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

Background: Pantoea species are increasingly recognized as opportunistic human pathogens. We describe a rare case of osteomyelitis that has developed slowly over two decades, with the identification of the causative agent as a novel species of Pantoea . Case presentation: A 37-year-old generally healthy woman with suspected chronic osteomyelitis presented at our hospital. 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 resulting in a full recovery. Bone biopsy cultures revealed 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 revealed conserved antibiotic resistance and virulence genes. Conclusion: A literature review uncovered only five cases of osteomyelitis caused by Pantoea species that have been reported in the past, all of which were attributed to Pantoea agglomerans . We suggest that 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 are discussed, emphasizing the need for further research into its clinical relevance.