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AutoMated tool for Antimicrobial resistance Surveillance System version 2.0 (AMASSv2.0)

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Version 5 2023-09-15, 16:50
Version 4 2022-11-25, 09:08
Version 3 2022-11-16, 09:03
Version 2 2022-08-18, 03:55
Version 1 2022-05-22, 14:14
posted on 2023-09-15, 16:50 authored by Cherry LimCherry Lim, Chalida RangsiwutisakChalida Rangsiwutisak, Direk LimmathurotsakulDirek Limmathurotsakul

Version 2.0

Release date: 15th September 2023

This version fixes a code issue present in the release from 16th November 2022, which was causing a failure to generate the complete Annex B on page 42.

This version fixes a typo in the R code of the release 16th August 2022 that caused inaccurate estimations of the proportion of patients with non-susceptible isolates against levofloxacin and carbapenem drugs. In addition, this version also allows users to choose whether an organism included for the AMR Surveillance Report is Acinetobacter spp. or Acinetobacter baumanii.

The current version of the AMASS application provides additional reports on notifiable bacterial diseases in Annex A and on data indicators (including proportion of contaminants and discordant AST results) in Annex B for the "microbiology_data" file that is used to generate this report. A careful review of the Annex B could help readers and data owners to identify potential errors in the microbiology data used to generate the report.

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.

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. 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.

This is the containing the AMASS application. Further, details on how to use the application can be found at


Wellcome Trust Institutional Translational Partnership Award- MORU