MacKenzie Katrin, Marshall Jacqueline, Wright Frank, Gunn George, Holden Nicola
Biomathematics & Statistics Scotland, Invergowrie, Dundee DD2 5DA, Scotland, UK.
The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.
Curr Res Microb Sci. 2021 Dec 20;3:100093. doi: 10.1016/j.crmicr.2021.100093. eCollection 2022.
Analysis of taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of isolated from a long-term spring barley field trial for their presence. While most isolates clustered into the enteric-clade, four of them clustered into Clade-V, and one in Clade-IV. The Clade -V isolates shared >96% intra-clade average nucleotide sequence identity but <91% with other clades. Although pan-genomics analysis confirmed their taxonomy as Clade -V (E. marmotae), retrospective phylogroup PCR did not discriminate them correctly. Differences in metabolic and adherence gene alleles occurred in the Clade -V isolates compared to sensu scricto. They also encoded the bacteriophage phage-associated cyto-lethal distending toxin (CDT) and antimicrobial resistance (AMR) genes, including an ESBL, blaOXA-453. Thus, the isolate collection encompassed a genetic diversity, and included cryptic clade isolates that encode potential virulence factors. The analysis has determined the phylogenetic relationship of cryptic clade isolates with sensu scricto and indicates a potential for horizontal transfer of virulence factors.
随着不同隐性进化枝的识别，分类学分析已扩展到一个复合种。一个关键问题是这些进化枝的进化轨迹以及它们与具有临床或兽医重要性的分离株之间的关系。由于它们与环境存在一定关联，我们从一个长期的春大麦田间试验中筛选了一批分离株，以检测它们的存在情况。虽然大多数分离株聚集在肠道进化枝中，但其中有4个聚集在进化枝V中，1个聚集在进化枝IV中。进化枝V的分离株在进化枝内的平均核苷酸序列同一性大于96%，但与其他进化枝的同一性小于91%。尽管泛基因组分析证实它们的分类地位为进化枝V（土拨鼠埃希菌），但回顾性系统发育群PCR未能正确区分它们。与狭义的[具体物种名称未提及]相比，进化枝V的分离株在代谢和黏附基因等位基因上存在差异。它们还编码噬菌体相关的细胞致死膨胀毒素（CDT）和抗菌抗性（AMR）基因，包括一种超广谱β-内酰胺酶blaOXA - 453。因此，该分离株集合具有遗传多样性，并且包括编码潜在毒力因子的隐性进化枝分离株。该分析确定了隐性进化枝分离株与狭义的[具体物种名称未提及]之间的系统发育关系，并表明毒力因子存在水平转移的可能性。
