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Accueil > Départements > Microbiologie > Michael DUBOW : Génomique et Biodiversité microbienne des biofilms

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  • CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

    27 mai, par Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, C Rocha EP, Vergnaud G, Gautheret D, Pourcel C
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    CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

    Nucleic Acids Res. 2018 May 22;:

    Authors: Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, C Rocha EP, Vergnaud G, Gautheret D, Pourcel C

    Abstract
    CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

    PMID: 29790974 [PubMed - as supplied by publisher]

  • Transposition Behavior Revealed by High-Resolution Description of Pseudomonas Aeruginosa Saltovirus Integration Sites.

    8 mai, par Vergnaud G, Midoux C, Blouin Y, Bourkaltseva M, Krylov V, Pourcel C
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    Transposition Behavior Revealed by High-Resolution Description of Pseudomonas Aeruginosa Saltovirus Integration Sites.

    Viruses. 2018 May 07;10(5):

    Authors: Vergnaud G, Midoux C, Blouin Y, Bourkaltseva M, Krylov V, Pourcel C

    Abstract
    Transposable phages, also called saltoviruses, of which the Escherichia coli phage Mu is the reference, are temperate phages that multiply their genome through replicative transposition at multiple sites in their host chromosome. The viral genome is packaged together with host DNA at both ends. In the present work, genome sequencing of three Pseudomonas aeruginosa transposable phages, HW12, 2P1, and Ab30, incidentally gave us access to the location of thousands of replicative integration sites and revealed the existence of a variable number of hotspots. Taking advantage of deep sequencing, we then designed an experiment to study 13,000,000 transposon integration sites of bacteriophage Ab30. The investigation revealed the presence of 42 transposition hotspots adjacent to bacterial interspersed mosaic elements (BIME) accounting for 5% of all transposition sites. The rest of the sites appeared widely distributed with the exception of coldspots associated with low G-C content segments, including the putative O-antigen biosynthesis cluster. Surprisingly, 0.4% of the transposition events occurred in a copy of the phage genome itself, indicating that the previously described immunity against such events is slightly leaky. This observation allowed drawing an image of the phage chromosome supercoiling into four loops.

    PMID: 29735891 [PubMed - in process]

  • Associations between Mycobacterium tuberculosis Beijing genotype and drug resistance to four first-line drugs : A survey in China.

    31 décembre 2017, par Liu H, Zhang Y, Liu Z, Liu J, Hauck Y, Liu J, Dong H, Liu J, Zhao X, Lu B, Jiang Y, Vergnaud G, Pourcel C, Wan K
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    Associations between Mycobacterium tuberculosis Beijing genotype and drug resistance to four first-line drugs: A survey in China.

    Front Med. 2017 Dec 29;:

    Authors: Liu H, Zhang Y, Liu Z, Liu J, Hauck Y, Liu J, Dong H, Liu J, Zhao X, Lu B, Jiang Y, Vergnaud G, Pourcel C, Wan K

    Abstract
    Investigations on the genetic diversity of Mycobacterium tuberculosis in China have shown that Beijing genotype strains play a dominant role. To study the association between the M. tuberculosis Beijing genotype and the drug-resistance phenotype, 1286 M. tuberculosis clinical isolates together with epidemiological and clinical information of patients were collected from the center for tuberculosis (TB) prevention and control or TB hospitals in Beijing municipality and nine provinces or autonomous regions in China. Drug resistance testing was conducted on all the isolates to the four first-line anti-TB drugs (isoniazid, rifampicin, streptomycin, and ethambutol). A total of 585 strains were found to be resistant to at least one of the four anti-TB drugs. The Beijing family strains consisted of 499 (53.20%) drug-sensitive strains and 439 (46.80%) drug-resistant strains, whereas the non-Beijing family strains comprised 202 (58.05%) drug-sensitive strains and 146 (41.95%) drug-resistant strains. No significant difference was observed in prevalence (χ2= 2.41, P > 0.05) between the drug-resistant and drugsensitive strains among the Beijing family strains. Analysis of monoresistance, multidrug-resistant TB, and geographic distribution of drug resistance did not find any relationships between the M. tuberculosis Beijing genotype and drug-resistance phenotype in China. Results confirmed that the Beijing genotype, the predominant M. tuberculosis genotype in China, was not associated with drug resistance.

    PMID: 29288283 [PubMed - as supplied by publisher]