Su Datt Lam, Sabrina Di Gregorio, Mia Yang Ang, Emma Griffiths, Tengku Zetty Maztura Tengku Jamaluddin, Sheila Nathan, Hui-Min Neoh
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引用次数: 0
摘要
抗菌素耐药性(AMR)对全球公共卫生构成重大威胁,到 2050 年,每年可能造成数百万人死亡。对 AMR 病原体的有效监控对于监测和预测它们对抗生素的反应至关重要。然而,许多公共卫生专业人员缺乏有效分析病原体基因组所需的生物信息学技能和资源。为了应对这一挑战,我们开发了AMRColab,这是一个在谷歌实验室(Google Colaboratory)上托管的开放式生物信息学分析套件。AMRColab 使受过有限或根本没有生物信息学培训的用户也能使用 "即插即用 "的方法检测病原体基因组中的 AMR 决定因素并将其可视化。该平台集成了 AMRFinderPlus 和 hAMRonization 等成熟的生物信息学工具,使用户能够轻松地分析、比较和可视化 AMR 病原体的趋势。使用耐甲氧西林金黄色葡萄球菌(MRSA)菌株进行的试运行表明,AMRColab 在确定 AMR 决定因素和促进菌株间比较分析方面非常有效。举办了一次研讨会,与会者的反馈表明,他们对使用 AMRColab 非常有信心,并愿意将其纳入自己的研究中。AMRColab 的用户友好界面和模块化设计使其适合不同人群使用,包括医学实验室技术人员、医生和公共卫生科学家,无论其生物信息学专业知识如何。AMRColab 未来的改进将包括增强可视化工具、多语言支持和建立在线社区平台。AMRColab 是实现 AMR 监测民主化和增强公共卫生专业人员有效防治 AMR 能力的重要一步。
AMRColab - a user-friendly antimicrobial resistance detection and visualization tool.
Antimicrobial resistance (AMR) poses a significant threat to global public health, with the potential to cause millions of deaths annually by 2050. Effective surveillance of AMR pathogens is crucial for monitoring and predicting their behaviour in response to antibiotics. However, many public health professionals lack the necessary bioinformatics skills and resources to analyse pathogen genomes effectively. To address this challenge, we developed AMRColab, an open-access bioinformatics analysis suite hosted on Google Colaboratory. AMRColab enables users with limited or no bioinformatics training to detect and visualize AMR determinants in pathogen genomes using a 'plug-and-play' approach. The platform integrates established bioinformatics tools such as AMRFinderPlus and hAMRonization, allowing users to analyse, compare and visualize trends in AMR pathogens easily. A trial run using methicillin-resistant Staphylococcus aureus (MRSA) strains demonstrated AMRColab's effectiveness in identifying AMR determinants and facilitating comparative analysis across strains. A workshop was conducted and feedback from participants indicated high confidence in using AMRColab and a willingness to incorporate it into their research. AMRColab's user-friendly interface and modular design make it accessible to a diverse audience, including medical laboratory technologists, medical doctors and public health scientists, regardless of their bioinformatics expertise. Future improvements to AMRColab will include enhanced visualization tools, multilingual support and the establishment of an online community platform. AMRColab represents a significant step towards democratizing AMR surveillance and empowering public health professionals to combat AMR effectively.
期刊介绍:
Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.