Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
Center for Biotechnology - CeBiTec, University of Bielefeld, Bielefeld, Germany.
Sci Rep. 2021 Jan 14;11(1):1370. doi: 10.1038/s41598-020-80592-8.
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 ~ 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.
新的铜绿假单胞菌菌株的分离和测序创建了一个广泛的封闭基因组数据集。许多公开可用的基因组仅在其原始出版物中使用，而基于与以前发表的基因组比较的其他计算信息则未被探索。在这项研究中，我们定义并研究了环境分离株铜绿假单胞菌 KRP1 的基因组，并将其与 100 多个公开的封闭铜绿假单胞菌基因组进行了比较。通过使用不同的基因组岛预测程序，我们总共可以鉴定出 17 个基因组岛和 8 个基因组小岛，这标志着涵盖总基因组约 12%的大多数附件基因组。基于株内比较，我们能够预测这种环境分离株的致病潜力。它与高度毒力的 PSE9 和 LESB58 菌株共享大量基因组信息。对于这两种菌株，其增加的毒力以前都直接与其辅助基因组有关。因此，综合使用以前发表的数据可以帮助减少昂贵且耗时的湿实验室工作，以确定病原体的潜力。
