sredobЗдоровье населения и среда обитания – ЗНиСОPublic Health and Life Environment – PH&LE2219-52382619-0788ФБУЗ ФЦГиЭ Роспотребнадзора10.35627/2219-5238/2019-317-8-39-44sredob-110Research ArticleСтатьиМолекулярно-генетическая характеристика штамма Cutibacterium (Propionibacterium) acnes A1-14 как представителя симбиотической микробиоты человекаMolecular-genetic characteristic Cutibacterium (Propionibacterium) acnes A1-14 strain as human symbiotic microbiota representativeАлексееваАнна ЕвгеньевнаAlekseevaA. E.a.e.alexeeva79@mail.ruБруснигинаН. Ф.BrusniginaN. F.noemail@neicon.ruКашниковА. Ю.KashnikovA. Yu.noemail@neicon.ruНовиковаН. А.NovikovaN. A.noemail@neicon.ruФБУН «Нижегородский научно-исследовательский институт эпидемиологии и микробиологии им. академика И.Н. Блохиной» РоспотребнадзораРоссияAcademician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and MicrobiologyRussian Federation201914042021083944Copyright © Алексеева А.Е., Бруснигина Н.Ф., Кашников А.Ю., Новикова Н.А., 20212021Алексеева А.Е., Бруснигина Н.Ф., Кашников А.Ю., Новикова Н.А.Alekseeva A.E., Brusnigina N.F., Kashnikov A.Y., Novikova N.A.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://zniso.fcgie.ru/jour/article/view/110

Бактерии вида Cutibacterium (ранее Propionibacterium) acnes, с одной стороны, являются представителями нормальной микробиоты кожи человека, а с другой, - способствуют развитию воспалительных процессов, таких как акне, инфекционные осложнения в посттравматический и постоперационный период глаза (эндофтальмит), сердечно-сосудистой системы (эндокардит), центральной нервной системы и опорно-двигательного аппарата (остеомиелит), имплант-ассоциированные инфекции. Используются различные молекулярно-генетические подходы для определения эпидемически значимых генотипов, обладающих высоким патогенетическим потенциалом и генотипов низкопатогенных комменсалов. Впервые проведено полногеномное секвенирование штамма C. acnes A1-14, выделенного из толстого кишечника здорового человека. В результате выравнивания и объединения нуклеотидная последовательность генома составила 2 484 560 пар нуклеотидов. Согласно результатам генотипирования штамм относится к филотипу II, риботипу 6 и сиквенс-типу 7 (схема McDowell A. с соавторами) или 73 (схема Lomholt H.B., Kilian M.). Показано, что в геноме С. acnes A1-14 отсутствуют мобильные элементы, детерминанты патогенности и антибиотикорезистентности, мутации в генах 16S рРНК, 23S рРНК, gyrA, gyrB, parC, parE, установлено наличие CRISPR-Cas структуры. Обнаружена внехромосомная последовательность, принадлежащая геному бактериофага семейства Syphoviridae. С использованием электронно-микроскопического метода исследования дана морфологическая характеристика вириона бактериофага, присутствие которого в виде экстрахромосомной структуры характерно для многих штаммов C. acnes. Таким образом, результаты, полученные в нашем исследовании, дополняют представления о молекулярно-генетических особенностях штаммов C. acnes, выделенных из различных биотопов человека и являющихся представителями симбиотической микробиоты.

The bacteria of the Cutibacterium (formerly Propionibacterium) acnes species are representatives of normal microbiota of human skin on the one hand and they contribute to the development of inflammatory processes, such as acne, infectious complications in the post-traumatic and postoperative period of the eye (endophthalmitis), the cardiovascular system (endocarditis), central nervous system and musculoskeletal system (osteomyelitis), implant-associated infections on the other hand. To identify epidemically significant genotypes with high pathogenetic potential and genotypes of low pathogenic commensals the different molecular genetic approaches are used. The whole genome sequencing of C. acnes A1-14 strain isolated from the large intestine of a healthy person was carried out for the first time. As a result of alignment and collection, the nucleotide sequence of the genome was 2,484,560 pairs of nucleotides.The strain belongs to a phylotype II, a ribotype 6 and sequence-type 7 (McDowell A. et al. scheme) or 73 (Lomholt H. B., Kilian M. scheme) according to the results of genotyping. We showed that there are no mobile elements, determinants of pathogenicity and antibiotic resistance, mutations in the 16S rRNA, 23S rRNA, gyrA, gyrB, parC, parE genes and established the presence of CRISPR-Cas structure in the genome of C. acnes A1-14. An extrachromosomal sequence belonging to the genome of the Syphoviridae family bacteriophage was found. The morphological characteristic of the bacteriophage virion, the presence of that as extrachromosomal structure is typical to many C. acnes strains, is given using the electronic microscopic method of research. Thus, the obtained in our study results complement the understanding of the molecular genetic features of C. acnes strains isolated from various human biotopes and which are symbiotic microbiota representatives.

