Description of <i>Pseudomonas imrae</i> sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel (<i>Scomber scombrus</i>)
Abstract
Three β-lactam resistant bacterial strains isolated from gut samples of wild Atlantic mackerel (<i>Scomber scombrus</i>) collected from the northern North Sea were characterized by polyphasic analyses. The strains were determined to belong to the genus <i>Pseudomonas</i> 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 <i>rpoD</i> sequence exhibited relatively low similarities to <i>Pseudomonas proteolytica</i> (93.4%) and other <i>Pseudomonas</i> 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 <i>Pseudomonas</i>. The three strains demonstrated ANIb values >99.5% with each other, confirming that all three strains (CCUG 74779<sup>T</sup> = CECT 30571<sup>T</sup>, 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 <i>Pseudomonas imrae</i> sp. nov., is proposed, with strain CCUG 74779<sup>T</sup> (=CECT 30571<sup>T</sup>) designated as the type strain. We report the complete genome sequence of the type strain of <i>P. imrae</i> 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.