Laboratoire Antibiotiques, Antifongiques: Physico-chimie, Synthèse et Activité Biologiques (LAPSAB), Faculté des Sciences de la Nature, de la Vie, de la Terre et de l'Univers, Université Abou Bekr Belkaid - Tlemcen, Bp 119, Tlemcen 13000, Algeria.
Aix-Marseille Université, URMITE CNRS-IRD, UMR 6236 INSERM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France.
J Med Microbiol. 2013 Jun;62(Pt 6):864-874. doi: 10.1099/jmm.0.049437-0. Epub 2013 Feb 28.
Antimicrobial resistance is on the rise, and its early detection and surveillance are critical to implement effective control measures. The aim of this study was to develop a rapid hierarchical clustering bioinformatic tool for application on antibiotic susceptibility testing (AST) results (resistant, intermediate, sensitive) of a series of Klebsiella pneumoniae clinical isolates from Algeria and from France for surveillance of antibiotic-resistance phenotypes. A total of 1011 K. pneumoniae strains were collected from August 2008 to December 2012: 221 clinical isolates from western Algeria and 790 clinical isolates from Marseille, France. AST against a panel of 16 antibiotics was done for all isolates. Results of AST were introduced into MultiExperiment Viewer (MeV) software to perform hierarchical clustering, with resistant, intermediate and sensitive being translated to 1, 0 and -1 values, respectively. Hierarchical clustering results were compared to standard resistance phenotypes to evaluate the accuracy of the method. Based on the AST results, the 221 K. pneumoniae strains from Algeria could be separated into six phenotype groups as regards their resistance to β-lactam compounds: extended spectrum β-lactamase (ESBL) (68.3 %), ESBL associated with cephalosporinase (13.1 %), cephalosporinase (0.9 %), penicillinase (3.6 %) and wild-type (14.0 %). Hierarchical clustering by the MeV software applied to the AST results for all 1011 isolates generated clusters that were significantly representative of phenotypic classification and geographical origin, in less than 1 min. Moreover, adding to the dataset the AST results of a K. pneumoniae NDM-1 positive strain, the only strain resistant to imipenem in the series, immediately generated a new branch in the dendrogram. We have developed a rapid and simple hierarchical clustering tool for application on AST results that was able to survey qualitatively and quantitatively the prevalence of known and unknown phenotypes. This tool could be easily implemented in routine clinical microbiology laboratories.
抗菌药物耐药性呈上升趋势，早期检测和监测对于实施有效的控制措施至关重要。本研究旨在开发一种快速层次聚类生物信息学工具，用于对来自阿尔及利亚和法国的一系列肺炎克雷伯菌临床分离株的抗生素药敏试验（AST）结果（耐药、中介、敏感）进行分析，以监测抗生素耐药表型。共收集了 1011 株肺炎克雷伯菌菌株，采集时间为 2008 年 8 月至 2012 年 12 月：来自阿尔及利亚西部的 221 株临床分离株和来自法国马赛的 790 株临床分离株。对所有分离株进行了针对 16 种抗生素的 AST。将 AST 结果输入 MultiExperiment Viewer（MeV）软件进行层次聚类，将耐药、中介和敏感分别翻译为 1、0 和-1 值。将层次聚类结果与标准耐药表型进行比较，以评估该方法的准确性。根据 AST 结果，来自阿尔及利亚的 221 株肺炎克雷伯菌可根据其对β-内酰胺类化合物的耐药性分为六个表型组：超广谱β-内酰胺酶（ESBL）（68.3%）、ESBL 与头孢菌素酶相关（13.1%）、头孢菌素酶（0.9%）、青霉素酶（3.6%）和野生型（14.0%）。MeV 软件应用于所有 1011 株分离株的 AST 结果进行的层次聚类在不到 1 分钟的时间内生成了与表型分类和地理来源显著相关的聚类。此外，在数据集上添加一株产 NDM-1 肺炎克雷伯菌的 AST 结果，该菌株是该系列中唯一对亚胺培南耐药的菌株，立即在树状图中生成了一个新的分支。我们开发了一种快速简便的层次聚类工具，用于 AST 结果分析，能够定性和定量地调查已知和未知表型的流行情况。该工具可以很容易地在常规临床微生物学实验室中实施。
