PlasmidNL：用于比较质粒流行病学与监测数据探索的交互式 R/Shiny 应用
PlasmidNL: an interactive R/Shiny application for comparative plasmid epidemiology and surveillance-based data exploration
PlasmidNL 是一个交互式 R/Shiny 应用，将预计算的质粒聚类结果与 PlasmidFinder、MOB-suite 分型输出、耐药基因谱和流行病学元数据整合到统一分析环境中，用于比较质粒流行病学研究。该平台支持在大型数据集上交互探索质粒种群结构、耐药决定因子分布及相关元数据，并可将用户自有数据集与荷兰国家监测收藏（2012 至 2022 年间收集的 4,596 个产碳青霉烯酶菌株质粒）进行背景比对。作者同时提供可复现的预处理流程以生成标准化输入文件。PlasmidNL 以网页服务和本地部署两种方式免费提供，代码以 MIT 许可公开。
来源：Bioinformatics Advances · doi.org
Summary
Plasmids are key drivers of antimicrobial resistance (AMR) dissemination via horizontal gene transfer, yet their epidemiological analysis remains challenging due to fragmented analytical workflows and limited integration of genomic and contextual metadata. We present PlasmidNL, an interactive R/Shiny-based application for comparative plasmid epidemiology. PlasmidNL integrates precomputed plasmid clustering results with plasmid typing outputs (PlasmidFinder and MOB-suite), antimicrobial resistance gene profiles, and epidemiological metadata within a unified analytical environment. The platform enables interactive exploration of plasmid population structure, distribution of resistance determinants, and associated metadata across large datasets. A key feature is the ability to contextualize user-provided datasets against a curated Dutch national surveillance collection comprising 4,596 plasmids from carbapenemase-producing organisms collected between 2012 and 2022. We additionally provide a reproducible preprocessing pipeline that generates standardized input files compatible with the application. PlasmidNL is freely available as both a web-based service and a locally deployable application.
Availability and implementation
PlasmidNL is implemented in R using the Shiny framework and is accessible online at https://apps.rivm.nl/bsr-ids-ienv/plasmidnl/. Source code is available at https://github.com/gidjes/PlasmidNL under an MIT license.