Skoulakis Anargyros, Kostoula Vasiliki, Daniilidis Konstantinos, Gkountinoudis Christos-Georgios, Petinaki Efthymia, Hatzigeorgiou Artemis G
DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, 35131, Greece.
Hellenic Pasteur Institute, Athens, 11521, Greece.
Nucleic Acids Res. 2025 Jul 7;53(W1):W20-W31. doi: 10.1093/nar/gkaf400.
Antimicrobial resistance (AMR) remains a critical challenge in public health and research. AmrProfiler is a comprehensive tool with three specialized modules: identifying acquired AMR genes, resistance-associated mutations, and ribosomal RNA (rRNA) gene mutations across nearly 18 000 bacterial species. By integrating and refining data from established databases, it provides a robust framework for AMR analysis. AmrProfiler is the first to systematically report mutations in rRNA genes, offering in-depth analysis of rRNA copy numbers and mutations-key for identifying potential rRNA-associated resistance mechanisms. Its curated database includes 7600 unique AMR gene entries and over 4300 resistance-related mutations. Supporting genome assemblies in multiple formats, AmrProfiler allows users to customize detection thresholds for AMR genes, mutations, and rRNA analysis. Validation with Acinetobacter baumannii,Escherichia coli,Klebsiella pneumoniae,Staphylococcus aureus, and Staphylococcus epidermidis demonstrated that AmrProfiler accurately identified all AMR genes and mutations reported by other tools while also detecting additional resistance markers and mutations not previously recognized. By bridging AMR genotypes and phenotypes, AmrProfiler provides actionable insights that advance both research and clinical applications in AMR. AmrProfiler is freely available as an open-access web server without login at https://dianalab.e-ce.uth.gr/amrprofiler.
抗菌药物耐药性（AMR）仍然是公共卫生和研究领域的一项严峻挑战。AmrProfiler是一个综合性工具，具有三个专门模块：识别近18000种细菌中的获得性AMR基因、耐药相关突变和核糖体RNA（rRNA）基因突变。通过整合和完善来自现有数据库的数据，它为AMR分析提供了一个强大的框架。AmrProfiler率先系统地报告rRNA基因中的突变，对rRNA拷贝数和突变进行深入分析，这是识别潜在rRNA相关耐药机制的关键。其精心策划的数据库包含7600个独特的AMR基因条目和超过4300个耐药相关突变。AmrProfiler支持多种格式的基因组组装，允许用户自定义AMR基因、突变和rRNA分析的检测阈值。通过对鲍曼不动杆菌、大肠杆菌、肺炎克雷伯菌、金黄色葡萄球菌和表皮葡萄球菌进行验证，结果表明AmrProfiler能够准确识别其他工具报告的所有AMR基因和突变，同时还能检测到以前未识别的其他耐药标记和突变。通过在AMR基因型和表型之间架起桥梁，AmrProfiler提供了可操作的见解，推动了AMR研究和临床应用的发展。AmrProfiler作为一个开放获取的网络服务器免费提供，无需登录，网址为https://dianalab.e-ce.uth.gr/amrprofiler 。
