dimensional structure
Marchler-Bauer, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.281 · Cited by 679
Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial
Lee, D. G., Urbach, J. M., Wu, G., Liberati, N. T., Feinbaum, R. L., Miyata, S., Diggins, L. T., He, J., Saucier, M., Déziel, E., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-10-r90 · Cited by 603
Cell Death in Pseudomonas aeruginosa Biofilm Development
Webb, J. S., Thompson, L. S., James, S., Charlton, T., Tolker-Nielsen, T., Koch, B., Givskov, M., & Kjelleberg, S. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.15.4585-4592.2003 · Cited by 599
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Self-citationPseudomonas genomes: diverse and adaptable
Silby, M. W., Winstanley, C., Godfrey, S. A. C., Levy, S. B., & Jackson, R. W. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00269.x · Cited by 960
Self-citationThe Accessory Genome of Pseudomonas aeruginosa
Kung, V. L., Ozer, E. A., & Hauser, A. R. (2010) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00027-10 · Cited by 334
Filamentous Bacteriophage Promote Biofilm Assembly and Function
Secor, P. R., Sweere, J. M., Michaels, L. A., Malkovskiy, A. V., Lazzareschi, D., Katznelson, E., Rajadas, J., Birnbaum, M. E., Arrigoni, A., Braun, K. R., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.013 · Cited by 331
Detecting genomic islands using bioinformatics approaches
Langille, M. G. I., Hsiao, W. W. L., & Brinkman, F. S. L. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2350 · Cited by 279
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Metadata
- Authors
- Winstanley, C., Langille, M. G. I., Fothergill, J. L., Kukavica-Ibrulj, I., Paradis-Bleau, C., Sanschagrin, F., Thomson, N. R., Winsor, G. L., Quail, M. A., Lennard, N., Bignell, A., Clarke, L., Seeger, K., Saunders, D., Harris, D., Parkhill, J., Hancock, R. E. W., Brinkman, F. S. L., & Levesque, R. C.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-12-01
- Volume
- 19
- Issue
- 1
- Pages
- 12-23
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2165913026
- Cited by
- 339
- References
- 57
- Type
- posted content
- Language
- en
- Open access
- hybrid
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- Winstanley, C., Langille, M. G. I., Fothergill, J. L., Kukavica-Ibrulj, I., Paradis-Bleau, C., Sanschagrin, F., Thomson, N. R., Winsor, G. L., Quail, M. A., Lennard, N., Bignell, A., Clarke, L., Seeger, K., Saunders, D., Harris, D., Parkhill, J., Hancock, R. E. W., Brinkman, F. S. L., & Levesque, R. C. (2009). Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Research. https://doi.org/10.1101/gr.086082.108
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