Genomic identification and characterization of prophages associated with Citrobacter freundii strains

Citrobacter freundii is a Gram-negative opportunistic bacterium that can cause infections, sepsis, and meningitis, predominantly in infants and immunocompromised adults. This study is aimed at investigating the distribution of prophages in C. freundii strains and their potential effects on the host strains using genomic characterization. In-silico analysis of 144 complete chromosomal sequences of C. freundii strains was performed, and 574 intact prophages were identified from 1178 prophages in the host. The genome sizes of the intact prophages were 6.74-115.15 kb; on average, the host chromosomes were predicted to have around 3.98% of intact prophage genomes. At least three intact prophages were most frequently predicted, while only three host chromosomes were found to have the highest number of nine intact prophages. The GC content of prophages is 50.75%, slightly lower than the average GC content (51.85%) of C. freundii. Most of the prophages in C. freundii strains were classified into four families, Myoviridae (48.16%), Siphoviridae (42%), Podoviridae (4.67%), Inoviridae (0.17%), and 5% of the intact prophages could not be assigned into any family. Phylogenomic analysis of intact prophages divided the genomes into three distinct clades. Virulence gene analysis revealed the variable distribution of 7 virulence genes (hcp, higB, hipA, msgA, rtx, yeeV, and ykfI) among the intact prophages. Overall, this study provides insights into the diversity and characteristics of prophages associated with C. freundii strains, which will help in understanding the genetic evolution and pathogenesis of the bacteria.