We report two uncommon identifications of patient colonization with multidrug-resistant, carbapenemase-encoding Phytobacter in Ireland. Phytobacter is a recently delineated genus within the Enterobacterales that is frequently misidentified in clinical laboratories. Two isolates were recovered from rectal swabs in 2024 and were initially identified as Phytobacter ursingii by MALDI-TOF. Whole-genome sequencing with in silico species typing (average nucleotide identity and digital DNA-DNA hybridization) resolved them as Phytobacter diazotrophicus E787336 and P. ursingii E980862. We reconstructed a genus-wide maximum-likelihood core-genome phylogeny and profiled all publicly available Phytobacter genomes to contextualize antimicrobial resistance (AMR) and plasmid content. Across the dataset, 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% (9/34) 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, yet susceptibility to carbapenems and colistin. These findings expand the clinical and genomic evidence that Phytobacter can act as an under-recognized colonizer and reservoir for plasmid-borne AMR, including carbapenemases, and underscore the need for improved clinical identification, genomic surveillance, and preparedness for limited therapeutic options.
Tumeo et al. (Sun,) studied this question.