Abstract：
Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains. Core genome multilocus sequence typing (cgMLST) is a powerful genotyping system commonly used to delineate pathogen transmission routes for disease surveillance and control. Except for Brucella melitensis, cgMLST schemes for Brucella species are currently not established. Here, we describe a novel cgMLST scheme that covers multiple Brucella species. We first determined the phylogenetic breadth of the genus using 612 Brucella genomes. We selected 1,764 genes that were particularly well conserved and typeable in at least 98% of these genomes. We tested the new scheme on 600 genomes and found high agreement with the whole-genome-based single nucleotide polymorphism (SNP) analysis. Next, we applied the scheme to reanalyze the genome of Brucella strains from epidemiologically linked outbreaks. We demonstrated the applicability of the new scheme for high-resolution typing required in outbreak investigations as previously reported with whole-genome SNP methods. We also used the novel scheme to define the global population structure of the genus using 1,322 Brucella genomes. Finally, we demonstrated the possibility of tracing distribution of Brucella strains by performing cluster analysis of cgMLST profiles and found nearly identical cgMLST profiles in different countries. Our results show that sequencing depth of more than 40-fold is optimal for allele calling with this scheme. In summary, this study describes a novel Brucella-wide cgMLST scheme that is applicable in Brucella molecular epidemiology and helps in accurately tracking and thus controlling the sources of infection. The scheme is publicly accessible and should represent a valuable resource for laboratories with limited computational resources and bioinformatics expertise.
摘要：
布鲁氏菌病对世界范围内的人类和动物健康构成重大负担。需要健全和协调的分子流行病学方法和人群研究，包括常规疾病筛查，以有效追踪布鲁氏菌菌株的起源和传播。核心基因组多位点序列分型（cgMLST）是一种强大的基因分型系统，通常用于描绘病原体传播途径以进行疾病监测和控制。除了布鲁氏菌,目前尚未建立针对布鲁氏菌物种的cgMLST计划。这里,我们描述了一种新的cgMLST方案，涵盖了多种布鲁氏菌物种。我们首先使用612个布鲁氏菌基因组确定了该属的系统发育宽度。我们选择了1,764个基因，这些基因在至少98％的基因组中特别保守和可键入。我们在600个基因组上测试了新方案，发现与基于全基因组的单核苷酸多态性（SNP）分析高度一致。接下来,我们应用该方案重新分析了与流行病学相关的暴发中的布鲁氏菌菌株的基因组。我们证明了先前报道的全基因组SNP方法在爆发调查中所需的高分辨率分型新方案的适用性。我们还使用了新方案，使用1,322个布鲁氏菌基因组来定义该属的全球种群结构。最后,我们通过对cgMLST谱进行聚类分析,证明了追踪布鲁氏菌菌株分布的可能性,并在不同国家发现了几乎相同的cgMLST谱.我们的结果表明，超过40倍的测序深度对于该方案的等位基因调用是最佳的。总之,这项研究描述了一种新的布鲁氏杆菌范围的cgMLST方案，该方案适用于布鲁氏杆菌分子流行病学，有助于准确跟踪并控制感染源。该方案可以公开访问，对于计算资源和生物信息学专业知识有限的实验室来说，应该是宝贵的资源。
