Table 3_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.

从北海北部海域采集的野生大西洋鲭鱼（Scomber scombrus）肠道样本中，分离得到3株β-内酰胺耐药（β-lactam resistant）细菌菌株，本研究通过多相分类分析（polyphasic analyses）对其进行了系统的特征鉴定。经鉴定，这些菌株隶属于假单胞菌属（Pseudomonas），但无法归类至任何已知物种。近乎完整的16S rRNA基因（16S rRNA gene）序列显示，其与4个不同物种的序列相似性最高（达99.9%）；而部分rpoD基因（rpoD gene）序列与解蛋白假单胞菌（Pseudomonas proteolytica）及其他假单胞菌属物种的相似性相对较低，仅为93.4%。基因组测序（genome sequencing）及后续的数字DNA-DNA杂交（digital DNA–DNA hybridization, dDDH）、平均核苷酸同源性（average nucleotide identity, ANI）分析与核心基因组分析（core genome analysis）证实，这些菌株代表假单胞菌属内的一个全新物种。这3株菌株之间的ANIb值均高于99.5%，确认3株菌株（CCUG 74779T = CECT 30571T、CCUG 74780与CCUG 74781）属于同一个基因种（genomospecies）。系统基因组学分析（phylogenomic analysis）证实，这些菌株构成一个独立的基因组进化枝（genomic clade），代表一个全新的分类学物种，现将其命名为假单胞菌imrae新种（Pseudomonas imrae sp. nov.），并指定菌株CCUG 74779T（=CECT 30571T）作为模式菌株（type strain）。本研究报道了P. imrae sp. nov.模式菌株的完整基因组序列，并发现其携带一段编码染色体编码的C类β-内酰胺酶（class C β-lactamase）新变体的基因，该变体已被命名为PFL-7。