Comprehensive genomic and phenotypic analysis of Enterobacter kobei Isolates from milk

An Enterobacter kobei strain, named as BCSIR-MEcoli, isolated from a milk sample, was subjected to comprehensive genomic analysis to elucidate its antibiotic resistance profile, mobile genetic elements (MGEs), and prophage content. Average Nucleotide Identity (ANI) analysis using FastANI 1.3.3 demonstrated a high nucleotide identity of 98.83% with E. kobei strain UCI 24, indicating close genetic relatedness. Whole-genome phylogenetic analysis placed BCSIR-MEcoli closer to E. kobei, DSM 13645, highlighting significant genomic similarities within the species. The Comprehensive Antibiotic Resistance Database (CARD) analysis revealed multiple resistance mechanisms, including efflux pumps, target modifications, and antibiotic inactivation, with resistance to macrolides, fluoroquinolones, cephalosporins, tetracyclines, and carbapenems. The ResFinder tool identified specific resistance to beta-lactams due to the blaACT-9 gene. Additionally, defense mechanisms, including CRISPR-Cas and toxin-antitoxin systems, were characterized, and mobile genetic elements were extensively analyzed, showing significant interactions with bacteriophages. Prophage analysis identified several prophage regions, with notable contributions from phage species such as PHAGE_Salmon_SP_004 and PHAGE_Escher_HK639 . Viral elements included both dsDNA and ssDNA phages. These findings provide a detailed genomic characterization of BCSIR-MEcoli, contributing valuable insights into its antibiotic resistance, adaptability, and evolutionary dynamics. • A novel Enterobacter kobei strain, BCSIR-MEcoli, was isolated from a milk sample and subjected to detailed genomic analysis. • ANI analysis showed 98.83% identity with E. kobei strain UCI 24, indicating close genetic similarity. • Comprehensive analysis revealed resistance to multiple antibiotic classes (macrolides, fluoroquinolones, cephalosporins, tetracyclines and carbapenems) via diverse mechanisms. • Extensive presence of MGEs was observed, with active interactions between these elements and bacteriophages. • The strain harbors CRISPR-Cas systems and toxin-antitoxin modules, suggesting strong genomic defense and stress response capabilities.