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两株奇异变形杆菌中新发现的 SGI1-LK 变体和 SGI1-HKL 基因组岛群的进化。

Two New SGI1-LK Variants Found in Proteus mirabilis and Evolution of the SGI1-HKL Group of Genomic Islands.

机构信息

Bacteriology Department, University Hospital Dijon, Dijon, France

UMR 6249, Chrono-Environnement, Dijon, France.

出版信息

mSphere. 2020 Mar 4;5(2):e00875-19. doi: 10.1128/mSphere.00875-19.

Abstract

Integrative mobilizable elements belonging to the SGI1-H, -K, and -L genomic island 1 (SGI1) variant groups are distinguished by the presence of an alteration in the backbone (IS replaces 2.8 kb of the backbone extending from within [S005] to within S009). Members of this SGI1-HKL group have been found in serovars and in Two novel variants from this group, designated SGI1-LK1 and SGI1-LK2, were found in the draft genomes of antibiotic-resistant isolates from two French hospitals. Both variants can be derived from SGI1-GUE, a configuration found previously in another isolate from France. SGI1-LK1 could arise via an IS-mediated inversion in the complex class 1 integron that duplicated the IS element and the target site in IS SGI1-LK1 also has a larger 8.59-kb backbone deletion extending from to within S013 and removing and However, SGI1-LK1 was mobilized by an IncC plasmid. SGI1-LK2 can be derived from a hypothetical progenitor, SGI1-LK0, that is related to SGI1-GUE but lacks the gene and one copy of IS The integron of SGI1-LK2 could arise via deletion of DNA adjacent to an IS and a deletion occurring via homologous recombination between duplicated copies of part of the integron 3'-conserved segment. SGI1-K can also be derived from SGI1-LK0. This would involve an IS-mediated deletion and an inversion via homologous recombination of a segment between inversely oriented ISs. Similar events can explain the configuration of the integrons in other SGI1-LK variants. Members of the SGI1-HKL subgroup of SGI1-type integrative mobilizable elements have a characteristic alteration in their backbone. They are widely distributed among multiply antibiotic-resistant serovars and isolates. The SGI1-K type, found in the globally disseminated multiply antibiotic-resistant serovar Kentucky clone ST198 (sequence type 198), and various configurations in the original SGI1-LK group, found in other multiresistant serovars and isolates, have complex and highly plastic resistance regions due to the presence of IS However, how these complex forms arose and the relationships between them had not been analyzed. Here, a hypothetical progenitor, SGI1-LK0, that can be formed from the simpler SGI1-H is proposed, and the pathways to the formation of new variants, SGI1-LK1 and SGI1-LK2, found in and other reported configurations via homologous recombination and IS-mediated events are proposed. This led to a better understanding of the evolution of the SGI1-HKL group.

摘要

属于 SGI1-H、-K 和 -L 基因组岛 1(SGI1)变体组的整合可移动元件通过其骨架中的改变来区分(IS 取代了从 [S005] 内延伸到 S009 内的 2.8kb 骨架)。该 SGI1-HKL 组的成员已在血清型和中发现。 来自该组的两个新变体,命名为 SGI1-LK1 和 SGI1-LK2,在来自法国两家医院的抗生素耐药 分离株的草图基因组中发现。这两个变体都可以从先前在法国另一个 分离株中发现的 SGI1-GUE 衍生而来。SGI1-LK1 可能是通过复杂的 class 1 整合子中的 IS 介导的反转产生的,该反转复制了 IS 元件和 IS 中的靶位点。 SGI1-LK1 也具有更大的 8.59kb 骨架缺失,从 延伸到 S013 内并去除了 和 。然而,SGI1-LK1 由 IncC 质粒动员。SGI1-LK2 可以从与 SGI1-GUE 相关但缺乏 基因和 IS 拷贝的假设祖先进化而来。 SGI1-LK2 的整合子可以通过删除与 IS 相邻的 DNA 以及通过整合子 3'保守片段的重复拷贝之间的同源重组发生的缺失而产生。SGI1-K 也可以从 SGI1-LK0 衍生而来。这将涉及 IS 介导的缺失和通过在相反取向的 IS 之间的同源重组进行的反转。类似的事件可以解释其他 SGI1-LK 变体中整合子的构型。SGI1 型整合可移动元件的 SGI1-HKL 亚组的成员在其骨架中有一个特征性的改变。它们在多种抗生素耐药 血清型和 分离株中广泛分布。在全球传播的多种抗生素耐药 血清型肯塔基克隆 ST198(序列类型 198)中发现的 SGI1-K 型和在其他多耐药 血清型和 分离株中发现的原始 SGI1-LK 组中的各种构型,由于存在 IS,具有复杂和高度可塑的耐药区域。然而,这些复杂形式是如何产生的以及它们之间的关系尚不清楚。在这里,提出了一个假设的祖先进化体 SGI1-LK0,可以从更简单的 SGI1-H 形成,并且通过同源重组和 IS 介导的事件提出了在 和其他报道的构型中形成新变体 SGI1-LK1 和 SGI1-LK2 的途径。这导致了对 SGI1-HKL 组进化的更好理解。

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