Pseudomonas carnis isolated from blue discolored fresh cheese and insights into the phylogeny.

Most Pseudomonas spp. are responsible for spoilage in refrigerated foods such as alteration in flavor, texture and appearance. Samples of Minas Frescal cheese with blue discoloration were analysed and contained a high Pseudomonas concentration (7.72 ± 0.36 log CFU/g). Out of the 26 Pseudomonas isolates that were analyzed in our study, 19 demonstrated the capability of producing a diffusible dark pigment. Thus, a pigment-producing isolate (C020) was selected by rep-PCR fingerprinting and subsequently subjected to whole-genome sequencing. The draft genome assembled comprises 42 contigs totaling 6,366,75 bp with an average G + C content of 59.97%, and the species prediction performed by TYGS server, based on the draft genome sequence, identified the C020 as Pseudomonas carnis. In order to investigate the phylogenetic relationships of this isolate with strains already identified of this species, we performed an analysis based on whole-genomic sequences. First, an analysis of all P. carnis genomes deposited in GenBank to date shows that 11% (4/37) are misidentified, and belong to the Pseudomonas paracarnis species. A comparative analysis based on phylogenomic analysis has showed that there is no evolutionary relationship between P. carnis strains carrying second copies of trp genes related to blue discoloration (trpABCDF). This finding reinforces the assertion that these genes are contained in a mobile genetic element. However, it is worth noting that all strains carrying these secondary gene copies have exclusively been isolated from food sources. This observation provides valuable insights into the potential origins and dispersion dynamics of this genetic trait within the species.