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Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

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Abstract
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers similar to 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.

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MLA
Berger, Carola, et al. “Estimation of Pathogenic Potential of an Environmental Pseudomonas Aeruginosa Isolate Using Comparative Genomics.” SCIENTIFIC REPORTS, vol. 11, no. 1, 2021, doi:10.1038/s41598-020-80592-8.
APA
Berger, C., Rueckert, C., Blom, J., Rabaey, K., Kalinowski, J., & Rosenbaum, M. A. (2021). Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. SCIENTIFIC REPORTS, 11(1). https://doi.org/10.1038/s41598-020-80592-8
Chicago author-date
Berger, Carola, Christian Rueckert, Jochen Blom, Korneel Rabaey, Joern Kalinowski, and Miriam A. Rosenbaum. 2021. “Estimation of Pathogenic Potential of an Environmental Pseudomonas Aeruginosa Isolate Using Comparative Genomics.” SCIENTIFIC REPORTS 11 (1). https://doi.org/10.1038/s41598-020-80592-8.
Chicago author-date (all authors)
Berger, Carola, Christian Rueckert, Jochen Blom, Korneel Rabaey, Joern Kalinowski, and Miriam A. Rosenbaum. 2021. “Estimation of Pathogenic Potential of an Environmental Pseudomonas Aeruginosa Isolate Using Comparative Genomics.” SCIENTIFIC REPORTS 11 (1). doi:10.1038/s41598-020-80592-8.
Vancouver
1.
Berger C, Rueckert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA. Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. SCIENTIFIC REPORTS. 2021;11(1).
IEEE
[1]
C. Berger, C. Rueckert, J. Blom, K. Rabaey, J. Kalinowski, and M. A. Rosenbaum, “Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics,” SCIENTIFIC REPORTS, vol. 11, no. 1, 2021.
@article{8704649,
  abstract     = {{The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers similar to 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.}},
  articleno    = {{1370}},
  author       = {{Berger, Carola and Rueckert, Christian and Blom, Jochen and Rabaey, Korneel and Kalinowski, Joern and Rosenbaum, Miriam A.}},
  issn         = {{2045-2322}},
  journal      = {{SCIENTIFIC REPORTS}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{14}},
  title        = {{Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics}},
  url          = {{http://dx.doi.org/10.1038/s41598-020-80592-8}},
  volume       = {{11}},
  year         = {{2021}},
}

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