AutoMated tool for Antimicrobial resistance Surveillance System (AMASS)

Version 1.1Release date: 12^th January 2021 AMASS 1.1 fixes a typo in the R codes of the AMASS 1.0 that caused inaccurate estimations of the proportion of non-susceptible isolates of <i>E. coli </i>and <i>K. pneumoniae</i> for ampicillin (page 9-10 and page 18-21 in the AMR surveillance report).<br>AutoMated tool for Antimicrobial resistance Surveillance System (AMASS) was developed as an offline, open−access and easy−to−use application that allows a hospital to perform data analysis independently and generate isolate−based and sample−based surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in R, which is a free software environment. The application has been placed within a user−friendly interface that only requires the user to double−click on the application icon. <br>AMASS performs data analysis and generates reports automatically. The raw data files required are hospital admission and microbiology databases. Firstly, the application cleans the microbiology data file and produces isolate−based and sample−based surveillance reports without stratification by infection origin. Secondly, the application then merges the microbiology and hospital admission data files, analyzes the merged data, and produces an isolated−based and sample−based surveillance reports with stratification by infection origin. Finally, the application then perform a statistical analysis to estimate all−cause mortality of patients with AMR infection and mortality attributable to AMR, which are automatically added into the AMR surveillance report.<br>AMASS aims to support the hospitals even those hospitals having only microbiology results. recorded electronica formats. For example, only isolate−based surveillance report without stratification by infection origin will be generated, if only microbiology data file is available and hospital admission data file is not available in the computer.<br> This is the AMASS.zip containing the AMASS application. Further, details on how to use the application can be found in https://www.amass.website

版本1.1，发布日期：2021年1月12日。AMASS 1.1修复了AMASS 1.0的R代码中的一处拼写错误，该错误导致氨苄青霉素药敏试验下大肠埃希菌（E. coli）与肺炎克雷伯菌（K. pneumoniae）非易感分离株比例的估算出现偏差（详见抗菌药物耐药性监测报告第9-10页及第18-21页）。
自动化抗菌药物耐药性监测系统（AutoMated tool for Antimicrobial resistance Surveillance System，简称AMASS）是一款离线、开源且易于使用的应用程序，支持医疗机构独立开展数据分析，并可基于常规收集的电子数据库，生成按感染来源分层的分离株级与样本级监测报告。该应用基于R语言（一款免费软件环境）开发，搭载了用户友好的图形界面，用户仅需双击应用图标即可启动使用。
AMASS可自动完成数据分析并生成报告，所需原始数据为医院入院数据库与微生物学数据库。具体流程如下：首先，应用将清理微生物学数据文件，生成未按感染来源分层的分离株级与样本级监测报告；其次，应用会合并微生物学数据与医院入院数据，对合并后的数据进行分析，并生成按感染来源分层的分离株级与样本级监测报告；最后，应用将执行统计分析，估算抗菌药物耐药（Antimicrobial Resistance，AMR）感染患者的全因死亡率及抗菌药物耐药相关归因死亡率，并将结果自动添加至抗菌药物耐药性监测报告中。
AMASS旨在为仅具备微生物学结果电子记录格式的医疗机构提供支持。例如，若计算机中仅提供微生物学数据文件而缺失医院入院数据文件，则应用将仅生成未按感染来源分层的分离株级监测报告。
本资源为包含AMASS应用程序的AMASS.zip压缩包。有关该应用程序的详细使用说明，可访问https://www.amass.website 查询。