PHYLOGENETIC ANALYSIS OF GENOMES OF VIBRIO CHOLERAE STRAINS ISOLATED ON THE TERRITORY OF ROSTOV REGION


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Abstract

Aim. Determination of origin of 2 Vibrio cholerae strains isolated on the territory of Rostov region by using full genome sequencing data. Materials and methods. Toxigenic strain 2011EL-301 V. cholerae O1 El Tor Inaba No. 301 (ctxAB+, tcpA+) and nontoxigenic strain V. cholerae О1 Ogawa P-18785 (ctxAB-, tcpA+) were studied. Sequencing was carried out on the MiSeq platform. Phylogenetic analysis of the genomes obtained was carried out based on comparison of conservative part of the studied and 54 previously sequenced genomes. Results. 2011EL-301 strain genome was presented by 164 contigs with an average coverage of100, N50 parameter was 132 kb, for strain P-18785 - 159 contigs with a coverage of69, N50 - 83 kb. The contigs obtained for strain 2011EL-301 were deposited in DDBJ/EMBL/GenBank databases with access code AJFN02000000, for strain P-18785 - ANHS00000000. 716 protein-coding orthologous genes were detected. Based on phylogenetic analysis strain P-18785 belongs to PG-1 subgroup (a group of predecessor strains of the 7 th pandemic). Strain 2011EL-301 belongs to groups of strains of the 7 th pandemic and is included into the cluster with later isolates that are associated with cases of cholera in South Africa and cases of import of cholera to the USA from Pakistan. Conclusion. The data obtained allows to establish phylogenetic connections with V. cholerae strains isolated earlier.

About the authors

K. V Kuleshov

Central Research Institute of Epidemiology, Moscow, Russia

M. L Markelov

Research Institute of Occupational Health, Moscow, Russia

V. G Dedkov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

S. O Vodopianov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

A. S Vodopianov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

A. V Kermanov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

R. V Pisanov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

V. D Kruglikov

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

A. B Mazrukho

Rostov Research Institute of Plague Control, Rostov-on-Don, Russia

V. V Maleev

Central Research Institute of Epidemiology, Moscow, Russia

G. A Shipulin

Central Research Institute of Epidemiology, Moscow, Russia

References

  1. Ломов Ю. М., Москвитина Э. А., Арешина О. А. Оценка эпидемиологической обстановки по холере в мире в современный период. Прогноз. Проблемы особо опасных инфекций. 2011, 107: 16-19.
  2. Онищенко Г. Г., Ломов Ю. M., Москвитина Э. А. и др. Холера, обусловленная Vibrio cholerae O1 ctxAB- tcpA+. Журн. микробиол. 2007, 1: 23-29.
  3. Смирнова Н. И., Заднова С. П., Шашкова А. В. и др. Вариабельность генома измененных вариантов Vibrio cholerae биовара Эль-Тор, изолированных на территории России в современный период. Мол. генет. микробиол. вирусол. 2011, 3: 11-18.
  4. Altschul S. F, Gish W, Miller W et al. Basic local alignment search tool. J. Mol. Biol. 1990, 215: 403-410.
  5. Binnewies T. T., Motro Y., Hallin P. F. et al. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct. Integr. Genomics. 2006, 6: 165-185.
  6. Chin C. S., Sorenson J., Harris J. B. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 2011, 364: 33-42.
  7. Chun J., Grim C. J., Hasan N. A. et al. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc. Natl. Acad. Sci. USA. 2009, 106: 15442-15447.
  8. Dasgupta A., Banerjee R., Das S. et al. Evolutionary perspective on the origin of Haitian cholera outbreak strain. J. Biomol. Struct. Dyn. 2012, 30: 338-346.
  9. Delcher A. L., Harmon D., Kasif S. et al. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27: 4636-4641.
  10. Edgar R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797.
  11. Hasan N. A., Choi S. Y, Eppinger M. et al. Genomic diversity of 2010 Haitian cholera outbreak strains. Proc. Natl. Acad. Sci. USA. 2012, 109: E2010- E2017.
  12. Li L., Stoeckert C. J., Jr., Roos D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13: 2178-2189.
  13. Reimer A. R., Van Domselaar G., Stroika S. et al. Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa. Emerg. Infect. Dis. 2011, 17: 2113-2121.
  14. Tamura K., Peterson D., Peterson N. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28: 2731-2739.
  15. Yamasaki S., Shimizu T., Hoshino K. et al. The genes responsible for O-antigen synthesis of Vibrio cholerae O139 are closely related to those of Vibrio cholerae O22. Gene. 1999, 237: 321-332.

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Copyright (c) 2013 Kuleshov K.V., Markelov M.L., Dedkov V.G., Vodopianov S.O., Vodopianov A.S., Kermanov A.V., Pisanov R.V., Kruglikov V.D., Mazrukho A.B., Maleev V.V., Shipulin G.A.

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