Table 1_Description of Pseudomonas imrae sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel (Scomber scombrus).xlsx

Three β-lactam resistant bacterial strains isolated from gut samples of wild Atlantic mackerel (Scomber scombrus) collected from the northern North Sea were characterized by polyphasic analyses. The strains were determined to belong to the genus Pseudomonas but could not be assigned to a known species. The nearly-complete 16S rRNA gene sequence showed the highest similarity (99.9%) to four different species, although partial rpoD sequence exhibited relatively low similarities to Pseudomonas proteolytica (93.4%) and other Pseudomonas spp. Genome sequencing and subsequent digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) analysis and core genome analysis confirmed that these strains represent a novel species within the genus Pseudomonas. The three strains demonstrated ANIb values >99.5% with each other, confirming that all three strains (CCUG 74779T = CECT 30571T, CCUG 74780 and CCUG 74781) belong to the same genomospecies. Phylogenomic analysis confirmed that the strains form a distinct genomic clade, representing a novel taxonomic species, for which the name Pseudomonas imrae sp. nov., is proposed, with strain CCUG 74779T (=CECT 30571T) designated as the type strain. We report the complete genome sequence of the type strain of P. imrae sp. nov. and show that it carries a gene encoding a novel variant of a chromosomally-encoded class C β-lactamase, which has been designated as PFL-7.

从北海北部采集的野生大西洋鲭（Scomber scombrus）肠道样本中分离得到的3株耐β-内酰胺（β-lactam）细菌菌株，经多相分类分析完成了分类鉴定。这些菌株被划归假单胞菌属（Pseudomonas），但无法归入已知物种。近乎完整的16S rRNA基因序列与4个不同物种的同源序列最高相似度达99.9%，不过部分rpoD基因序列与解蛋白假单胞菌（Pseudomonas proteolytica）及其他假单胞菌属（Pseudomonas spp.）物种的同源性相对较低，仅为93.4%。基因组测序及后续的数字化DNA-DNA杂交（dDDH）、平均核苷酸同源性（ANI）分析和核心基因组分析证实，这些菌株属于假单胞菌属内的一个新物种。3株菌株之间的ANIb值均大于99.5%，证实3株菌株（CCUG 74779ᵀ = CECT 30571ᵀ、CCUG 74780及CCUG 74781）属于同一个基因种。系统基因组学分析证实，这些菌株构成一个独立的基因组进化枝，代表一个新的分类学物种，故提议将其命名为伊雷假单胞菌（Pseudomonas imrae sp. nov.），模式菌株为CCUG 74779ᵀ（=CECT 30571ᵀ）。本研究报道了伊雷假单胞菌模式菌株的完整基因组序列，并发现其携带一个编码染色体编码的C类β-内酰胺酶（class C β-lactamase）新型变体的基因，该变体已被命名为PFL-7。