First case of Kosakonia radicincitans bacteremia in Japan, with comparative genome analysis of clinical and plant-associated isolates

ABSTRACT Background Kosakonia radicincitans is a plant-associated gram-negative bacterium that rarely causes human infection. Only a few cases of bacteremia have been reported worldwide, and no cases have been documented in Japan. Routine clinical identification methods may misidentify this organism as closely related Enterobacter species. Case Summary A 77-year-old woman with pancreatic cancer and multiple liver metastases, undergoing chemotherapy, presented with chills and fever 1 week after treatment. Blood cultures were positive in three of four bottles, yielding gram-negative rods. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry suggested K. radicincitans as the top candidate, whereas API 20E identified the isolate as Enterobacter cloacae . Final identification was established by 16S rRNA gene sequencing, which showed 100% identity with the type strain. Whole-genome sequencing of the isolate, designated YUH003903, yielded two contigs of 5.48 Mb and 118 kb. Comparative genome analysis showed 99.2%–99.4% average nucleotide identity with clinical and plant-derived K. radicincitans strains. Single nucleotide polymorphism (SNP)-based phylogenetic analysis did not clearly distinguish clinical isolates from plant-derived strains. The isolate showed low MICs to most antimicrobial agents tested, and the patient recovered after levofloxacin treatment. Conclusion This is the first reported case of K. radicincitans bacteremia in Japan. Genome analysis indicated that the clinical isolate was highly similar to both clinical and plant-derived strains and revealed no obvious genomic feature specifically associated with human pathogenicity. These findings suggest that K. radicincitans may act as an opportunistic pathogen in susceptible hosts and that accurate identification requires molecular and genomic approaches when routine diagnostic methods yield inconsistent results.