Cutibacterium (Propionibacterium) acnesполногеномное секвенированиеMLSTгенотипированиефакторы патогенностиCRISPR-CasбактериофагCutibacterium (Propionibacterium) acneswhole genome sequencingMLSTgenotypingpathogenicity factorsCRISPR-CasbacteriophageReferencesВирусология. Методы // Под редакцией Б. Мейхи. М.: Мир, 1988. 172 сВирусология. Методы // Под редакцией Б. Мейхи. М.: Мир, 1988. 172 сAchermann Y., Goldstein E.J.C., Coenye T., Shirtliffa M.E. Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen. Clin. Microbiol. Rev., 2014, no. 3,pp. 419-440.Achermann Y., Goldstein E.J.C., Coenye T., Shirtliffa M.E. Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen. Clin. Microbiol. Rev., 2014, no. 3,pp. 419-440.Bae Y., Ito T., Iida T., Uchida K., Sekine M., Nakajima Y. et al. Intracellular Propionibacterium acnes infection in glandular epithelium and stromal macrophages of the prostate with or without cancer. PLoS ONE, 2014, no. 2 (9), 11 p. Available at: https://doi.org/10.1371/joumal.pone.0090324 (accessed: 17.01.2017).Bae Y., Ito T., Iida T., Uchida K., Sekine M., Nakajima Y. et al. Intracellular Propionibacterium acnes infection in glandular epithelium and stromal macrophages of the prostate with or without cancer. PLoS ONE, 2014, no. 2 (9), 11 p. Available at: https://doi.org/10.1371/joumal.pone.0090324 (accessed: 17.01.2017).Brbggemann H. Insights in the pathogenic potential of Propionibacterium acnes from its complete genome. Semin. Cutan. Med. Surg., 2005, no. 2 (24), pp. 67-72.Brbggemann H. Insights in the pathogenic potential of Propionibacterium acnes from its complete genome. Semin. Cutan. Med. Surg., 2005, no. 2 (24), pp. 67-72.Brbgemann H., Lomholt H.B., Tettelin H., Kilian M. CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS ONE, 2012, no. 3 (7), 10 p. Available at: https://doi.org/10.1371/journal.pone.0034171 (accessed: 17.01.2017).Brbgemann H., Lomholt H.B., Tettelin H., Kilian M. CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS ONE, 2012, no. 3 (7), 10 p. Available at: https://doi.org/10.1371/journal.pone.0034171 (accessed: 17.01.2017).Eishi Y., Suga M., Ishige I., Kobayashi D., Yamada T., Takemura T. et al. Quantitative analysis of mycobacterial and propionibacterial DNA in lymph nodes of Japanese and European patients with sarcoidosis. J. Clin. Microbiol., 2002, no. 40, pp. 198-204.Eishi Y., Suga M., Ishige I., Kobayashi D., Yamada T., Takemura T. et al. Quantitative analysis of mycobacterial and propionibacterial DNA in lymph nodes of Japanese and European patients with sarcoidosis. J. Clin. Microbiol., 2002, no. 40, pp. 198-204.Fitz-Gibbon S., Tomida S., Chiu B.-H., Nguyen L., Du C., Liu M. et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J. Invest. Dermatol., 2013, no. 9, pp. 2152-2160.Fitz-Gibbon S., Tomida S., Chiu B.-H., Nguyen L., Du C., Liu M. et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J. Invest. Dermatol., 2013, no. 9, pp. 2152-2160.Ghachi M.E., Bouhss A., Blanot D., Mengin-Lecreulx D. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. J. Biol. Chem., 2004, no. 29 (279), pp. 30106-30113.Ghachi M.E., Bouhss A., Blanot D., Mengin-Lecreulx D. The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity. J. Biol. Chem., 2004, no. 29 (279), pp. 30106-30113.Jakab E., Zbinden R, Gubler J., Ruef C., von Graevenitz A., Krause M. Severe infections caused by Propionibacterium acnes: an underestimated pathogen in late postoperative infections. Yale J Biol Med., 1996, no. 6 (69), pp. 477-482.Jakab E., Zbinden R, Gubler J., Ruef C., von Graevenitz A., Krause M. Severe infections caused by Propionibacterium acnes: an underestimated pathogen in late postoperative infections. Yale J Biol Med., 1996, no. 6 (69), pp. 477-482.Lodes M.J., Secrist H., Benson D.R., Jen S., Shanebeck K.D., Guderian J. et al. Variable expression of immunoreactive surface proteins of Propionibacterium acnes. Microbiology, 2006, no. 12, pp. 3667-3681.Lodes M.J., Secrist H., Benson D.R., Jen S., Shanebeck K.D., Guderian J. et al. Variable expression of immunoreactive surface proteins of Propionibacterium acnes. Microbiology, 2006, no. 12, pp. 3667-3681.Lomholt H.B., Kilian M. Population genetic analysis of Propionibacterium acnes identifies a subpopulation and epidemic clones associated with acne. PLoS ONE, 2010, no. 8, 10 p. Available at: https://doi.org/10.1371/joumal. pone.0012277 (accessed: 20.01.2017)Lomholt