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

Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA (Unpublished) .

Preprint | Unveröffentlicht | Englisch
 
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Autor*in
Berger, Carola; Rückert, ChristianUniBi ; Blom, Jochen; Rabaey, Korneel; Kalinowski, JörnUniBi; Rosenbaum, Miriam A.
Abstract / Bemerkung
Background: New strains of Pseudomonas aeruginosa are continuously being isolated and sequenced to increase the genomic accessibility of this important pathogen. This has led to the generation of an impressive dataset of closed P. aeruginosa genomes. To understand the difference between the strains, investigations are focused on the accessory genome, thereby constantly extending the known pan genome of P. aeruginosa as a species. Apart from follow-up studies, 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. Results: Pseudomonas spp. KRP1 could clearly be identified as a P. aeruginosa isolate, via comparative genomics. By using different genomic island prediction programs, we could identify a total of 25 genomic islands that cover ~12% of the genome of P. aeruginosa KRP1. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of its genomic information with the highly virulent PSE9 and LESB58 strains. For both of these clones, their increased virulence has been directly linked to their accessory genome before. Conclusions: Here we show, how the integrated use of previously published genomic data today, can help to replace expensive and time consuming wetlab work to determine the pathogenetic potential of environmental isolates. This knowledge is vital to understand what makes an isolate a potential pathogen as it helps design effective treatment.
Erscheinungsjahr
2020
Page URI
https://pub.uni-bielefeld.de/record/2949924

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Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA. Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Unpublished.
Berger, C., Rückert, C., Blom, J., Rabaey, K., Kalinowski, J., & Rosenbaum, M. A. (Unpublished). Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. doi:10.21203/rs.2.22505/v1
Berger, C., Rückert, C., Blom, J., Rabaey, K., Kalinowski, J., and Rosenbaum, M. A. (Unpublished). Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.
Berger, C., et al., Unpublished. Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.
C. Berger, et al., “Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics”, Unpublished.
Berger, C., Rückert, C., Blom, J., Rabaey, K., Kalinowski, J., Rosenbaum, M.A.: Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. (Unpublished).
Berger, Carola, Rückert, Christian, Blom, Jochen, Rabaey, Korneel, Kalinowski, Jörn, and Rosenbaum, Miriam A. “Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics”. (Unpublished).

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