In silico identification of tandem repeats in Ureaplasma diversum genome: potential application to develop a MLVA scheme for typing of the agent
Abstract
Ureaplasma diversum is a pathogenic microorganism detected in cattle
and pigs. Different genetic types of the agent have previously been identified with
techniques producing poor reproducible or inconclusive results. The objective of
the present study was to identify in silico tandem (TR) repeated regions in the
genome of U. diversum. The genome of the strain ATCC 49782 was analyzed, identifying
tandem repeated regions (TR). For each of the identified TR, specific primers
were designed, an in silico PCR was performed and the products were aligned
against BLAST database to determine their specificity. Of the 51 species-specific TR
identified, 54.9% (28) encoding hypothetical proteins, and the rest is located in intergenic
regions. The size of the identified TR varied from 2 to 102 base pairs (bp),
repeated between 1.8 and 21.5 times, which would allow to discriminate them by
electrophoresis or sequencing. The identification of a wide repertoire of TR is the
first step for the genotyping of the agent by a Multiple-Locus Variable Number Tandem
Repeat Analysis (MLVA), which would constitute a faster, more practical and
reproducible method than other typing methods previously reported.
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References
Benson G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (2): 573-580.
Burgher Y., Miranda L., Rodriguez-Roche R., de Almeida Campos A.C., Lobo E., Neves T., Martínez O., Timenetsky J. (2014). Ureaplasma diversum in pneumonic lungs of swine. Infect Genet Evol. 21:486-488. doi: 10.1016/j.meegid.2013.07.003.
Buzinhani M., Buim M.R., Yamaguti M., Oliveira R.C., Mettifogo E., Timenetsky, J.. (2007) Genotyping of Ureaplasma diversum isolates using pulsed-field electrophoresis. Vet J.; 73(3): 688–690. S1090-0233(06)00039-6 [pii] doi: 10.1016/j.tvjl.2006.02.001
Dos Santos L.F., Clavijo M.J., Sreevatsan S., Rovira A., Moreira M.A., Pieters M. (2015) Genotyping of Mycoplasma hyorhinis using multiple-locus variable number tandem repeat analysis. J Microbiol Methods. 111:87-92. doi: 10.1016/j.mimet.2015.02.003.
Hata E., Suzuki K., Hanyu H., Itoh M., Higuchi H., Kobayashi H. (2014). Molecular epidemiology of cases of Mycoplasma californicum infection in Japan. Appl Environ Microbiol. 80 (24): 7717-7724. doi: 10.1128/AEM.02488-14.
Joukhadar, R. y Jighly, A. (2012). Microsatellites grant more stable flanking genes. BMC Res Notes 5:556. doi: 10.1186/1756-0500-5-556.
Lindstedt, B.A. (2005). Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis. 26 (13): 2567-2582.
Marques L.M., Buzinhani M., Guimaraes A.M., Marques, R.C., Farias S.T., Neto R.L., Yamaguti M., Oliveira R.C., Timenetsky J. (2011). Intraspecific sequence variation in 16S rRNA gene of Ureaplasma diversum isolates. Vet microbiol 152(1–2): 205–211. doi: 10.1016/j.vetmic.2011.04.007
Marques L.M., Guimarães A.M., Martins H.B., Rezende I.S., Barbosa M.S., Campos G.B., do Nascimento N.C., Dos Santos A.P., Amorim A.T., Santos V.M., Messick J.B., Timenetsky J. (2015). Genome Sequence of Ureaplasma diversum Strain ATCC 49782. Genom Announc. 3(2). pii: e00314-15. doi: 10.1128/genomeA.00314-15.
Miller R., Chelmonska-Soyta A., Smits B., Foster R., Rosendal S. (1994). Ureaplasma diversum as a cause of reproductive disease in cattle. Vet Clin North Am: Food Anim Pract. 10, 479-490.
Pinho L., Thompson G., Rosenbusch R., Carvalheira J. (2012). Genotyping of Mycoplasma bovis isolates using multiple-locus variable-number tandem-repeat analysis. J Microbiol Methods. 88 (3):377-385. doi: 10.1016/j.mimet.2012.01.003.
Seitz J., Sticotti E., Giruado J., Tamiozzo P. (2018). [Detection of Ureaplasma diversum in cows with and without granular vulvovaginitis from Argentina]. Ab Intus. 1, 89-92.
Vranckx K., Maes D., Calus D., Villarreal I., Pasmans F., Haesebrouck, F. (2011). Multiple-locus variable-number tandem-repeat analysis is a suitable tool for differentiation of Mycoplasma hyopneumoniae strains without cultivation. J Clin Microbiol. 49 (5): 2020-2023. doi: 10.1128/JCM.00125-11.
Zhou K., Aertsen A., Michiels C.W. (2014). The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev. 38 (1): 119-141. doi: 10.1111/1574-6976.12036.
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