Comparative Genomic Analysis of Citrobacter and Key Genes Essential for the Pathogenicity of Citrobacter koseri

species are opportunistic bacterial pathogens that have been implicated in both nosocomial and community-acquired infections. Among the genus , is often isolated from clinical material, and has been known to cause meningitis and brain abscess in neonates and immunocompromised individuals. The virulence determinants of , however, remain largely unknown. Based on traditional methods, the genus has been divided into 11 species, but this has been problematic. Here, we determined an improved, detailed, and more accurate phylogeny of the genus based on whole genome sequence (WGS) data from 129 genomes, 31 of which were sequenced in this study. A maximum likelihood (ML) phylogeny constructed with core genome single-nucleotide polymorphisms (SNPs) classified all isolates into 11 distinct groups, with all strains clustering into a single group. For comprehensive and systematic comparative genomic analyses, we investigated the distribution of virulence factors, resistance genes, and macromolecular secretion systems among the genus. Moreover, combined with group-specific genes analysis, we identified a key gene cluster for iron transport, which is present in the group, but absent in other the groups, suggesting that the high-pathogenicity island (HPI) cluster may be important for the pathogenicity of . Animal experiments showed that loss of the HPI cluster significantly decreased virulence in mice and rat. Further, we provide evidence to explain why is less susceptible than to several antibiotics . Overall, our data reveal novel virulence clusters specific to the predominantly pathogenic strains, which form the basis for elucidating the virulence mechanisms underlying these important pathogens.