Camargo Anny, Guerrero-Araya Enzo, Castañeda Sergio, Vega Laura, Cardenas-Alvarez María X, Rodríguez César, Paredes-Sabja Daniel, Ramírez Juan David, Muñoz Marina
Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
Faculty of Health Sciences, Universidad de Boyacá, Tunja, Colombia.
Front Microbiol. 2022 Jul 22;13:952081. doi: 10.3389/fmicb.2022.952081. eCollection 2022.
is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of ; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the genomes found in publicly available databases were derived from food ( = 85) and bird ( = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%). The most frequently found virulence factors based on > 70% coverage and 99.95% identity were (100%), (99%), (99%), and (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while (39.5%) and (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of as a one of the most common causes of foodborne illness.
是人和动物许多肠道毒性疾病的病原体，存在于多种环境中（土壤、食物、污水和水）。多位点序列分型（MLST）和全基因组测序（WGS）提供了一种关于其遗传多样性的通用方法；然而，这些研究仅限于特定地点，且通常包含的基因组数量有限。在本研究中，使用来自多个地点和来源的372个基因组来评估该病原体的遗传多样性和系统发育相关性。MLST用于对分离株进行分型，并根据与创始株最多相差双位点变异的等位基因谱将所得序列类型（ST）分配到克隆复合体（CC）。进行了泛基因组分析，并创建了基于核心基因组的系统发育树来定义系统发育组。此外，分别使用ABRicate针对毒力因子数据库（VFDB）、TOXiper和Resfinder鉴定关键毒力因子、毒素型和抗生素抗性基因。公开可用数据库中发现的大多数基因组来自食品（n = 85）和鸟类（n = 85）分离株。总共195个ST，其中一些在食品和人类、马和狗以及环境和鸟类等来源之间共享，被分为25个CC，并分布在五个系统发育组中。53%的基因组被归为毒素型A，其次是F（32%）和G（7%）。基于>70%覆盖率和99.95%同一性最常发现的毒力因子是（100%）、（99%）、（99%）和（98%），它们分别编码一种α毒素、一种唾液酸酶、一种α-梭菌蛋白酶和一种胶原酶，而介导四环素抗性决定簇的（39.5%）和（36.2%）是检测到的最常见抗生素抗性基因。此处进行的分析更好地展示了该病原体在多个宿主物种中的存在情况。它们还证实，其遗传多样性基于大量在系统发育组之间变化的毒力因子以及抗生素抗性标记，尤其是对四环素、氨基糖苷类和大环内酯类的抗性标记。这些特征突出了作为食源性疾病最常见病因之一的重要性。
