IS6110 element distribution in Tunisian clinical strains and phylogenetic relationship generated by its mobility
Keywords:
Mycobacterium tuberculosis,IS6110 element,Clinical strains,PhylogenyAbstract
The dynamics of IS6110 transposition is a valuable epidemiological tool in tuberculosis studies. In the present work, we studied IS6110 distribution along the genome of 58 unrelated clones and go over phylogenetic relationship between them by performing a molecular study with GL-PCR methodology. A total number of 309 insertion sites have been detected showing that IS6110 integration in samples studied crossed randomly several positions through the Mycobacterium tuberculosis genome. These sites were divided into 232 sequences having homologous in reference strains mainly in M. tuberculosis H37Rv strain and 77 other unique regions that did not have counterparts in reference strains fully sequenced and available in global databases. Most insertions occurred in coding regions. 114 insertions took place in the direction of the replication fork and 118 insertions were oriented against the direction of the replication fork, carried by the complementary strand of the chromosome. No clustered patterns have been illustrated. Several genetic statistical tests have been performed with language R package software to study the distribution and the symmetry of IS6110 insertion events. Our data confirm that IS6110 element prevalence and effect on genome function demonstrate the potential of this transposon as an evolutionary marker and as the best indicator of essential/virulence genes. In fact, survey of patterns of IS6110 insertions in circulating isolates may provide useful information for populational studies mainly in epidemic situations.
References
Alonso, H., Aguilo, J.I., Samper, S., Caminero, J.A., Campos-Herrero, M.I., Gicquel, B., Brosch, R., Martín, C., Otal, O., 2011. Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis., 91, 117-126.
Adams, L.V., Kreiswirth, B.N., Arbeit, R.D., Soini, H., Mtei, L., Matee, M., Bakari, M., Lahey, T., Wieland-Alter, W., other authors., 2012. Molecular Epidemiology of HIV-Associated Tuberculosis in Dar es Salaam, Tanzania: Strain Predominance, Clustering, and Polyclonal Disease. J. Clin. Microbiol., 50, 2645 - 2650.
Aryan, E., Makvandi, M., Farajzadeh, A., Huygen, K., Bifani, P., Mousavi, S.L., Fateh, A., Jelodar, A., Gouya, M.M., Romano, M., 2010. A novel and more sensitive loop-mediated isothermal amplification assay targeting IS6110 for detection of Mycobacterium tuberculosis complex. J. Microbiol. Res., 165, 211-220.
Barrios-Payán, J., Saqui-Salces, M., Jeyanathan, M., Alcántara-Vazquez, A., Castañon-Arreola, M., Rook, G., Hernandez-Pando, R., 2012. Extrapulmonary Locations of Mycobacterium tuberculosis DNA During Latent Infection. J. Infect. Dis., 206, 1194 - 1205.
Blaschitz, M., Hasanacevic, D., Hufnagl, P., Hasenberger, P., Pecavar, V., Meidlinger, L., Konrad, M., Allerberger, F., Indra, A., 2011. Real-time PCR for single-nucleotide polymorphism detection in the 16S rRNA gene as an indicator for extensive drug resistance in Mycobacterium tuberculosis. J. Antimicrob. Chemother., 66, 1243 – 1246.
Brosch, R., Wolfgang, J.P., Stavropoulos, E., Colston, M.J., Cole, S.T., Gordon, S.V., 1999. Genomic Analysis Reveals Variation between Mycobacterium tuberculosis H37Rv and the Attenuated M. tuberculosis H37Ra Strain. Infect Immun., 67, 5768 – 5774.
Casart, Y., Turcios, L., Florez, I., Jaspe, R., Guerrero, E., de Waard, J., Aguilar, D., Hernandez-Pando, R., Salazar, L., 2008. IS6110 in oriC affects the morphology and growth of Mycobacterium tuberculosis and attenuates virulence in mice. Tuberculosis (Edinb)., 88, 545 -552.
Cole, S.T., Barrell, B.G., 1998. Analysis of the genome of Mycobacterium tuberculosis H37Rv. Novartis. Found. Symp., 217, 160–172.
Dalla Costa, E.R., Lazzarini, L.C.O., Perizzolo, P.F., Díaz, C.A., Spies, F.S., Laux Costa, L., Ribeiro, A.W., Barroco, C., Schuh, S.J., other authors., 2013. Mycobacterium tuberculosis of the RDRio Genotype Is the Predominant Cause of Tuberculosis and Associated with Multidrug Resistance in Porto Alegre City, South Brazil. J. Clin. Microbiol., 51, 1071-1077.
de Beer, J.L., van Ingen, a.J., de Vries, b.G., Erkens, c.d.C., Sebek, d.M., Mulder, d.A., Sloot, a.R., van den Brandt, e.A.M., Enaimi, a.f.M., other authors., 2013. Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey. J. Clin. Microbiol., 51, 1193 - 1198.
Durmaz, R., Zozio, T., Gunal, S., Allix, C., Fauville-Dufaux, M., Rastogi, N., 2007. Population-Based Molecular Epidemiology Study of Tuberculosis in Malatya, Turkey. J. Clin. Microbiol., 45, 4027-4035.
