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.

幼芽孢杆菌引起美洲臭虫（AFB），这是一种具有高度传染性和破坏性的蜜蜂疾病。全基因组测序（WGS）已越来越多地用于细菌病原体分型，但很少用于研究流行病学幼虫。为此，我们使用了125幼虫代表全物种多样性的全基因组，以构建由5745个基因座组成的稳定的全基因组多基因座序列分型（wgMLST）方案。共51个幼虫来自斯洛文尼亚AFB爆发的分离株用于评估已开发的wgMLST计划在流行病学上的适用性。此外，将wgMLST与核心基因组MLST（cgMLST）和全基因组单核苷酸多态性（wgSNP）分析进行了比较。所有这三种方法都成功地确定了与暴发相关菌株的群，这些群明显与流行病学上没有联系的分离株分离开了。揭示了基于WGS的分析与常规分型方法（ERIC-PCR和MLST）的高水平向后可比性；但是，这两种传统方法都缺乏足够的区分力来区分爆发群。开发的wgMLST方案可更好地了解暴发期间暴发期间和暴发期间的遗传多样性幼虫 并代表了这一重要蜜蜂病原体的基因组流行病学研究的重要进展。