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AutoMated tool for Antimicrobial resistance Surveillance System version 3.0 (AMASSv3.0)

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modified on 2024-01-10, 02:44

Version 3.0 (BETA) Build 3026

Release date: 8 January 2024

The AMASS Version 3.0 (BETA) Build 3026 provides updates including:

  1. Add Table S10A and S10B in data verification log report to display list of ward data values in microbiology data file and hospital admission data file per configuration in dictionary for ward.
  2. Add white space trimming process to column names and data values in microbiology data file and hospital admission data file as well as values configured in dictionaries for better translate of data for process in AMASS per configuration in dictionaries.
  3. Support Thai language in 1) Table S10A and S10B of data_verification_log, 2) Table S1 of supplementary_Annex_C reports, and 3) exported CSV files which are located in the report_with_patientidentifier folder
  4. Fix Table S3 in data verification log report to show the correct number of observations contains S, I, and R per antibiotics data value in microbiology data file.
  5. Fix the process for loading a dictionaries to avoid error from extra text or data in columns and rows which are not part of the dictionary template.
  6. Fix wrong typo in AMR surveillance reports.


The current version of the AMASS Version 3.0 (BETA) application provides updates including

  1. Add “Annex C: Cluster signals”. This supplementary report shows the information of potential clusters which are identified using the SatScan (www.satscan.org);
  2. Add processed data files in the folder “Report_with_patient_identifiers” so that users can use the processed data files (e.g. deduplicated and merged data files for each AMR pathogen) for any further analysis and internal use;
  3. Enterococcus faecalis and E. faecium are explicitly included in the pathogens under the survey (while Enterococcus spp. are used in the AMASS version 2.0);
  4. Add a few antibiotics in the list of antibiotics for a few pathogens under the survey;
  5. Use only Python rather than R + Python (as used in the AMASS version 2.0);
  6. Include patients who have missing discharge dates in the analysis by truncating the day at risk using the last date of specimen date in the data set (e.g. a patient who was admitted on 30 Dec 2023, had blood specimen collected for culture on 31 Dec 2023, and were still in the hospital on 10 Jan 2024. Then, the microbiology data file and hospital admission date file were exported on 10 Jan 2024 for the data of year 2023 [specimen dates and hospital admission dates from 1 Jan 2023 to 31 Jan 2023]. This patient would be included in the analysis, assuming that the days at risk of BSI was from 30 Dec to 31 Dec 2023, and the specimen collected on 31 Dec 2023 would be included in the analysis. In the AMASS version 2.0, this patient would not be included in the analysis as the code for truncation among patients who were not discharged was not included in the AMASS version 2.0).

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 antimicrobial resistance (AMR) surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in Python, 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 the AMR 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 the AMR surveillance reports with stratification by infection origin. Finally, the application then performs 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 uses a tier-based approach. In cases when only the microbiology data file with the results of culture positive samples is available, only the AMR surveillance report without stratification by infection origin will be generated.

Further, details on how to use the application can be found at https://www.amass.website.

Funding

Wellcome Trust Institutional Translational Partnership Award- MORU