Whole-genome sequencing of Pseudomonas koreensis isolated from diseased Tor tambroides

Abstract

BackgroundPseudomonas koreensis have been reported as a pathogen in freshwater fish. Unlike environmental P. koreensis from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis from fish has been assessed only to a very limited extent. This is the first draft genome of P. koreensis CM-01 isolated from the internal organs of diseased Tor tambroides.ResultsHerein, we report the morphological and biochemical characteristics, as well as whole genome sequences of a newly identified P. koreensis strain. We achieved a high-quality draft genome of P. koreensis CM-01 with a N50 value of 233,601 bp and 99.5% BUSCO completeness. The total size of P. koreensis CM-01 genome contains 6,171,880 bp and has a G+C content of 60.5%. Besides, the genome sequence includes 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 predicted in the P. koreensis CM-01 genome. 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.ConclusionsThis study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain. Further study will be necessary to fully understand any correlation between the bacteria and the occurrences of diseases in Tor tambroides.

Phenotypic and genomic insights into the pathogenicity and antimicrobial resistance of an Enterobacter roggenkampii strain isolated from diseased silver arowana (Osteoglossum bicirrhosum)

“…The presence of multiple fimbriae genes associated with type I fimbriae and type IV pili indicated that EOBSR_19 was likely able to adhere to and colonize a rather wide range of hosts or environments. Similar genes are also reported earlier in other strains, including E. roggenkampii ED5 (Guo et al., 2020), E. cloacae ATCC13047 (Liu et al., 2013), Vibrio parahaemolyticus TJA114 (Zhang et al., 2021), Pseudomonas koreensis CM‐01 (Kho et al., 2023), and Aeromonas veronii A8‐AHP (Tyagi et al., 2022).…”

“…Some of the efflux pump showed resistance activity in response to pathogenic bacterium that have been previously reported to P. koreensis CM‐01 (Kho et al., 2023) and A. veronii JC529 (Sheng et al., 2021). AcrAB‐TolC is a resistance‐nodulation‐cell division (RND) multiple drug efflux pump complex and it mediates the resistance against fluoroquinolone and tetracycline antibiotics, which is essential for intrinsic bacterial antibiotic resistance (Andersen et al., 2015; Hocquet et al., 2003; Li et al., 2015; Masuda et al., 2000; Swick et al., 2011).…”