CAPTURA Dataset download and analysis using QAAPT and WHONET

In this tutorial, we'll walk you through QAAPT, which stands for Quick Analysis of AMR Patterns and Trends. QAAPT is a tool developed by the CAPTURA team for the analysis of Antimicrobial Susceptibility Testing data. Using QAAPT, you may interpret and visualize AMR data downloaded from WHONET.

Let’s get started with downloading items from QAAPT.

In this video, we will show you how to download items from QAAPT.

First, go to . To access and download the CAPTURA report and the cleaned dataset, you must login using a username and password we’ve provided for your laboratory. The Login Dashboard can be found on the right-hand side. Click on the login dashboard, and you can see the login panel.

QAAPT Website

Please enter your provided username and password here to complete the login.

CAPTURA report download

Once you’re logged in, the first screen you will see is the QAAPT Dashboard. To download the dataset and the CAPTURA facility report, select the item you want to download by clicking the drop-down menu on the right-hand side of the screen, and then click on the blue Download button.

CAPTURA report download

Next, to download the cleaned dataset, select the “AMR Cleaned Dataset” from the drop-down menu. Depending on your need, you may download the dataset in either the WHONET or CSV format. Using this dataset, you may conduct your own analysis using WHONET. We recommend using the cleaned dataset for WHONET analysis, but the original dataset is also available to download for your reference.

In this tutorial, we have shown you how to download your facilityreport and data set. In the following videos, we will show you how to use the dashboard and other functions in QAAPT, and also how to use WHONET software to analyze your downloaded dataset.

In this video, we will give you an overview of the QAAPT dashboard and other functions that comes with QAAPT.

Once you have logged in to QAAPT, the Dashboard is the first screen you will see. CAPTURA developed this predefined dashboard that offers visualizations of the following items:

Data set summary:

QAAPT Dashboard Summary

Descriptive statistics which include:

  • Number of records by year
  • Variable completeness status, and
  • Specimen types by all records, positive culture, negative culture, and contamination/mixed flora/no growth and others
QAAPT Descriptive Statistics

Data distributions that include:

  • Monthly distribution
  • Yearly distribution
  • Sex and age group distribution
  • Records by departments
QAAPT Data Distribution

Organism statistics that include:

  • Organism as True Pathogens, No-growth, Contamination and others
  • Most common organisms, and
  • Top five organisms by specimens such as urine, soft tissue and body fluids, blood, respiratory, genital and stool
QAAPT organism statistics

The next section of the dashboard shows:

  • Resistance pattern by most common organisms
  • Antibiogram by organism shown in percentage of resistance
  • Gram positive and negative organisms and distributions
  • List of Data variables
QAAPT resistant pattern

There is a filter function which can be used to generate the dashboard by all records or positive records only.

QAAPT dashboard filter

This dashboard is automatically generated from your laboratory’s cleaned dataset. Currently, it is not possible for you to upload your own data.

In addition to the Dashboard, QAAPT offers a number of other analyses you can customize. In the next video, we will show you how to use the custom reporting function on QAAPT.

In this video, we will show you several ways in which you can generate custom reports using QAAPT. You can use these functions to conduct further analysis beyond the automatic analyses presented on the Dashboard. The QAAPT analyses should be taken as an example and reference, and we recommend consulting microbiologists and AMR experts in your circle to better understand the relevance and credibility of such analyses.

QAAPT can help you generate custom reports for analyses that include:

  • Antimicrobial Pattern Analysis
  • Antimicrobial Susceptibility Trends Analysis
  • Hospital Antibiogram
  • Antibiogram by Organism

First, we will dive into Antimicrobial Pattern Analysis. The Antimicrobial Pattern analysis report can help you analyze the antimicrobial patterns according to organism.

  • First, select a data set in the first drop-down menu
  • The second dropdown will populate the list of top organisms. Please select only one organism here
  • Select the antibiotics you’re interested in
  • You can change the threshold 30 to any other values; it means the minimum isolates per test is 30 and click on the search button

This will generate three result figures:

  • A table with antibiotics, percentage of resistance, number of tested resistance and number of total test for the organisms
  • Cumulative resistance pattern with bar graph
  • Pattern by year
QAAPT resistant pattern

The next custom report you can generate with QAAPT is Antimicrobial Susceptibility Trends Analysis . This report will show you the half-yearly proportion of susceptibility by organism.

  • First, select a dataset of interest
  • The second dropdown will populate the list of top organisms. Please select only one organism here
  • Select the antibiotics you’re interested in
  • You can change the threshold 30 to any other values; it means the minimum isolates per test is 30 and click on the search button

This will generate two results figures:

  • Susceptibility trends line graph by half yearly trends, and
  • Two-by-Two table with % susceptibility, numerator and denominator
QAAPT resistant trends

Next, we will show you how to generate antibiograms, using QAAPT. You can understand the patterns of resistance in organisms of your choice using this function.

  • First, select your dataset from the drop-down menu and it will generate the report automatically

This report will help you generate your hospital antibiogram with following tables:

  • Distribution of Bacterial growth in different specimen
  • Pattern of organisms isolated
  • Distribution of bacteria Isolated from OPD, IPD
  • Distribution of sex and specimens
  • Antibiotic susceptibility pattern of major gram-positive organisms
  • Antibiotic susceptibility pattern of major gram-negative organisms
  • Distribution of organism and specimens
QAAPT antibiogram

Lastly, we will show you how to generate antibiogram by organism using QAAPT.

First, in the first drop-down menu, select the dataset of your interest. Next, in the second drop-down menu, choose which organism you’re interested in.

This will generate a table that shows specimen by antibiotic antibiogram. the percentage of resistance, numerator, and denominators can be seen in the following table using the color codes.

QAAPT antibiogram by organisms

That brings us to the end of QAAPT tutorial videos. If you would like to learn about how you can use WHONET to analyze your own data, please watch the videos below.

In the above QAAPT tutorial video, you have downloaded your cleaned dataset onto your computer. Go to your download location, copy the data file, and paste it onto your Desktop folder.

To begin, you must download the WHONET software from the website. You can get 32/64 bit installers from the website's "Software" tab. You can download either 32 bit or 64 bit, depending on your computer's configuration. How to grasp your computer's operating system is now the question. Check it by right clicking "This PC/My Computer" and looking at the properties. You can now see the operating system configuration.

We hope that this tutorial has helped you locate the CAPTURA report and that your lab can use the WHONET and QAAPT software to explore your own data.