Genomic Characterization of Intestinal Colonizing Pseudomonas juntendi Strains Harboring bla _VIM-2

To characterize the genomic architecture of carbapenemase-producing Pseudomonas juntendi harboring bla _VIM-2, elucidate genetic mechanisms underlying carbapenem resistance, and evaluate mobile genetic element (MGE)-mediated dissemination pathways using Oxford Nanopore and Illumina sequencing were combined for hybrid genome assembly approaches.

Hybrid Nanopore-Illumina whole-genome sequencing was applied on two P. juntendi isolates (L2353hy/L2891hy) recovered from distinct human fecal samples. L2353hy and L2891hy were identified as P. juntendi by ANI analysis. Comparative pangenomics identified resistance determinants and phylogenetic relationships, and SNP distances were calculated using SNP-dists. Plasmid profiles were verified using S1 nuclease pulsed-field gel electrophoresis (S1-PFGE).

Both strains exhibited a multidrug resistance profile, comprising 13 antimicrobial resistance genes (ARGs), including bla _VIM-2, bla _OXA-246, and tet(A). Core genome phylogeny demonstrated clonal propagation of two VIM-producing P. juntendi strains. Notably, these two isolates were closely linked to P. juntendi yb_3 (a fish intestinal isolate; Wenzhou, China).

This study reports two clonally related P. juntendi strains harboring bla _VIM-2 isolated from human fecal microbiota, expanding the genomic understanding of carbapenem-resistant P. juntendi. The close phylogenetic relationship between these human isolates and an animal-derived strain (P. juntendi yb_3) underscores bidirectional resistance gene flow at the human-animal interface. Our findings support a One Health-oriented surveillance approach to mitigate the dissemination of carbapenemase-producing pathogens.