ArticleBMC genomics2020
Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 21 citations in OpenAlex.
- Phenotypic and genotypic features of the Mycobacterium tuberculosis lineage 1 subgroup in central Vietnam.Scientific reports · 2021Trial
- Genomic Characterization and Taxonomic Classification ofInternational journal of molecular sciences · 2026Article
- Beyond adaptive immunity: Functional diversity of the type III-A CRISPR-Cas system inCell insight · 2026Review
- Future Research Directions on Mycobacterium tuberculosis Proteins.Advances in experimental medicine and biology · 2026Review
- Mycobacterium tuberculosis complex Lineage 1: A neglected cause of tuberculosis.PLoS neglected tropical diseases · 2025Review
- Genomic survey reveals no detectable bacteriophage activity in Mycobacterium bovis across a large population.FEMS microbiology ecology · 2025Article
- The future of CRISPR in Mycobacterium tuberculosis infection.Journal of biomedical science · 2023Review
- Features ofMicroorganisms · 2023Article
- Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory.Genes · 2022Article
- Development, Evaluation, and Implementation of a House-Made Targeted Next-Generation Sequencing Spoligotyping in a French Laboratory.International journal of molecular sciences · 2022Article
- Consistency of Mycobacterium tuberculosis Complex Spoligotyping between the Membrane-Based Method andMicrobiology spectrum · 2022Article
- Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a newEpidemiology and infection · 2022Article
- Biodiversity ofMicroorganisms · 2022Article
- ISFrontiers in microbiology · 2022Article
- CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.PLoS computational biology · 2021Article
- Comparative Genomic Analysis ofmSystems · 2021Article
- Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array.Frontiers in microbiology · 2021Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDiversity 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.
resultsWe 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.
conclusionThis 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.
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