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PLoS One. 2016 May 5;11(5):e0154937. doi: 10.1371/journal.pone.0154937. eCollection 2016.

A Novel Computerized Cell Count Algorithm for Biofilm Analysis.

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Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany.
Computer Vision Group, Friedrich-Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany.
Institute of Pharmacy, Friedrich-Schiller University Jena, Otto-Schott-Strasse 41, 07745, Jena, Germany.
InfectoGnostics Forschungscampus Jena e.V., Zentrum für Angewandte Forschung Jena, Philosophenweg 7, 07743, Jena, Germany.


Biofilms are the preferred sessile and matrix-embedded life form of most microorganisms on surfaces. In the medical field, biofilms are a frequent cause of treatment failure because they protect the bacteria from antibiotics and immune cells. Antibiotics are selected according to the minimal inhibitory concentration (MIC) based on the planktonic form of bacteria. Determination of the minimal biofilm eradicating concentration (MBEC), which can be up to 1,000-fold greater than the MIC, is not currently conducted as routine diagnostic testing, primarily because of the methodical hurdles of available biofilm assessing protocols that are time- and cost-consuming. Comparative analysis of biofilms is also limited as most quantitative methods such as crystal violet staining are indirect and highly imprecise. In this paper, we present a novel algorithm for assessing biofilm resistance to antibiotics that overcomes several of the limitations of alternative methods. This algorithm aims for a computer-based analysis of confocal microscope 3D images of biofilms after live/dead stains providing various biofilm parameters such as numbers of viable and dead cells and their vertical distributions within the biofilm, or biofilm thickness. The performance of this algorithm was evaluated using computer-simulated 2D and 3D images of coccal and rodent cells varying different parameters such as cell density, shading or cell size. Finally, genuine biofilms that were untreated or treated with nitroxoline or colistin were analyzed and the results were compared with quantitative microbiological standard methods. This novel algorithm allows a direct, fast and reproducible analysis of biofilms after live/dead staining. It performed well in biofilms of moderate cell densities in a 2D set-up however the 3D analysis remains still imperfect and difficult to evaluate. Nevertheless, this is a first try to develop an easy but conclusive tool that eventually might be implemented into routine diagnostics to determine the MBEC and to improve outcomes of patients with biofilm-associated infections.

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