Web-Based Tools Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis

Antimicrobial resistance (AMR) is a serious threat to global public health, necessitating rapid and precise diagnostic tools. The prevalence of novel antibiotic resistance genes (ARGs) has increased due to microbial sequencing, resulting in the need to extract vital information from vast amounts of data. Although many AMR prediction tools exist, only a few are accurate and scalable. We examined 20 widely used AMR prediction tools and chose 4 web-based tools for antimicrobial resistance surveillance over standalone software due to their easy accessibility, portability, and centralized data management, eliminating the need for complex installation and maintenance. CGE (Center for Genomic Epidemiology) provides bioinformatics tools and promotes open data sharing. At the same time, CARD (Comprehensive Antibiotic Resistance Database) is a valuable resource for antibiotic resistance gene information, collectively contributing to our understanding and management of antibiotic resistance. We highlighted web-based AMR prediction tools and performed a case study using the Pseudomonas aeruginosa complete plasmid sequence (CPS) to identify strengths and weaknesses in the system. Our study explored four web-based antibiotic resistance gene prediction tools: ResFinder, KmerResistance, ResFinderFG, and RGI. ResFinder excelled at finding acquired antimicrobial resistance genes as well as maintaining a database up to date. KmerResistance identified resistance genes using k-mer analysis. esFinderFG offered a unique perspective, excelling in detecting a broad range of resistant phenotypes, due to its inclusion of sequences discovered through functional metagenomics. RGI was versatile in detecting a wide range of resistance genes and provided extensive resistance mechanism information. Researchers must understand the capabilities and trade-offs of these tools to make well-informed choices for efficient resistance gene identification and surveillance as the antibiotic resistance landscape evolves.