diskImageR: quantification of resistance and tolerance to antimicrobial drugs using disk diffusion assays
diskImageR: quantification of resistance and tolerance to antimicrobial drugs using disk diffusion assays
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DOI：
10.1099/mic.0.000295
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发表时间：
2016-07-01
期刊：
影响因子：
2.8
通讯作者：
Berman, Judith
中科院分区：
文献类型：
--
作者：
Gerstein, Aleeza C.;Rosenberg, Alexander;Berman, Judith
微生物病原体对人类健康的威胁越来越大。虽然许多感染可以成功治疗和清除，但耐药性是一个普遍存在的问题。“耐受性”细胞亚群的存在（其中一部分群体能够在群体抗性水平以上生长）可能会增加治疗失败率;然而，现有的测量亚群效应的方法很麻烦。在这里，我们描述了diskImageR，一个计算管道，分析磁盘扩散试验的照片，以确定药物敏感性的程度[抑制半径，（RAD）]，和两个方面的亚群生长[生长分数（FoG）在抑制区，（Z 01），和生长的变化率从无药物到抑制药物浓度，（SLOPE）]。diskImageR用于检查人类真菌病原体白色念珠菌对抗真菌药物氟康唑在不同菌株背景和生长条件下的反应。在临床和实验室标准化协会（CLSI）条件下进行的纸片扩散试验比使用富培养基条件进行的试验敏感性更高，耐受性更低。我们还使用diskImageR来量化三种药物与氟康唑组合的效果，发现所有三种组合都会影响耐受性，其中一种药物（多西环素）的效果非常依赖于菌株。三种药物对敏感性的影响不同，强力霉素一般没有影响，氯喹一般增加敏感性和双羟萘酸吡维铵一般降低敏感性。同时定量微生物药物反应的不同方面的能力将促进在抗菌药物存在下亚群反应机制的研究。
Microbial pathogens represent an increasing threat to human health. Although many infections can be successfully treated and cleared, drug resistance is a widespread problem. The existence of subpopulations of 'tolerant' cells (where a fraction of the population is able to grow above the population resistance level) may increase the rate of treatment failure; yet, existing methods to measure subpopulation effects are cumbersome. Here we describe diskImageR, a computational pipeline that analyses photographs of disk diffusion assays to determine the degree of drug susceptibility [the radius of inhibition, (RAD)], and two aspects of subpopulation growth [the fraction of growth (FoG) within the zone of inhibition, (Z01), and the rate of change in growth from no drug to inhibitory drug concentrations, (SLOPE)]. diskImageR was used to examine the response of the human fungal pathogen Candida albicans to the antifungal drug fluconazole across different strain backgrounds and growth conditions. Disk diffusion assays performed under Clinical and Laboratory Standards Institute (CLSI) conditions led to more susceptibility and less tolerance than assays performed using rich medium conditions. We also used diskImageR to quantify the effects of three drugs in combination with fluconazole, finding that all three combinations affected tolerance, with the effect of one drug (doxycycline) being very strain dependent. The three drugs had different effects on susceptibility, with doxycycline generally having no effect, chloroquine generally increasing susceptibility and pyrvinium pamoate generally reducing susceptibility. The ability to simultaneously quantitate different aspects of microbial drug responses will facilitate the study of mechanisms of subpopulation responses in the presence of antimicrobial drugs.