Whole-genome sequencing provides insights into a novel species: associated with urinary tract infections.

is a clinically significant opportunistic pathogen that is involved in urinary tract infections. Due to the resolution limitations of identification, distinguishing from closely related species is challenging by commercial biochemical test systems. Here, we first reported a novel species, , which had been misidentified as . Exhibiting ≤91.97% average nucleotide identity (ANI) and ≤46.10% in silico DNA-DNA hybridization values with all known species, falls well beneath the established species-defining thresholds. We conducted a population genomics analysis of isolates worldwide. Our study revealed that has emerged in many countries and has formed several transmission clusters. We found that shared the highest ANI values (91.54% and 91.97%) with and , respectively. The pan-genome analysis revealed that these three species possessed a similar component of pan-genomes. Two genes associated with metabolism, and , were identified to be specific to . Furthermore, we also observed that carbapenem-resistance genes frequently occur in with the being the most prevalent (46.15%; 36/78). The emergence of is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, and calls for tailored surveillance of this species as a clinically relevant species in the future. IMPORTANCE Our study has identified and characterized a novel species, , which is associated with urinary tract infections and was previously misidentified as . Through this study, we have identified specific genes unique to , which could serve as marker genes for rapid PCR identification. Additionally, our findings suggest that the emergence of is often accompanied by extended-spectrum β-lactamase and carbapenem-resistance genes, emphasizing the need for attention to clinical management and the importance of accurate species identification and proper drug use.