Phenotypic and Genotypic Profile of Enterobacteriaceae Isolated at a Teaching Hospital in Ghana

Antibiotic resistance in Enterobacteriaceae continues to rise, and its implications for healthcare delivery have intensified. We investigated the genetic basis of antimicrobial resistance (AMR), virulence genes, and associated plasmids in Enterobacteriaceae isolates from a teaching hospital in Ghana. Antimicrobial susceptibility testing was performed using archived isolates. Whole genome sequencing was performed on a subset of the isolates, that were either multidrug resistant or extended-spectrum β-lactamase (ESBL)-producing. Bioinformatics analyses were performed for speciation, identification of AMR and virulence genes, and associated plasmids. The 100 Enterobacteriaceae isolates included in this study showed high phenotypic resistance to ß-lactams and susceptibility to aminoglycosides. Nineteen of the 20 WGS isolates were genotypically identified using the housekeeping genes as Escherichia coli (8/20, 40%), Klebsiella pneumoniae (8/20, 40%), Enterobacter cloacae (2/20, 10%), and Salmonella enterica (1/20, 5%). These strains harboured 139 unique antibiotic resistance genes (ARGs) encoding resistance against ß-lactams (64/139), aminoglycosides (23/139), fluoroquinolones (45/139), tetracyclines (37/139), phenicols (27/139), and sulphonamides (9/139). Subsequent AST revealed that (74/79, 94%) were ESBL producers, and (9/79,11%) were carbapenem resistant Enterobacteriaceae (CRE). The isolates expressed 8 categories of virulence factors (VFs), including effector delivery systems, adherence, and metabolic factors. Additionally, 26 unique plasmid replicons of both the I-complex and colicin plasmids were detected. We observed phenotypic and genotypic evidence of antimicrobial resistance to common antibiotics in the isolates driven by CTX-M-15 and in some K. pneumoniae, the NDM-1. These findings highlight the urgent need to improve antibiotic stewardship, surveillance and control at the hospital.