AutoMated Antimicrobial resistance Surveillance System version 2.0

Principal Investigator : Cherry Lim

Project Status : On-going

Project Summary

Antimicrobial susceptibility test (AST) results of bacterial isolates identified from clinical samples need to be verified before reporting to doctors and before being included in a cumulative AST report. This is because accurate AST results are crucial not only for selecting the appropriate treatment for individual patients, but also for a precise understanding on the disease burdens at a population level. However, data quality checks do not always happen in all laboratories, especially those in low and middle-income countries (LMICs). This is because AST data are often stored, on daily basis, in paper logbooks, in Microsoft Excel, or in-house laboratory information systems (LIS) with no functions to automatically verify the AST results or highlight the results that need to be confirmed. For example, Escherichia coli isolates that are resistant to amikacin but susceptible to both gentamicin and tobramycin should be confirmed as such an observation is likely the result of laboratory errors. Commercial LIS with functions to support data verification are unaffordable for many hospitals in LMICs. The open-access WHONET program has functions to support data quality checks. However, no open-access tool has yet been developed to produce printable PDF data verification reports.


We recently developed an open-access, easy-to-use application, named AutoMated tool for Antimicrobial resistance Surveillance System (AMASS website), that utilizes retrospective data in Excel format to generate cumulative AST reports. AMASS shortens the time needed to clean and de-duplicate routinely collected data, and automatically generates a cumulative AST report in PDF format. We have implemented the application in seven hospitals, and the reports generated from those hospitals are shared on an open-access data depository website. The hospitals needed to manually export their data from their existing LIS before using AMASS, and AMASS version 1.0 does not have the function to support data verification.