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 local hospitals including those that have only microbiology results recorded in electronic 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