Antibiogramj: A tool for analysing images from disk diffusion tests
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.
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].
References (29)
ORB: an efficient alternative to SIFT or SURF
Proceedings of International Conference on Computer Vision
(2011)Laboratory automation in clinical bacteriology: what system to choose?
Clin. Microbiol. Infect.
(2016)Comparison of the accuracy of disk diffusion zone diameters obtained by manual zone measurements to that by automated zone measurements to determine antimicrobial susceptibility
J. Microbiol. Methods
(2008)- et al.
Telemicrobiology: focusing on quality in an era of laboratory consolidation
Clin. Microbiol. Newsl.
(2016) - et al.
Evaluation of the BIOMIC video reader system for routine use in the clinical microbiology laboratory
Diagn. Microbiol. Infect. Dis.
(2000) - vlab.amrita.edu, Quantification of bacterial colonies on an agar plate, 2012Last accessed on 24th November...
- et al.
Evaluation of the BIOMIC video reader system for determining interpretive categories of isolates on the basis of disk diffusion susceptibility results
J. Clin. Microbiol.
(1998) - et al.
Current concepts in laboratory testing to guide antimicrobial therapy
Mayo Clin. Proc.
(2012) - et al.
Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories
Clin. Microbiol. Infect.
(2014) - et al.
Antibiotic susceptibility testing by a standardized single disk method
Am. J. Clin. Pathol.
(1966)