DiskimageR: Quantification of resistance and tolerance to antimicrobial drugs using disk diffusion assays

Microbiology (United Kingdom)

Volumn 162, Issue 7, 2016, Pages 1059-1068

  Gerstein, Aleeza C ^a,b,c   Rosenberg, Alexander ^a   Hecht, Inbal ^a   Berman, Judith ^a,b,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

Author keywords

Broth microdilution; C. albicans; Drug synergism; Fluconazole; ImageJ; R Programming Language

Indexed keywords

CHLOROQUINE; DOXYCYCLINE; FLUCONAZOLE; PYRVINIUM EMBONATE; ANTIFUNGAL AGENT;

ANTIBIOTIC SENSITIVITY; ANTIFUNGAL RESISTANCE; ANTIFUNGAL SUSCEPTIBILITY; ARTICLE; BROTH DILUTION; CANDIDA ALBICANS; CONTROLLED STUDY; DISK DIFFUSION; DRUG POTENTIATION; DRUG TOLERANCE; FUNGUS GROWTH; GROWTH INHIBITION; IMAGE ANALYSIS; INHIBITION ZONE; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; DRUG EFFECTS; GROWTH, DEVELOPMENT AND AGING; HUMAN; ISOLATION AND PURIFICATION; PROCEDURES; SOFTWARE;

ANTIFUNGAL AGENTS; CANDIDA ALBICANS; CHLOROQUINE; DISK DIFFUSION ANTIMICROBIAL TESTS; DOXYCYCLINE; DRUG RESISTANCE, FUNGAL; FLUCONAZOLE; HUMANS; PYRVINIUM COMPOUNDS; SOFTWARE;

EID: 84981290681     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.000295     Document Type: Article

References (37)

