Nykrynova Marketa, Barton Vojtech, Sedlar Karel, Bezdicek Matej, Lengerova Martina, Skutkova Helena
Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia.
Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.
Front Microbiol. 2021 Feb 3;12:631605. doi: 10.3389/fmicb.2021.631605. eCollection 2021.
Genotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g., local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also non-coding regions are examined.
基因分型方法用于区分同一物种的细菌菌株。因此，在全球范围内、不同国家之间或一个国家内的不同地区之间区分细菌菌株是可行的。然而，经过高度筛选的细菌群体（例如医院内的本地群体）通常关系密切且多样性较低。因此，目前使用的分型方法无法区分各个菌株。在此，我们提出了一种新颖的流程，用于检测高度可变的基因片段，以对密切相关的细菌群体进行基因分型。该方法基于分析序列中的无序程度，可用序列熵来表示。通过识别出的可变序列，可以找出高毒力和多重耐药菌株的传播途径和来源。所提出的方法可用于任何细菌群体，并且由于其覆盖全基因组范围，也会对非编码区域进行检测。
