Patient colonization with Phytobacter spp. co-harboring blaIMP-4, blaSHV-12, and mcr-9.1 highlights its role as an under-recognized reservoir of antimicrobial resistance.

We report two uncommon cases of patient colonization with multidrug-resistant, carbapenemase-encoding Phytobacter species in Ireland. Phytobacter is a recently delineated genus within the Enterobacterales that is commonly misidentified in clinical laboratories. Two isolates were recovered from rectal swabs in 2024 and were initially identified as Phytobacter ursingii by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Whole-genome sequencing combined with in silico species typing (average nucleotide identity and digital DNA-DNA hybridization) resolved them as Phytobacter diazotrophicus E787336 and Phytobacter ursingii E980862. We reconstructed a genus-wide maximum-likelihood core genome phylogeny and profiled all publicly available Phytobacter genomes to contextualize antimicrobial resistance and plasmid content. Across the data set, we detected 22 plasmid replicon types and a resistome comprising 71 genes, over half predicted to be plasmid-borne. These included carbapenemases in 26.5% (nine of 34) of the genomes and disinfectant-associated resistance determinants in 29.5%. E787336 and E980862 represent the first Phytobacter isolates identified to co-harbor plasmid-borne blaIMP-4, blaSHV-12, and mcr-9.1 in association with IncHI2A plasmid reconstructions. Phenotypic testing confirmed resistance to aztreonam, aminoglycosides, cephalosporins, fluoroquinolones, and piperacillin-tazobactam and susceptibility to carbapenems and colistin. These findings strengthen the clinical and genomic evidence that Phytobacter acts as an under-recognized colonizer and reservoir for plasmid-borne antimicrobial resistance, including carbapenemases, and highlight the need for improved clinical identification, genomic surveillance, and preparedness for limited therapeutic options.