Webb Andrew L, Kruczkiewicz Peter, Selinger L Brent, Inglis G Douglas, Taboada Eduardo N
Agriculture and Agri-Food Canada, 5403 - 1st Avenue S, Lethbridge, AB, Canada.
Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.
BMC Microbiol. 2015 May 7;15:94. doi: 10.1186/s12866-015-0426-4.
Molecular typing methods are critical for epidemiological investigations, facilitating disease outbreak detection and source identification. Study of the epidemiology of the emerging human pathogen Arcobacter butzleri is currently hampered by the lack of a subtyping method that is easily deployable in the context of routine epidemiological surveillance. In this study we describe a comparative genomic fingerprinting (CGF) method for high-resolution and high-throughput subtyping of A. butzleri. Comparative analysis of the genome sequences of eleven A. butzleri strains, including eight strains newly sequenced as part of this project, was employed to identify accessory genes suitable for generating unique genetic fingerprints for high-resolution subtyping based on gene presence or absence within a strain.
A set of eighty-three accessory genes was used to examine the population structure of a dataset comprised of isolates from various sources, including human and non-human animals, sewage, and river water (n=156). A streamlined assay (CGF40) based on a subset of 40 genes was subsequently developed through marker optimization. High levels of profile diversity (121 distinct profiles) were observed among the 156 isolates in the dataset, and a high Simpson's Index of Diversity (ID) observed (ID > 0.969) indicate that the CGF40 assay possesses high discriminatory power. At the same time, our observation that 115 isolates in this dataset could be assigned to 29 clades with a profile similarity of 90% or greater indicates that the method can be used to identify clades comprised of genetically similar isolates.
The CGF40 assay described herein combines high resolution and repeatability with high throughput for the rapid characterization of A. butzleri strains. This assay will facilitate the study of the population structure and epidemiology of A. butzleri.
分子分型方法对于流行病学调查至关重要，有助于疾病暴发检测和源头识别。新兴人类病原体布氏嗜冷杆菌的流行病学研究目前因缺乏一种可在常规流行病学监测中轻易应用的分型方法而受阻。在本研究中，我们描述了一种用于布氏嗜冷杆菌高分辨率和高通量分型的比较基因组指纹图谱（CGF）方法。我们对11株布氏嗜冷杆菌的基因组序列进行了比较分析，其中包括作为本项目一部分新测序的8株菌株，以鉴定适合基于菌株内基因存在与否生成独特遗传指纹用于高分辨率分型的辅助基因。
使用一组83个辅助基因来检查一个数据集的群体结构，该数据集由来自各种来源的分离株组成，包括人类和非人类动物、污水和河水（n = 156）。随后通过标记优化开发了一种基于40个基因子集的简化检测方法（CGF40）。在数据集中的156株分离株中观察到高水平的图谱多样性（121种不同图谱），并且观察到的高辛普森多样性指数（ID）（ID > 0.969）表明CGF40检测具有高鉴别力。同时，我们观察到该数据集中的115株分离株可被归入29个分支，图谱相似度为90%或更高，这表明该方法可用于识别由遗传相似的分离株组成的分支。
本文所述的CGF40检测方法结合了高分辨率、可重复性和高通量，可快速鉴定布氏嗜冷杆菌菌株。该检测方法将有助于布氏嗜冷杆菌群体结构和流行病学的研究。
