Antibiogramj: A tool for analysing images from disk diffusion tests

https://doi.org/10.1016/j.cmpb.2017.03.010Get rights and content

Highlights

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    AntibiogramJ determines, measures and categorises inhibition zones of antibiograms.

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    AntibiogramJ deals with images captured with any device that incorporates a camera.

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    AntibiogramJ is user-friendly, open-source, guides users, learns, and stores results.

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    AntibiogramJ provides the benefits of automated readers but without any investment.

Abstract

Background and objectives

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow.

Methods

Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation.

Results

We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result.

Conclusions

AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory.

Section snippets

Background

Determining the antimicrobial susceptibility of microorganisms is of great importance in clinical microbiology not only to guide therapeutic decisions in infectious diseases, but also to investigate the evolution and epidemiology of resistance [1] — which is essential for implementing hospital prevention programs. Antimicrobial susceptibility tests are used to examine the in vitro activity of different antimicrobial agents against a specific microorganism. There are a variety of methods for

Implementation

AntibiogramJ has been developed as a Java application. It relies on two third-party libraries widely applied in bioinformatics: ImageJ [12], that provides functionality for image processing, and OpenCV [13], that features several computer vision and machine-learning algorithms. The combination of those two libraries was possible thanks to the IJ-OpenCV library (http://joheras.github.io/IJ-OpenCV/). Additionally, AntibiogramJ includes an embedded database provided by the JavaDB library [14].

Results

In this section, we compare AntibiogramJ’s automatic procedure to categorise inhibition zones with the results obtained manually by an expert microbiologist. For this study, we employed a battery of 86 plates-images corresponding to 27 enterobacterial, enterococcal, staphylococcal, pseudomonal and acinetobacterial clinical isolates prepared on Mueller Hinton (MH) agar plates. A total of 29 different antimicrobial agents were used.

From the 86 plates-images, 43 images were captured with a digital

Discussion

There are two kinds of automated or semi-automated inhibition zone readers: integrated instruments that combine hardware and software; and software tools that work with plate-images captured with a camera device.

For the first kind of inhibition zone readers, a variety of instruments have been introduced over the years to automate the measurement of inhibition zones in order to determine antimicrobial susceptibility [11], [21], [22], [23]. Nowadays, these systems usually consists of three

Conclusions

In this paper, we have presented AntibiogramJ, a Java application designed for determining, measuring and categorising zone of growth inhibition from plate-images captured with any camera device, including digital cameras, smartphones and tablets. AntibiogramJ is a user-friendly, platform-independent, open-source, and free-tool. Up to the best of our knowledge, AntibiogramJ is the most complete software tool for antibiogram analysis without requiring any particular hardware system. Besides, the

Availability and requirements

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    Project name: AntibiogramJ.

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    Project home page: https://sourceforge.net/projects/antibiogramj/.

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    Operating system(s): Platform independent.

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    Programming language: Java.

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    Other requirements: Java 8.

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    License: GNU GPL v3.

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    Any restrictions to use by non-academics: restrictions specified by GNU GPL v3.

AntibiogramJ does not require installation. To run AntibiogramJ, the user should download AntibiogramJ from the project home page, unzip the downloaded file, and run the program antibiogramJv1*.jar. The only

Competing interests

The authors declare that they have no competing interests.

Acknowledgement

This work was partially supported by Ministerio de Economía y Competitividad [MTM2014-54151-P].

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