In silico Study on Antimicrobial Resistance (AMR) in Escherichia coli: A Pilot Study

Abstract

Escherichia coli (E. coli) is a Gram-negative, facultative anaerobic bacterium commonly found in the gastrointestinal tract of humans and animals. While most strains are commensals, some exhibit pathogenic traits, leading to infections such as urinary tract infections, neonatal meningitis, and diarrheal diseases. The adaptability of E. coli is largely attributed to its genomic plasticity, enabling the acquisition and dissemination of antimicrobial resistance (AMR) genes through horizontal gene transfer mechanisms. The increasing prevalence of multidrug-resistant (MDR) E. coli strains, facilitated by mobile genetic elements such as plasmids, transposons, and integrons, poses a severe global health concern. This study utilizes publicly available E. coli genomic sequences from the NCBI Sequence Read Archive (SRA) to investigate the distribution and diversity of AMR genes across various environmental and biological sources, including wastewater, soil, poultry cloacal swabs, and raw milk. A structured bioinformatics workflow was employed, incorporating tools like FastQC, SPAdes, QUAST, and the Resistance Gene Identifier (RGI) within the Comprehensive Antibiotic Resistance Database (CARD). The analysis revealed a high prevalence of AMR genes conferring resistance to fluoroquinolones, tetracyclines, aminoglycosides, and beta-lactams. Efflux pumps and enzymatic modification mechanisms were the dominant resistance strategies across all sample types. The widespread occurrence of resistance genes underscores the potential for horizontal gene transfer and environmental dissemination. This study highlights the necessity for continuous genomic surveillance and a One Health approach to combat the  spread of AMR in E. coli, ultimately aiding in the development of effective mitigation strategies.