Integrative Genomics and Immunoinformatic Reveal Putative Drug Targets and Vaccine Candidates Against Enterococcus faecalis Isolated from Patient with Colorectal Cancer

Colorectal cancer (CRC) affects more than two million people annually and remains a leading cause of cancer-related mortality. Its increasing incidences are associated with lifestyle factors, gut microbiota dysbiosis, and microbial contributions to tumorigenesis through chronic inflammation. The aim of the current study was to perform a genome analysis of the multidrug resistant bacterial strains derived from patients with CRC following the identification of potential drug targets by subtractive genomics and vaccine development by reverse vaccinology. The multidrug-resistant strain was named as the E. faecalis strain rwlp. The genome contains 2955 protein-coding genes, including 65 conserved virulence factors and 38 antibiotic resistance genes corresponding to sixteen principal classes of antibiotics. Moreover, subtractive genomics revealed two proteins, DNA gyrase subunit A with protein id 9GBV and DNA topoisomerase with protein id 2NOV, that emerged as potential drug targets. Among the four extracellular proteins, i.e., autolysin, gelatinase, thiol-activated cytolysin, and WxL domain surface protein, on the basis of their strong antigenicity and adequate stability profile, the gelatinase protein was selected as the final candidate for vaccine construction. High-affinity cytotoxic T-lymphocyte, helper T-lymphocyte, and B-cell epitopes specific to their corresponding HLA alleles were screened, prioritized, and subsequently assembled into a multiepitope construct using the EAAAK linker. Molecular dynamics simulations of the vaccine construct and the human immune receptor TLR2 docked complex confirmed the stability of the complex. Codon optimization and in silico cloning supported efficient vaccine expression in E. coli. To the best of our knowledge, this is the first study to report the whole-genome sequence of E. faecalis isolated from a patient with CRC and to elucidate its virulence and antibiotic resistance, while identifying potential vaccine candidates and drug targets for future therapeutic development.