H.B., Kilian M. Population genetic analysis of Propionibacterium acnes identifies a subpopulation and epidemic clones associated with acne. PLoS ONE, 2010, no. 8, 10 p. Available at: https://doi.org/10.1371/joumal. pone.0012277 (accessed: 20.01.2017)Lomholt H.B., Scholz C.F.P., BrBggemann H., Tettelin H., Kilian M. A comparative study of Cutibacterium (Propionibacterium) acnes clones from acne patients and healthy controls. Anaerobe, 2017, vol. 47, pp. 57-63.Lomholt H.B., Scholz C.F.P., BrBggemann H., Tettelin H., Kilian M. A comparative study of Cutibacterium (Propionibacterium) acnes clones from acne patients and healthy controls. Anaerobe, 2017, vol. 47, pp. 57-63.Lood R., Collin M. Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny. BMC Genomics, 2011, no. 12 (198), 14 p. Available at: https:// doi.org/10.1186/1471-2164-12-198 (accessed: 20.04.2015)Lood R., Collin M. Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny. BMC Genomics, 2011, no. 12 (198), 14 p. Available at: https:// doi.org/10.1186/1471-2164-12-198 (accessed: 20.04.2015)Makarova K.S., Wolf Y.I., Alkhnbashi O.S., Costa F., Shah S.A., Saunders S.J. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol., 2015, no. 11 (13), pp. 722-736.Makarova K.S., Wolf Y.I., Alkhnbashi O.S., Costa F., Shah S.A., Saunders S.J. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol., 2015, no. 11 (13), pp. 722-736.McDowell A., Perry A.L., Lambert P.A., Patrick S. A new phylogenetic group of Propionibacterium acnes. J. Med. Microbiol., 2008, no. 57, pp. 218-224.McDowell A., Perry A.L., Lambert P.A., Patrick S. A new phylogenetic group of Propionibacterium acnes. J. Med. Microbiol., 2008, no. 57, pp. 218-224.McDowell A., Barnard E., Nagy I., Gao A., Tomida S., Li H. et al. An expanded multilocus sequence typing scheme for Propionibacterium acnes: investigation of «pathogenic», «commensal» and antibiotic resistant strains. PLoS ONE, 2012, no. 7, 14 p. Available at: https://doi.org/10.1371/ journal.pone.0041480 (accessed: 20.01.2017)McDowell A., Barnard E., Nagy I., Gao A., Tomida S., Li H. et al. An expanded multilocus sequence typing scheme for Propionibacterium acnes: investigation of «pathogenic», «commensal» and antibiotic resistant strains. PLoS ONE, 2012, no. 7, 14 p. Available at: https://doi.org/10.1371/ journal.pone.0041480 (accessed: 20.01.2017)Romanyuk L.V., Tovkach F.I., Ivanitsa T.V., Kushkina A.I., Ostapchuk A.N., Gorb T.E. Abortive infection in Erwinia carotovora J2, as a source of nanoparticles of phage nature. Мiкробiологiчний журнал, 2010, no. 6, pp. 51-57. (In Ukrain.)Romanyuk L.V., Tovkach F.I., Ivanitsa T.V., Kushkina A.I., Ostapchuk A.N., Gorb T.E. Abortive infection in Erwinia carotovora J2, as a source of nanoparticles of phage nature. Мiкробiологiчний журнал, 2010, no. 6, pp. 51-57. (In Ukrain.)Schaeverbeke T., Lequen L., de Barbeyrac B., Labbe L., Bebear C.M., Momer Y. et al. Propionibacterium acnes isolated from synovial tissue and fluid in a patient with oligoarthritis associated with acne and pustulosis. Arthritis Rheum., 1998, no. 10 (41), pp. 1889-1893.Schaeverbeke T., Lequen L., de Barbeyrac B., Labbe L., Bebear C.M., Momer Y. et al. Propionibacterium acnes isolated from synovial tissue and fluid in a patient with oligoarthritis associated with acne and pustulosis. Arthritis Rheum., 1998, no. 10 (41), pp. 1889-1893.Scholz C.F., Kilian M. The natural history of cutaneous propionibacteria and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int. J. Syst. Evol. Microbiol., 2016, no. 11 (66), pp. 4422-4432.Scholz C.F., Kilian M. The natural history of cutaneous propionibacteria and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int. J. Syst. Evol. Microbiol., 2016, no. 11 (66), pp. 4422-4432.Tomida S., Nguyen L., Chiu B.-H., Liu J., Sodergren E., Weinstock G.M. et al. Pan-genome and comparative genome analyses of Propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. mBio., 2013, no. 3 (4), 11 p. Available at: http://mbio.asm. org/content/4/3/e00003-13 (accessed: 27.01.2017).Tomida S., Nguyen L., Chiu B.-H., Liu J., Sodergren E., Weinstock G.M. et al. Pan-genome and comparative genome analyses of Propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. mBio., 2013, no. 3 (4), 11 p. Available at: http://mbio.asm. org/content/4/3/e00003-13 (accessed: 27.01.2017).

The authors declare that there are no conflicts of interest present.