COMPARATIVE GENOMICS OF CLINICAL AND ENVIRONMENTAL ENTEROBACTER CLOACAE REVEALS NICHE-SPECIFIC ADAPTATION AND EXTENSIVE GENE FLOW OF AMR DETERMINANTS

Enterobacter cloacae is an emerging multidrug-resistant (MDR) pathogen within the ESKAPE group, able to thrive in both clinical and environmental niches. Its ability to acquire, maintain, and mobilize resistance determinants through horizontal gene transfer (HGT) presents a significant global health challenge. This study carried out a comprehensive comparative genomic analysis of 100 E. cloacae strains (62 clinical and 38 environmental) to investigate niche-specific genomic adaptations and evolutionary relationships. An integrated bioinformatics pipeline, including Prokka for genome annotation, Roary for pangenome analysis, ABRicate for AMR, plasmid, and virulence profiling, IntegronFinder and MobileElementFinder for mobile genetic element (MGE) characterization, and BRIG for genome alignment, revealed genomic distinctions between the two niches. Clinical isolates exhibited a larger, more open pangenome (25,673 genes) reflecting extensive genomic plasticity and strong selective pressures typical of hospital environments. These isolates carried a more diverse repertoire of AMR genes, including β-lactamases, aminoglycoside-modifying enzymes, and efflux pump components, as well as high-risk plasmid replicons (IncF, IncHI, IncX3), commonly linked to carbapenemase dissemination. In contrast, environmental isolates possessed a more conserved pangenome (18,955 genes) but contained unique plasmid types and low-level resistance determinants, indicating their role as reservoirs of ancestral gene pools. Virulence profiling revealed a shared backbone of adhesion, motility, and iron acquisition genes across both niches, although toxin-associated genes were were enriched in clinical strains. Integron and MGE analyses showed extensive diversity and shared integron structures, supporting active bidirectional gene flow between environments. BRIG visualizations further confirmed a conserved genomic core among environmental isolates alongside variable genomic islands associated with adaptive functions. These findings reveal that E. cloacae populations form a genetically interconnected continuum shaped by ecological pressures, mobile genetic elements, and horizontal gene transfer, underscoring the need for One Health–based genomic surveillance to curb MDR emergence.