Pantoea osteomyelitidis sp. nov., a novel human opportunistic pathogen isolated from a patient with chronic osteomyelitis: case report, genomic characterization and literature review

Purpose : Pantoea species are increasingly recognized as human opportunistic pathogens. We describe a rare case of osteomyelitis that has been developed over years, with the identification of the causing agent as a novel species of Pantoea . Case presentation: A 37-year-old generally healthy woman presented to our hospital with suspected chronic osteomyelitis. The condition was possibly related to an incident that occurred two decades before the onset of symptoms, involving a tibia fracture with a large open bleeding wound. The patient had undergone two aggressive debridement operations, systemic ciprofloxacin treatment, and local aminoglycoside therapy, eventually exhibiting full recovery. Bone biopsy cultures grew gram-negative coccobacilli that could not be identified by conventional clinical microbiology methods. Whole-genome sequencing and subsequent taxonomic and phylogenetic analyses revealed genetic relatedness to several Pantoea species. Comparative genomic analyses identified conserved antibiotic resistance and virulence genes. Conclusion: A literature review search uncovered only five cases of osteomyelitis caused by Pantoea species that have been reported in the past, all attributed to Pantoea agglomerans . We suggest this new strain belongs to a yet unidentified Pantoea species, which we have named Pantoea osteomyelitidis . sp.nov. The high diversity of Pantoea and the obscured potential pathogenicity of this genus is discussed, emphasizing the need for further research into its clinical relevance.