Braun Sascha D, Rezk Shahinda, Brandt Christian, Reinicke Martin, Diezel Celia, Müller Elke, Frankenfeld Katrin, Krähmer Domenique, Monecke Stefan, Ehricht Ralf
Leibniz Institute of Photonic Technology, Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany.
InfectoGnostics Research Campus Jena, Center for Applied Research, 07743 Jena, Germany.
Antibiotics (Basel). 2024 Dec 5;13(12):1185. doi: 10.3390/antibiotics13121185.
The rise in carbapenem-resistant (CRE) in Egypt, particularly in hospital settings, poses a significant public health challenge. This study aims to develop a combined epidemiological surveillance tool utilizing the Microreact online platform (version 269) and molecular microarray technology to track and analyze carbapenem-resistant strains in Egypt. The objective is to integrate molecular diagnostics and real-time data visualization to better understand the spread and evolution of multidrug-resistant (MDR) bacteria.
The study analyzed 43 isolates collected from Egyptian hospitals between 2020 and 2023. Nanopore sequencing and microarray analysis were used to identify carbapenemase genes and other resistance markers, whereas the VITEK2 system was employed for phenotypic antibiotic susceptibility testing. Microreact was used to visualize epidemiological data, mapping the geographic and temporal distribution of resistant strains.
We found that 72.09% of the isolates, predominantly from pediatric patients, carried the NDM-5 gene, while other carbapenemase genes, including OXA-48 and VIM, were also detected. The microarray method demonstrated 92.9% diagnostic sensitivity and 87.7% diagnostic specificity compared to whole-genome sequencing. Phenotypic resistance correlated strongly with next-generation sequencing (NGS) genotypic data, achieving 95.6% sensitivity and 95.2% specificity.
This method establishes the utility of combining microarray technology, NGS and real-time data visualization for the surveillance of carbapenem-resistant especially . The high concordance between genotypic and phenotypic data underscores the potential of DNA microarrays as a cost-effective alternative to whole-genome sequencing, especially in resource-limited settings. This integrated approach can enhance public health responses to MDR bacteria in Egypt.
在埃及，耐碳青霉烯类肠杆菌（CRE）的出现，尤其是在医院环境中，对公共卫生构成了重大挑战。本研究旨在开发一种结合流行病学监测工具，利用Microreact在线平台（版本269）和分子微阵列技术来追踪和分析埃及的耐碳青霉烯类菌株。目的是整合分子诊断和实时数据可视化，以更好地了解多重耐药（MDR）细菌的传播和演变。
该研究分析了2020年至2023年期间从埃及医院收集的43株分离株。使用纳米孔测序和微阵列分析来鉴定碳青霉烯酶基因和其他耐药标记，而VITEK2系统用于表型抗生素敏感性测试。Microreact用于可视化流行病学数据，绘制耐药菌株的地理和时间分布。
我们发现72.09%的分离株主要来自儿科患者，携带NDM-5基因，同时还检测到其他碳青霉烯酶基因，包括OXA-48和VIM。与全基因组测序相比，微阵列方法显示出92.9%的诊断敏感性和87.7%的诊断特异性。表型耐药性与下一代测序（NGS）基因型数据密切相关，敏感性达到95.6%，特异性达到95.2%。
该方法确立了结合微阵列技术、NGS和实时数据可视化用于监测耐碳青霉烯类细菌的实用性。基因型和表型数据之间的高度一致性强调了DNA微阵列作为全基因组测序的经济有效替代方法的潜力，特别是在资源有限的环境中。这种综合方法可以加强埃及对MDR细菌的公共卫生应对。
