Table_2_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.

巴氏芽孢杆菌群，亦称广义的巴氏芽孢杆菌（s.l.），是一个包含众多密切相关的谱系的物种复合体，其在人类和动物中引发疾病的能力各不相同。对广义的巴氏芽孢杆菌（s.l.）分离株进行物种水平的分类单元划分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，但这种划分并非总是一帆风顺。近期提出的一种基因组物种-亚基因组物种-生物变种分类框架旨在为这一物种复合体提供标准化的命名法，但高度依赖全基因组测序（WGS）。因此，尚不清楚流行的、低成本的分型方法（例如，单核苷酸多态性和多位点序列分型）是否与所提出的分类学相一致。在此，我们利用计算机模拟方法对2,231个广义的巴氏芽孢杆菌（s.l.）基因组进行了特征描述，包括：（i）基于平均核苷酸身份（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）单位点泛C群归属，（v）rpoB等位基因分型，以及（vi）毒力因子检测。我们发现，使用MLST分配的序列型（STs）可以用于基因组物种归属，并提供了ST/基因组物种关联的详尽列表。对于泛C群归属，我们表明，经过调整的八组框架大体上与所提出的八个基因组物种分类学相一致，尽管并不完美，因为泛C群本身可能无法区分（i）巴氏芽孢杆菌（B. luti）与第二组的巴氏镶嵌杆菌（B. mosaicus）以及（ii）巴氏芽孢杆菌（B. paramycoides）与第六组的巴氏芽孢杆菌（B. mycoides）。此外，我们还提供了一份可以用于未来序列分型工作的捕获全基因组巴氏芽孢杆菌（s.l.）系统发育拓扑结构的位点列表。对于能够访问全基因组测序（WGS）、MLST和/或泛C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）如何用于将广义的巴氏芽孢杆菌（s.l.）分离株归属到所提出的框架中的分类单元，而无需或仅需少量用户干预或对广义的巴氏芽孢杆菌（s.l.）分类学的专业知识。我们还概述了一种将广义的巴氏芽孢杆菌（s.l.）基因组归属到所提出的基因组物种中的伪基因流单元的新方法。本研究所呈现的结果突出了近期提出的基因组物种-亚基因组物种-生物变种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使用所提出的命名法进行有效操作的必要条件。