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

Abstract

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 74779^T = CECT 30571^T, 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 74779^T (=CECT 30571^T) 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.

Keywords: Pseudomonas fluorescens group; Pseudomonas gessardii subgroup; novel species; phylogenomics; polyphasic taxonomy; whole-genome sequencing; β-lactamase novel variant.

Figure 1

Holotomographic microscopy image of strain 16FHM2^T showing different morphological features of the cells, indicated by different color arrows. The lower part of the figure shows a dividing cell. The colors represent different refractive index ranges (see Supplementary Figure 1 for the refractive index scale). Strain 16FHM2^T was cultivated on Blood Agar medium, for 1 day, at 30°C.

Figure 2

Dendrogram generated from whole-genome sequence ANIb determinations, demonstrating the estimated relationships of the three strains of the proposed novel species and type strains of species of the P. gessardii and P. fluorescens subgroups.

Figure 3

Core genome-based phylogenomic tree of the three strains of the proposed novel species and type strains of species of the P. gessardii and P. fluorescens subgroups. The tree was constructed, using Maximum Likelihood and the Shimodaira-Hasegawa-like approximate likelihood-ratio test (SH-aLRT). The numbers at the nodes indicate the SH-aLRT support values.