Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, United Kingdom.
Genome Biol Evol. 2014 Jan;6(1):36-52. doi: 10.1093/gbe/evt204.
The symptoms of Clostridium difficile infection are caused by toxins expressed from its 19 kb pathogenicity locus (PaLoc). Stable integration of the PaLoc is suggested by its single chromosomal location and the clade specificity of its different genetic variants. However, the PaLoc is variably present, even among closely related strains, and thus resembles a mobile genetic element. Our aim was to explain these apparently conflicting observations by reconstructing the evolutionary history of the PaLoc. Phylogenetic analyses and annotation of the regions spanning the PaLoc were performed using C. difficile population-representative genomes chosen from a collection of 1,693 toxigenic (PaLoc present) and nontoxigenic (PaLoc absent) isolates. Comparison of the core genome and PaLoc phylogenies demonstrated an eventful evolutionary history, with distinct PaLoc variants acquired clade specifically after divergence. In particular, our data suggest a relatively recent PaLoc acquisition in clade 4. Exchanges and losses of the PaLoc DNA have also occurred, via long homologous recombination events involving flanking chromosomal sequences. The most recent loss event occurred ∼30 years ago within a clade 1 genotype. The genetic organization of the clade 3 PaLoc was unique in containing a stably integrated novel transposon (designated Tn6218), variants of which were found at multiple chromosomal locations. Tn6218 elements were Tn916-related but nonconjugative and occasionally contained genes conferring resistance to clinically relevant antibiotics. The evolutionary histories of two contrasting but clinically important genetic elements were thus characterized: the PaLoc, mobilized rarely via homologous recombination, and Tn6218, mobilized frequently through transposition.
艰难梭菌感染的症状是由其 19kb 致病性基因座（PaLoc）表达的毒素引起的。PaLoc 稳定整合的证据来自于其单一的染色体位置和不同遗传变异体的进化枝特异性。然而，PaLoc 的存在是可变的，即使在密切相关的菌株之间也是如此，因此它类似于一种移动遗传元件。我们的目的是通过重建 PaLoc 的进化历史来解释这些明显矛盾的观察结果。使用从 1693 株产毒（存在 PaLoc）和非产毒（不存在 PaLoc）分离株组成的集合中选择的艰难梭菌种群代表性基因组，对跨越 PaLoc 的区域进行了系统发育分析和注释。PaLoc 核心基因组和系统发育分析的比较表明，它具有一个丰富的进化历史，不同的 PaLoc 变异体在进化枝特异性分化后获得。特别是，我们的数据表明，在进化枝 4 中，PaLoc 的获得是相对较新的事件。通过涉及侧翼染色体序列的长同源重组事件，也发生了 PaLoc DNA 的交换和丢失。最近的一次丢失事件发生在大约 30 年前，发生在进化枝 1 基因型中。进化枝 3 PaLoc 的遗传组织是独特的，它包含一个稳定整合的新型转座子（命名为 Tn6218），在多个染色体位置发现了其变体。Tn6218 元件与 Tn916 相关，但不能进行接合，偶尔含有赋予临床相关抗生素抗性的基因。因此，对两个具有对比性但具有重要临床意义的遗传元件的进化历史进行了描述：PaLoc 很少通过同源重组发生转移，而 Tn6218 则通过转座频繁发生转移。