Fang, Z., Forbes, K.J., 1997. A Mycobacterium tuberculosis IS6110 preferential locus (ipl) for insertion into the genome. J. Clin. Microbiol., 35, 479-481.
Fleischmann, R.D., Alland, D., Eisen, J.A., Carpenter, L., White, O., Peterson, J., DeBoy, R., Dodson, R., Gwinn, M., other authors., 2002. Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains. J. Bacteriol., 184, 5479–5490.
Green, E.P., Tizard, M.L.V., Moss, M.T., Thompson, J., Winterbourne, D.J., McFadden, J.J., Hermon-Taylor, J., 1989. Sequence and characteristics of IS900, an insertion element identified in a human Crohn’s disease isolate of Mycobacterium paratuberculosis. Nucleic. Acid. Res., 17, 9063-9073.
Haldar, S., Sharma, N., Gupta, V.K., Tyagi, J.S., 2009. Efficient diagnosis of tuberculous meningitis by detection of Mycobacterium tuberculosis DNA in cerebrospinal fluid filtrates using PCR. J. Med. Microbiol., 58, 616-624.
Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic. Acids. Symp. Ser., 41, 98.
Kamerbeek, J., Schouls, L., Kolk, A., van Agterveld, M., van Soolingen, D., Kuijper, S., Bunschoten, A., Molhuizen, H., Shaw, R., other authors., 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol., 35, 907-914.
Kempsell, K.E., JI, Y.E., Estrada-G, I.C.E., Colston, M.J., Cox, R.A., 1992. The nucleotide sequence of the promoter, 16s rRNA and spacer region of the ribosomal RNA operon of Mycobacterium tuberculosis and comparison with Mycobacterium leprae precursor rRNA. J. Gen. Microbiol., 138, 1717–1727.
Lari, N., Rindi, L., Bonanni, D., Rastogi, N., Sola, C., Tortoli, E., Garzelli, C., 2007. Three-Year Longitudinal Study of Genotypes of Mycobacterium tuberculosis Isolates in Tuscany, Italy. J. Clin. Microbiol., 45, 1851-1857.
Lazzeri, E., Santoro, F., Oggioni, M.R., Iannelli, F., Pozzi, G., 2012. Novel Primer-Probe Sets for Detection and Identification of Mycobacteria by PCR-Microarray Assay. J. Clin. Microbiol., 50, 3777-3779.
Namouchi, A., Mardassi, H., 2006. A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis. J. Microbiol. Methods., 67, 202-211.
Namouchi, A., Haltiti, R., Hawari, D., Mardassi, H., 2010. Re-emergence of the Progenitors of a Multidrug-Resistant Outbreak Strain of Mycobacterium tuberculosis Among the Post-Outbreak Case-Patients. J. Infect. Dis., 201, 390-398.
Namouchi, A., Karboul, A., Mhenni, B., Khabouchi, N., Haltiti, R., Ben Hassine, R., Louzir, B., Chabbou, A., Mardassi, H., 2008. Genetic profiling of Mycobacterium tuberculosis in Tunisia : predominance and evidence for the establishment of a few genotypes. J. Med. Microbiol., 57, 864-872.
Pérez-Osorio, A.C., Boyle, D.S., Ingham, Z.K., Ostash, A., Gautom, R.K., Colombel, C., Houze, Y., Leader, B.T., 2012. Rapid Identification of Mycobacteria and Drug-Resistant Mycobacterium tuberculosis by Use of a Single Multiplex PCR and DNA Sequencing. J. Clin. Microbiol., 50, 326-336.
Reyes, A., Sandoval, A., Cubillos-Ruiz, A., Varley, K.E., Hernández-Neuta, I., Samper, S., Martín, C., Garcí, M.J., Ritacco, V., other authors., 2012. IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. BMC. Genomics., 13, 249.
Thierry, D., Brisson-Noel, A., Vincent-Lévy-Frébault, V., Nguyen, S., Guesdon, J.L., Gicquel, B., 1990. Characterization of Mycobacterium tuberculosis Insertion Sequence, IS6110, and Its Application in Diagnosis. J. Clin. Microbiol., 28, 2668-2673.
Thorne, N., Borrell, S., Evans, J., Magee, J., De Viedma, D.G., Bishop, C., Gonzalez-Martin, J., Gharbia, S., Arnold, C., 2010. IS6110-based global phylogeny of Mycobacterium tuberculosis. Infect. Genet. Evol., 11, 132-138.
Thorne, N., Evan, J.T., Smith, E.G., Hawkey, P.M., Gharbia, S., Arnold, C., 2007. An IS6110-targeting fluorescent amplified fragment length polymorphism alternative to IS6110 restriction fragment length polymorphism analysis for Mycobacterium tuberculosis DNA fingerprinting. Clin. Microbiol. Infect., 13, 964-970.
Van Embden, J.D.A., Cave, M.D., Crawford, J.T., Dale, J.W., Eisenach, K.D., Gicquel, B., Hermans, P., Martin, C., McAdam, R., other authors., 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol., 31, 406-409.
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