Data_Sheet_3_Analysis of the Global Population Structure of Paenibacillus larvae and Outbreak Investigation of American Foulbrood Using a Stable wgMLST Scheme.PDF

Paenibacillus larvae causes the American foulbrood (AFB), a highly contagious and devastating disease of honeybees. Whole-genome sequencing (WGS) has been increasingly used in bacterial pathogen typing, but rarely applied to study the epidemiology of P. larvae. To this end, we used 125 P. larvae genomes representative of a species-wide diversity to construct a stable whole-genome multilocus sequence typing (wgMLST) scheme consisting of 5745 loci. A total of 51 P. larvae isolates originating from AFB outbreaks in Slovenia were used to assess the epidemiological applicability of the developed wgMLST scheme. In addition, wgMLST was compared with the core-genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analyses. All three approaches successfully identified clusters of outbreak-associated strains, which were clearly separated from the epidemiologically unlinked isolates. High levels of backward comparability of WGS-based analyses with conventional typing methods (ERIC-PCR and MLST) were revealed; however, both conventional methods lacked sufficient discriminatory power to separate the outbreak clusters. The developed wgMLST scheme provides an improved understanding of the intra- and inter-outbreak genetic diversity of P. larvae and represents an important progress in unraveling the genomic epidemiology of this important honeybee pathogen.

幼虫芽孢杆菌（Paenibacillus larvae）可引发美洲幼虫腐臭病（AFB），这是一种极具传染性且破坏性极强的蜜蜂病害。全基因组测序（WGS）在细菌病原分型领域的应用日益广泛，但极少被用于幼虫芽孢杆菌的流行病学研究。为此，我们选取了代表该物种全谱系多样性的125株幼虫芽孢杆菌基因组，构建了一套包含5745个基因座的稳定全基因组多位点序列分型（wgMLST）方案。我们进一步使用源自斯洛文尼亚美洲幼虫腐臭病暴发事件的51株幼虫芽孢杆菌分离株，对所开发的wgMLST方案的流行病学适用性进行评估。此外，我们将wgMLST与核心基因组多位点序列分型（cgMLST）、全基因组单核苷酸多态性（wgSNP）分析展开对比。三种分析方法均成功识别出与暴发相关的菌株聚类簇，且此类聚类簇与流行病学上无关联的分离株界限清晰。研究结果显示，基于WGS的分析方法与传统分型方法（ERIC-PCR与多位点序列分型（MLST））具备高度的向后兼容性；不过，两种传统分型方法均缺乏足够的分辨能力以区分暴发相关聚类簇。本研究开发的wgMLST方案有助于更深入地解析幼虫芽孢杆菌在暴发内与暴发间的遗传多样性，为阐明这一重要蜜蜂病原的基因组流行病学特征迈出了关键一步。