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Description of Pseudomonas imrae sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel (Scomber scombrus)
RISE Research Institutes of Sweden, Materials and Production, Methodology, Textiles and Medical Technology. University of Gothenburg, Sweden; Sahlgrenska University Hospital, Sweden.ORCID iD: 0000-0003-0173-560X
IMR Institute of Marine Research, Norway.
University of Gothenburg, Sweden; Sahlgrenska University Hospital, Sweden.
University of Gothenburg, Sweden; Sahlgrenska University Hospital, Sweden.
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2025 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 16, article id 1530878Article in journal (Refereed) Published
Abstract [en]

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. 

Place, publisher, year, edition, pages
Frontiers Media SA , 2025. Vol. 16, article id 1530878
Keywords [en]
antibiotic agent; beta lactamase; fatty acid ester; meropenem; RNA 16S; antibiotic resistance; antibiotic sensitivity; Article; Atlantic mackerel; average nucleotide identity; bacterial strain; bacterium isolate; bacterium isolation; DNA DNA hybridization; DNA extraction; gene sequence; genetic variability; genome analysis; intestine; matrix assisted laser desorption ionization time of flight mass spectrometry; microscopy; North Sea; nucleotide sequence; phenotype; phylogenetic tree; phylogenomics; phylogeny; polyphasic taxonomy; Pseudomonas brenneri; Pseudomonas fluorescens; Pseudomonas gessardii; Pseudomonas imrae; Pseudomonas mucidolens; Pseudomonas proteolytica; Pseudomonas shahriarae; sequence alignment; sequence analysis; whole genome sequencing
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Biological Sciences
Identifiers
URN: urn:nbn:se:ri:diva-78613DOI: 10.3389/fmicb.2025.1530878Scopus ID: 2-s2.0-105004803578OAI: oai:DiVA.org:ri-78613DiVA, id: diva2:1965405
Note

 The computations were performed, using resources provided by the Swedish National Infrastructure for Computing (SNIC), through the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), under project SNIC 2019/8-176.

Available from: 2025-06-09 Created: 2025-06-09 Last updated: 2025-06-09Bibliographically approved

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Salvà Serra, Francisco

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