Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes. We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs. We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats. This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.

中文翻译：

---

CRISPR 的意外多样性揭示了结核分枝杆菌中重复序列的一些进化模式

自 1997 年以来，出于分子流行病学目的，人们一直在研究结核分枝杆菌复合体 CRISPR 基因座的多样性。通过仅针对两个首先测序的基因组（H37Rv 和 BCG）中存在的 43 个间隔区，它给出了 CRISPR 多样性的偏见，并忽略了邻近 cas 基因的多样性。我们建立了定制的管道来探索短读中 CRISPR-cas 位点的多样性。我们分析了 198 个临床分离株的代表性数据，并通过充分表征的 SNP 来证明。我们发现间隔区的多样性相对较低：我们仅恢复了 2000 年描述的 68 个间隔区。我们在序列中没有发现部分或全局倒置，使直接变异重复 (DVR) 始终保持相同的顺序。相比之下，我们发现了意想不到的多样性，其形式如下：间隔区和直接重复中的 SNP、不同长度的重复、IS6110 插入序列不同位置的插入以及 DVR 删除块。这种多样性在一定程度上是针对血统的。当重建该位点的进化步骤时，我们没有发现 SNP 逆转的证据。DVR 删除与 IS6110 插入之间或直接重复序列之间的重组有关。这项工作明确表明，自有毒谱系的最后一个最近的共同祖先以来，结核分枝杆菌的 CRISPR 基因座并不是通过经典的 CRISPR 适应（新间隔区的掺入）而进化的。我们发现的进化机制可能与细菌适应有关，但具体方式仍有待确定。