Table_5_No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods.XLSX

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.

枯草芽孢杆菌属（Bacillus cereus group），亦称为广义上的B. cereus（sensu lato，简称s.l.），是一个包含众多密切相关的谱系的物种复杂群，其在人类和动物中引起疾病的能力各异。将广义上的B. cereus（s.l.）分离株归类于物种水平的分类单元，对于促进微生物学家、临床医生、公共卫生官员和产业专业人士之间的沟通至关重要，但这一过程并不总是直接明了。近期提出的一种基因组物种-亚基因组物种-生物变体分类框架旨在为这一物种复杂群提供标准化的命名法，但其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（例如单核苷酸多态性分析和多位点序列分型）是否与所提出的分类学相吻合。在本研究中，我们采用多种方法对2,231个广义上的B. cereus（s.l.）基因组进行特征描述，包括：（i）基于平均核苷酸一致性（ANI）的基因组物种归属，（ii）基于ANI的亚基因组物种归属，（iii）七基因多位点序列分型（MLST），（iv）单位点panC群归属，（v）rpoB等位基因分型，以及（vi）致病因子检测。我们证明了通过MLST分配的序列类型（STs）可用于基因组物种归属，并提供了一个完整的ST/基因组物种关联列表。对于panC群归属，我们展示了调整后的八群框架在很大程度上（尽管并非完全）与所提出的八个基因组物种分类学相吻合，因为panC本身可能无法区分（i）B. luti与II组B. mosaicus，以及（ii）B. paramycoides与VI组B. mycoides。此外，我们还提供了一份可捕捉全基因组广义上的B. cereus（s.l.）系统发育拓扑结构的位点列表，这些位点可用于未来的序列分型工作。对于能够访问WGS、MLST和/或panC数据的科研人员，我们展示了我们最近发布的软件BTyper3（https://github.com/lmc297/BTyper3）如何被用于将广义上的B. cereus（s.l.）分离株归入该框架内的分类单元，而几乎无需用户干预或对广义上的B. cereus（s.l.）分类学有特定的专业知识。我们还概述了一种将广义上的B. cereus（s.l.）基因组归入所提出的基因组物种内假基因流单位的新方法。本文所展示的结果突出了近期提出的基因组物种-亚基因组物种-生物变体分类框架的向后兼容性和易用性，并说明了全基因组测序并非微生物学家有效使用所提出的命名法的必要条件。