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The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin

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Abstract

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with “domain C” composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.

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Acknowledgments

This work was supported by the Russian Science Foundation (RSF), grant no. 15-15-00158. This publication made use of the Viridans.eMLSA.net database (http://viridans.emlsa.net/) and the Streptococcus pneumoniae MLST database (http://spneumoniae.mlst.net/), hosted at the Department of Infectious Disease Epidemiology, Imperial College London.

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Authors and Affiliations

  1. Research Institute of Physical-Chemical Medicine, Ministry of Public Health of Russian Federation, 119992, Malaya Pirogovskaya str., 1a, Moscow, Russia

    L. N. Ikryannikova, D. S. Ischenko, A. V. Kanygina, I. Y. Karpova, E. S. Kostryukova, E. N. Ilina & V. M. Govorun

  2. Federal State Budgetary Institute “Scientific Center of Children Health” of RAMS, Moscow, Russia

    G. G. Lominadze & N. A. Mayansky

  3. Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121, Russia

    V. S. Skvortsov

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  1. L. N. Ikryannikova
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  2. D. S. Ischenko
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  3. G. G. Lominadze
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  4. A. V. Kanygina
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  6. E. S. Kostryukova
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  8. V. S. Skvortsov
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  9. E. N. Ilina
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  10. V. M. Govorun
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Correspondence to L. N. Ikryannikova.

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Submission of manuscript: All authors have contributed sufficiently to the scientific work presented in this manuscript and, therefore, share collective responsibility for the results. All authors agree with the final version of the manuscript under submission. This manuscript is not under consideration by any other journal. No parts of the data have been previously submitted for publication.

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Ikryannikova, L.N., Ischenko, D.S., Lominadze, G.G. et al. The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin. Eur J Clin Microbiol Infect Dis 35, 119–130 (2016). https://doi.org/10.1007/s10096-015-2516-5

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  • DOI: https://doi.org/10.1007/s10096-015-2516-5

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