AUTHOR=Yuan Chao , Yin Zhiqiu , Wang Junyue , Qian Chengqian , Wei Yi , Zhang Si , Jiang Lingyan , Liu Bin 

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

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02774

DOI=10.3389/fmicb.2019.02774

ISSN=1664-302X

ABSTRACT=<p><italic>Citrobacter</italic> species are opportunistic bacterial pathogens that have been implicated in both nosocomial and community-acquired infections. Among the genus <italic>Citrobacter</italic>, <italic>Citrobacter koseri</italic> 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 <italic>Citrobacter</italic>, however, remain largely unknown. Based on traditional methods, the genus <italic>Citrobacter</italic> has been divided into 11 species, but this has been problematic. Here, we determined an improved, detailed, and more accurate phylogeny of the genus <italic>Citrobacter</italic> based on whole genome sequence (WGS) data from 129 <italic>Citrobacter</italic> genomes, 31 of which were sequenced in this study. A maximum likelihood (ML) phylogeny constructed with core genome single-nucleotide polymorphisms (SNPs) classified all <italic>Citrobacter</italic> isolates into 11 distinct groups, with all <italic>C. koseri</italic> 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 <italic>Citrobacter</italic> genus. Moreover, combined with group-specific genes analysis, we identified a key gene cluster for iron transport, which is present in the <italic>C. koseri</italic> group, but absent in other the groups, suggesting that the high-pathogenicity island (HPI) cluster may be important for the pathogenicity of <italic>C. koseri</italic>. Animal experiments showed that loss of the HPI cluster significantly decreased <italic>C. koseri</italic> virulence in mice and rat. Further, we provide evidence to explain why <italic>Citrobacter freundii</italic> is less susceptible than <italic>C. koseri</italic> to several antibiotics <italic>in silico</italic>. Overall, our data reveal novel virulence clusters specific to the predominantly pathogenic <italic>C. koseri</italic> strains, which form the basis for elucidating the virulence mechanisms underlying these important pathogens.</p>