Exhaustive reconstruction of the CRISPR locus in<i>Mycobacterium tuberculosis</i>complex using short reads

Guyeux, Christophe; Sola, Christophe; Refrégier, Guislaine

doi:10.1101/844746

Cited by 3 publications

(6 citation statements)

References 25 publications

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“…We set up a method to identify not only variants of known spacers but also unknown spacers from M. tuberculosis CRISPR locus. Surprisingly, despite having explored more than 1000 sequencing data [35], we found no new spacers as compared to the 68 described previously for M. tuberculosis sensu stricto (excluding M. canettii or the new L0 and L8 lineages) [34]. The only new spacers that could be identified were found in M. canettii (data not shown).…”

Section: Exhaustive Catalog Of Spacers In M Tuberculosis Complex Strcontrasting

confidence: 64%

“…One hundred ninety-eight (n = 198) Sequence Reads Archives obtained by paired-end sequencing with Illumina technology were selected from a local database of more than 3500 genome sequences based on their representativeness of M. tuberculosis lineages [35]. Namely, the following numbers of data were included for each lineage: 55 for Lineage 1, 20 for Lineage 2, 17 from Lineage 3, 60 from Lineage 4, 25 from Lineage 5, 7 from Lineage 6, 10 from Lineage 7, 1 from M. bovis, 1 from M. caprae, 1 from M. microti, 1 from M. pinnipedii.…”

Section: Data Collectionmentioning

confidence: 99%

“…3) the sequences found between these bordering genes and first or last DR; 4) the beginning and the end of each Cas gene; 5) sequences in the neighbouring genes (Cas or others) when these sequences were found besides an IS6110 sequence during reconstruction -see below-(for more details; see [35].…”

Section: Identification and Cataloging Of Crispr Subsequences Of Intementioning

confidence: 99%

“…The method is described and was fully validated using in silico simulated CRISPR in our methodological paper [35].…”

Section: Identification and Cataloging Of Crispr Subsequences Of Intementioning

confidence: 99%

“…We recently set up a pipeline to reconstruct reliably CRISPR locus of M. tuberculosis [35]. We selected Short Reads Archives (SRA) from the more than 60,000 available today to represent clinical isolates diversity and derived their CRISPR locus structure.…”

Section: Introductionmentioning

confidence: 99%

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Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

2020

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Background 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. Results 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. Conclusion 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.

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Section: Exhaustive Catalog Of Spacers In M Tuberculosis Complex Strcontrasting

confidence: 64%

Section: Data Collectionmentioning

confidence: 99%

Section: Identification and Cataloging Of Crispr Subsequences Of Intementioning

confidence: 99%

“…The method is described and was fully validated using in silico simulated CRISPR in our methodological paper [35].…”

Section: Identification and Cataloging Of Crispr Subsequences Of Intementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

2020

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Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences inMycobacterium tuberculosis

Refrégier

Sola

Guyeux

2019

Preprint

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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.

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Mycobacterium bovis: From Genotyping to Genome Sequencing

Guimarães

Zimpel

2020

Microorganisms

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Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sectors, especially in developing countries and in high-income nations with wildlife reservoirs. Current bTB control programs are mostly based on test-and-slaughter, movement restrictions, and post-mortem inspection measures. In certain settings, contact tracing and surveillance has benefited from M. bovis genotyping techniques. More recently, whole-genome sequencing (WGS) has become the preferential technique to inform outbreak response through contact tracing and source identification for many infectious diseases. As the cost per genome decreases, the application of WGS to bTB control programs is inevitable moving forward. However, there are technical challenges in data analyses and interpretation that hinder the implementation of M. bovis WGS as a molecular epidemiology tool. Therefore, the aim of this review is to describe M. bovis genotyping techniques and discuss current standards and challenges of the use of M. bovis WGS for transmission investigation, surveillance, and global lineages distribution. We compiled a series of associated research gaps to be explored with the ultimate goal of implementing M. bovis WGS in a standardized manner in bTB control programs.

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Exhaustive reconstruction of the CRISPR locus inMycobacterium tuberculosiscomplex using short reads

Cited by 3 publications

References 25 publications

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences inMycobacterium tuberculosis

Mycobacterium bovis: From Genotyping to Genome Sequencing

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