Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.
Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia Province, Egypt.
J Clin Microbiol. 2022 Aug 17;60(8):e0031122. doi: 10.1128/jcm.00311-22. Epub 2022 Jul 19.
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.
布鲁氏菌病对全球人类和动物健康构成重大负担。需要强大且协调一致的分子流行病学方法和包括常规疾病筛查的人群研究，以有效地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）是一种常用的基因分型系统，用于描绘疾病监测和控制的病原体传播途径。除了布鲁氏菌 melitensis 外，目前尚未建立布鲁氏菌属的 cgMLST 方案。在这里，我们描述了一种新的涵盖多种布鲁氏菌物种的 cgMLST 方案。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广度。我们选择了 1764 个在至少 98%的这些基因组中特别保守且可分型的基因。我们在 600 个基因组上测试了新方案，发现与基于全基因组单核苷酸多态性（SNP）分析的结果高度一致。接下来，我们应用该方案重新分析了流行病学相关暴发的布鲁氏菌菌株的基因组。我们证明了该新方案在先前报道的全基因组 SNP 方法中所需的高分辨率分型方面的适用性。我们还使用新方案使用 1322 个布鲁氏菌基因组定义了该属的全球种群结构。最后，我们通过对 cgMLST 图谱进行聚类分析来证明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 图谱。我们的结果表明，该方案的等位基因调用最佳测序深度超过 40 倍。总之，本研究描述了一种新的适用于布鲁氏菌分子流行病学的布鲁氏菌属 cgMLST 方案，有助于准确跟踪和控制感染源。该方案是公开的，对于计算资源有限和缺乏生物信息学专业知识的实验室来说，应该是一个有价值的资源。