1. Bednár, M. (2000). New formula for calculating antibiotic critical concentration by the disk diffusion method. Med Sci Monitor 6, 168-170
2. Berghaus, L. J., Giguère, S., Guldbech, K., Warner, E., Ugorji, U. & Berghaus, R. D. (2014). Comparison of Etest, disk diffusion, and broth macrodilution for in vitro susceptibility testing of Rhodococcus equi. JCM 53, 314-318
3. Bigger, J. W. (1944). Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 244, 497-500
4. Butts, A. & Krysan, D. J. (2012). Antifungal drug discovery: something old and something new. PLoS Pathogens 8, e1002870
5. Butts, A., DiDone, L., Koselny, K., Baxter, B. K., Chabrier-Rosello, Y., Wellington, M. & Krysan, D. J. (2013). A repurposing approach identifies off-patent drugs with fungicidal cryptococcal activity, a common structural chemotype, and pharmacological properties relevant to the treatment of cryptococcosis. Euk Cell 12, 278-287.
6. CLSI (2008). Reference method from broth dilution antifungal susceptibility testing of yeasts; Approved standard, 3rd edn. CLSI Document M27-A3 Wayne, PA: Clinical and Laboratory Standards Institute.
7. Center for Disease Dynamics & Policy (2015). State of the World’s Antibiotics. Washington, DC: CDDEP.
8. Chen, G., Mulla, W. A., Kucharavy, A., Tsai, H. J., Rubinstein, B., Conkright, J., McCroskey, S., Bradford, W. D., Weems, L. & other authors (2015). Targeting the adaptability of heterogeneous aneuploids. Cell 160, 771-784
9. Cohen, N. R., Lobritz, M. A. & Collins, J. J. (2013). Microbial persistence and the road to drug resistance. Cell Host Microbe 13, 632-642
10. Coorevits, L., Boelens, J. & Claeys, G. (2015). Direct susceptibility testing by disk diffusion on clinical samples: a rapid and accurate tool for antibiotic stewardship. Eur J Clin Microbiol 34, 1207-1212
11. Cowen, L. E., Sanglard, D., Calabrese, D., Sirjusingh, C., Anderson, J. B. & Kohn, L. M. (2000). Evolution of drug resistance in experimental populations of Candida albicans. J Bacteriol 182, 1515-1522
12. Driscoll, A. J., Bhat, N., Karron, R. A., O’Brien, K. L. & Murdoch, D. R. (2012). Disk diffusion bioassays for the detection of antibiotic activity in body fluids: applications for the Pneumonia Etiology Research for Child Health project. Clin Infect Dis 54, S159-S164
13. Fiori, A. & Van Dijck, P. (2012). Potent synergistic effect of doxycycline with fluconazole against Candida albicans is mediated by interference with iron homeostasis. Antimicrob Agents Chemother 56, 3785-3796.
14. FitzJohn, R. G. (2012). Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol Evol 3, 1084-1092
15. Fonzi, W. A. & Irwin, M. Y. (1993). Isogenic strain construction and gene mapping in Candida albicans. Genetics 134, 717-728
16. Fothergill, A. W. (2011). In Antifungal Susceptibility Testing: Clinical Laboratory and Standards Institute (CLSI) Methods, pp. 65-74 Totowa, NJ: Humana Press.
17. Huys, G., D’Haene, K. & Swings, J. (2002). Influence of the culture medium on antibiotic susceptibility testing of food-associated lactic acid bacteria with the agar overlay disc diffusion method. Lett Appl Microbiol 34, 402-406
18. Jensen, K. T., Schønheyder, H., Gottschau, A. & Thomsen, V. F. (1994). Impact of the agar medium and disc type on disc diffusion susceptibility testing against teicoplanin and vancomycin. APMIS 102, 94-102
19. Lee, D.-H. & Palsson, B. O. (2010). Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-1,2-propanediol. Appl Environ Microb 76, 4158-4168
20. Lewis, K. (2010). Persister cells. Annu Rev Microbiol 64, 357-372
21. Li, Y., Wan, Z., Liu, W. & Li, R. (2015). Synergistic activity of chloroquine with fluconazole against fluconazole-resistant isolates of candida species. Antimicrob Agents Chemother 59, 1365-1369
22. Liu, S., Hou, Y., Chen, X., Gao, Y., Li, H. & Sun, S. (2014). Combination of fluconazole with non-antifungal agents: A promising approach to cope with resistant Candida albicans infections and insight into new antifungal agent discovery. Int J Antimicrob Agents 43, 395-402
23. Lockhart, S. R., Pujol, C., Daniels, K. J., Miller, M. G., Johnson, A. D., Pfaller, M. A. & Soll, D. R. (2002). In Candida albicans, white-opaque switchers are homozygous for mating type. Genetics 162, 737-745
24. Marr, K. A., White, T. C., van Burik, J. A. & Bowden, R. A. (1997). Development of fluconazole resistance in Candida albicans causing disseminated infection in a patient undergoing marrow transplantation. Clin Infect Dis 25, 908-910
25. Matar, M. J., Ostrosky-Zeichner, L., Paetznick, V. L., Rodriguez, J. R., Chen, E. & Rex, J. H. (2003). Correlation between E-test, disk diffusion, and microdilution methods for antifungal susceptibility testing of fluconazole and voriconazole. Antimicrob Agents Chemother 47, 1647-1651
26. Odds, F. C., Bougnoux, M.-E., Shaw, D. J., Bain, J. M., Davidson, A. D., Diogo, D., Jacobsen, M. D., Lecomte, M., Li, S.-Y. & other authors (2007). Molecular phylogenetics of Candida albicans. Euk Cell 6, 1041-1052.
27. NCCLS (2004). Reference Method for Antifungal Disk Diffusion Susceptibility Testing of Yeasts; Approved Guideline. Wayne, PA: NCCLS Document M44-a. National Committee for Clinical Laboratory Standards.
28. Pfaller, M. A. (2012). Antifungal drug resistance: mechanisms, epidemiology, and consequences for treatment. Am J Med 125, S3-S13.
29. R Core Team. (2014). R: a Language and Environment for Statistical Computing. Austria: Vienna. http://www.R-project.org/.
30. Redding, S., Smith, J., Farinacci, G., Rinaldi, M., Fothergill, A., Rhine-Chalberg, J. & Pfaller, M. (1994). Resistance of Candida albicans to fluconazole during treatment of oropharyngeal candidiasis in a patient with AIDS: documentation by in vitro susceptibility testing and DNA subtype analysis. Clin Infect Dis 18, 240-242
31. Rex, J. H. & Pfaller, M. A. (2002). Has antifungal susceptibility testing come of age? Clin Infect Dis 35, 982-989
32. Sanglard, D., Kuchler, K., Ischer, F., Pagani, J. L., Monod, M. & Bille, J. (1995). Mechanisms of resistance to azole antifungal agents in Candida albicans isolates from AIDS patients involve specific multidrug transporters. AAC 39, 2378-2386
33. Sanglard, D. & Odds, F. C. (2002). Resistance of Candida species to antifungal agents: molecular mechanisms and clinical consequences. Lancet Infect Dis 2, 73-85
34. Sharma, S. V., Lee, D. Y., Li, B., Quinlan, M. P., Takahashi, F., Maheswaran, S., McDermott, U., Azizian, N., Zou, L. & other authors (2010). A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 141, 69-80
35. Siles, S. A., Srinivasan, A., Pierce, C. G., Lopez-Ribot, J. L. & Ramasubramanian, A. K. (2013). High-throughput screening of a collection of known pharmacologically active small compounds for identification of Candida albicans biofilm inhibitors. Antimicrob Agents Chemother 57, 3681-3687
36. Wu, W., Lockhart, S. R., Pujol, C., Srikantha, T. & Soll, D. R. (2007). Heterozygosity of genes on the sex chromosome regulates Candida albicans virulence. Mol Microbiol 64, 1587-1604
37. Zeidler, U., Bougnoux, M. E., Lupan, A., Helynck, O., Doyen, A., Garcia, Z., Sertour, N., Clavaud, C., Munier-Lehmann, H. & other authors (2013). Synergy of the antibiotic colistin with echinocandin antifungals in Candida species. J Antimicrob Chemother 68, 1285-1296.