Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
Department of Biological Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Malaysia.
Curr Microbiol. 2023 Jun 25;80(8):255. doi: 10.1007/s00284-023-03354-5.
Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.
与已被广泛研究其促进植物生长作用的土壤中分离出的环境朝鲜假单胞菌不同，从鱼类中分离出的致病性朝鲜假单胞菌鲜有报道。因此，我们调查并分离了可能导致 Tor tambroides 患病的病原体。在此，我们报道了一株新鉴定的朝鲜假单胞菌 CM-01 的形态学和生化特征以及全基因组序列。我们组装了高质量的朝鲜假单胞菌 CM-01 草图基因组，其连续体 N50 值为 233601bp，99.5%的 BUSCO 完整性。CM-01 基因组组装由 6171880bp 组成，GC 含量为 60.5%。基因组注释鉴定出 5538 个蛋白编码基因、3 个 rRNA 基因、54 个 tRNA，未发现质粒。此外，还预测了 39 个散布重复序列和 141 个串联重复序列、6 个噬菌体、51 个基因组岛、94 个插入序列、4 个成簇规则间隔短回文重复序列、5 个抗生素抗性基因和 150 个毒力基因。基于培养的方法表明，CM-01 菌株对氨苄西林、氨曲南、克林霉素和头孢西丁表现出抗性，其计算的多重抗生素耐药性 (MAR) 指数值为 0.4。此外，组装的 CM-01 基因组成功地在蛋白同源簇数据库、基因本体数据库和京都基因与基因组百科全书通路数据库中进行了注释。CM-01 与 3 株代表性的朝鲜假单胞菌的比较分析表明，这四个基因组中有 92%的直系同源簇是保守的，只有 CM-01 菌株具有与致病性和毒力相关的独特元件。本研究为新鉴定的朝鲜假单胞菌菌株提供了基本的表型和基因组信息。
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