Complete genome sequence of Pseudomonas sp. PK-RTE-24 isolated from lettuce

Fresh vegetables can harbor diverse bacteria, including Pseudomonas spp. In routine diagnostics, isolates are often identified by MALDI-TOF MS, but novel or unreferenced taxa can be misidentified. Here, we report the WGS of Pseudomonas sp. strain PK-RTE-24, initially assigned by MALDI-TOF MS to a known species. The aim was to generate genomic data that clarify the taxonomic assignment of PK-RTE-24 that is not linked to any described species and to highlight the discrepancy between MALDI-TOF MS identification and WGS analysis.

PK-RTE-24 was isolated from ready-to-eat lettuce during screening for extended-spectrum β-lactamase (ESBL)-producing bacteria. MALDI-TOF MS reported Pseudomonas koreensis. Using Illumina and Oxford Nanopore technologies a complete 5,847,647-bp genome, with 60.04% GC content, and encoding 5,285 predicted genes, was assembled. Phylogenomic analysis and average nucleotide identity showed that PK-RTE-24 did not match any described Pseudomonas sp. and fell below the species threshold, grouping within an environment-associated clade. Antimicrobials testing revealed β-lactams non-susceptibility, consistent with a chromosomally-encoded class C β-lactamase (AmpC) gene (1,167-bp). The 388 amino-acid protein shared 96.9% identity with an AmpC from Pseudomonas sp. RG1. The PK-RTE-24's genome sequence provides valuable data for classifying environment-associated Pseudomonas spp. and elucidating β-lactam resistance in non-clinical strains.