The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.

这蜡样芽孢杆菌组，也称为B. cereus 意义（斯尔），是一个物种复合体，由许多密切相关的谱系组成，这些谱系在人类和动物中引起疾病​​的能力各不相同。的分类蜡状芽孢杆菌 sl将分离株划分为物种级分类单位对于促进微生物学家、临床医生、公共卫生官员和行业专业人士之间的沟通至关重要，但并不总是那么简单。最近提出的基因种-亚种-生物变种分类框架旨在为该物种复合体提供标准化命名法，但在很大程度上依赖于全基因组测序（WGS）。因此，尚不清楚流行的低成本分型方法（例如单基因座和多基因座序列分型）是否与提议的分类法保持一致。在这里，我们描述了 2,231蜡状芽孢杆菌 sl基因组使用组合计算机模拟(i) 基于平均核苷酸同一性 (ANI) 的基因种分配，(ii) 基于 ANI 的亚种分配，(iii) 七基因多位点序列分型 (MLST)，(iv) 单位点泛C小组作业，(v)rpoB等位基因分型，以及（vi）毒力因子检测。我们表明，使用 MLST 分配的序列类型 (ST) 可用于基因组分配，并且我们提供了 ST/基因组关联的完整列表。为了泛C组分配，我们表明调整后的八组框架虽然不完美，但在很大程度上与拟议的八基因组分类法一致，因为泛C单独可能无法区分 (i)B. 卢蒂来自第二组马赛克 B.(二)副丝状芽孢杆菌来自第六组蕈状芽孢杆菌。我们还提供了捕获全基因组拓扑的基因座列表蜡状芽孢杆菌 sl系统发育可能用于未来的序列分型工作。对于能够访问 WGS、MLST 和/或泛C数据，我们展示了我们最近发布的软件 BTyper3 (https://github.com/lmc297/BTyper3），可用于赋值蜡状芽孢杆菌 sl在这个提议的框架内分离到分类单元，几乎没有用户干预或特定领域的知识蜡状芽孢杆菌 sl分类。我们还概述了一种新的分配方法蜡状芽孢杆菌 sl基因组到拟议基因种内的伪基因流单位。这里提出的结果强调了最近提出的基因种-亚种-生物变种分类框架的向后兼容性和可访问性，并说明对于想要有效使用所提出的命名法的微生物学家来说，WGS 并不是必需的。