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AutoMated tool for Antimicrobial resistance Surveillance System (AMASS)

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modified on 2021-09-06, 12:55

Version 1.1

Release date: 12th 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 E. coli and K. pneumoniae for ampicillin (page 9-10 and page 18-21 in the AMR surveillance 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 in


Epidemiology and health burdens of antimicrobial resistant bacterial infection in Southeast Asia and impact of antibiotic use on patient survival

Wellcome Trust

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