Israeli Ofir, Makdasi Efi, Cohen-Gihon Inbar, Zvi Anat, Lazar Shirley, Shifman Ohad, Levy Haim, Gur David, Laskar Orly, Beth-Din Adi
Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.
Future Sci OA. 2020 Apr 29;6(6):FSO476. doi: 10.2144/fsoa-2020-0013.
High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, , and spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5-5.9 orders of magnitude, in samples with bacteria spiked-in at 10-10 CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8-9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.
全血样本中病原体的高通量DNA测序（HTS）受到高宿主/病原体核酸比例的阻碍。我们描述了一种新颖且快速的细菌富集程序，该程序在模拟菌血症人类血液样本中的实施情况得到了例证。该程序包括宿主DNA的去除、快速HTS和生物信息学分析。按照此程序，在每毫升加入10⁻¹⁰至10⁻⁹CFU细菌的样本中，加入[具体细菌名称1]、[具体细菌名称2]和[具体细菌名称3]的样本显示宿主/病原体DNA比例提高了2.5至5.9个数量级。本研究中描述的程序能够在8至9小时内对病原体进行快速且详细的宏基因组分析，规避了菌血症血液中高背景以及样本性质未知所带来的挑战。
