FEATURES OF THE MICROBIOME OF THE UPPER RESPIRATORY TRACT IN CHILDREN WITH RECURRENT RESPIRATORY DISEASES
- Authors: Shabaldin A.V.1,2, Shabaldina E.V.1, Simbirtsev A.S.3
-
Affiliations:
- Kemerovo State Medical Academy of Ministry of Health of Russia, Kemerovo
- Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
- State Research Institute of Highly Pure Biopreparations FMBA of Russia, St. Petersburg
- Issue: Vol 7, No 4 (2017)
- Pages: 341-349
- Section: REVIEWS
- Submitted: 20.01.2018
- Accepted: 20.01.2018
- Published: 20.01.2018
- URL: https://iimmun.ru/iimm/article/view/591
- DOI: https://doi.org/10.15789/2220-7619-2017-4-341-349
- ID: 591
Cite item
Full Text
Abstract
Studies of the metagenome of the upper respiratory tract in children showed the presence of five major bacterial phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria. Were revealed population differences in the distribution of weights of the above listed phyla, but subject to the dominance of the Firmicutes. Proved the role of environmental factors and time of year for representation in these biotopes of the phyla: Firmicutes, Proteobacteria, Bacteroidetes. Recurrent respiratory infections, hypertrophy of the tonsils of the lymphoid pharyngeal ring, secretory middle ear infections in children is associated with carriage of Haemophilus (H.) parainfluenzae, H. paraphrohaemolyticus, Gemella (G.) haemolysans, G. morbillorum, G. sanguinis, Streptococcus (S.) pneumoniae, S. pseudopneumoniae, S. intermedius, S. agalactiae.
About the authors
A. V. Shabaldin
Kemerovo State Medical Academy of Ministry of Health of Russia, Kemerovo;Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo
Author for correspondence.
Email: weit2007@ya.ru
PhD, MD (Medicine), Leading Researcher, Laboratory of Cell Technologies, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russian Federation; Professor of Department of Otolaryngology and Clinical Immunology, Kemerovo State Medical Academy Россия
E. V. Shabaldina
Kemerovo State Medical Academy of Ministry of Health of Russia, Kemerovo
Email: weit2007@ya.ru
PhD, MD (Medicine), Associate Professor, Head of the Department of Otorhinolaryngology and Clinical Immunology, Kemerovo State Medical Academy Россия
A. S. Simbirtsev
State Research Institute of Highly Pure Biopreparations FMBA of Russia, St. Petersburg
Email: weit2007@ya.ru
RAS Corresponding Member, PhD, MD (Biology), Professor, Deputy Director on Science of State Research Institute of Highly Pure Biopreparations Россия
References
- Альбицкий В.Ю., Баранов А.А. Часто болеющие дети. Клинико-социальные аспекты. Пути оздоровления. Саратов: Саратовский национальный исследовательский государственный университет им. Н.Г. Чернышевского, 1986. 184 с. [Albitsky V.Yu., Baranov A.A. Chasto boleyushchie deti. Kliniko-sotsial’nye aspekty. Puti ozdorovleniya [Frequently ill children. Clinical and social aspects. The road to recovery]. Saratov: N.G. Chernyshevsky Saratov National Research University, 1986. 184 p.]
- Бонч-Осмоловская Е.А., Равин Н.В. Анализ полных геномов — очередной этап в развитии микробиологии // Вестник Российской академии наук. 2010. Т. 80, № 11. С. 977–984. [Bonch-Osmolovskaya E.A., Ravin N.V. Analysis of complete genome as successive stage in development of microbiology review. Vestnik Rossiiskoi akademii nauk = Herald of the Russian Academy of Sciences, 2010, vol. 80, no. 11, pp. 977–984. (In. Russ.)]
- Волкова Р.А., Сколетнева Е.С., Эльберт Е.В., Мыца Е.Д., Давыдов Д.С., Мовсесянц А.А., Меркулов В.А., Бондарев В.П., Борисевич И.В. Проблемы генотипирования микроорганизмов // БИОпрепараты. Профилактика, диагностика, лечение. 2016. Т. 16, № 3 (59). С. 139–144. [Volkova R.A., Skoletneva E.S., El’bert E.V., Mytsa E.D., Davydov D.S., Movsesyants A.A., Merkulov V.A., Bondarev V.P., Borisevich I.V. Genotyping problems of microorganisms. BIOpreparaty. Profilaktika, diagnostika, lechenie = BIO Preparations. Prevention, Diagnosis, Treatment, 2016, vol. 16, no. 3 (59), pp. 139–144. (In Russ.)]
- Карпова Е.П., Тулупов Д.А. Хронический аденоидит у детей: пособие для врачей. М.: РМАПО, 2009. 54 с. [Karpova E.P., Tulupov D.A. Khronicheskii adenoidit u detei: posobie dlya vrachei [Chronic adenoiditis in children: manual for physicians]. Moscow: Russian Medical Academy, 2009. 54 p.]
- Кушнарева М.В., Виноградова Т.В., Кешишян Е.С., Парфенов В.В., Кольцов В.Д., Брагина Г.С., Паршина О.В., Гусева Т.С. Особенности иммунного статуса и системы интерферона у детей раннего возраста // Российский вестник перинатологии и педиатрии, 2016. Т. 61, № 3. С. 12–21. [Kushnareva M.V., Vinogradova T.V., Keshishian E.S., Parfenov V.V., Koltsov V.D., Bragina G.S., Parshina O.V., Guseva T.S. Specific features of the immune status and interferon system of infants. Rossiyskiy vestnik perinatologii i pediatrii = Russian Bulletin of Perinatology and Pediatrics, 2016, vol. 61, no. 3, pp. 12–21. doi: 10.21508/1027-4065-2016-61-3-12-21 (In. Russ.)]
- Раввин Н.В., Шестаков С.В. Геном прокариот // Вавиловский журнал генетики и селекции. 2013. Т. 17, № 4/2. С. 972– 984. [Ravvin N.V., Shestakov S.V. The Genome of prokaryotes. Vavilovskii zhurnal genetiki i selektsii = Vavilov Journal of Genetics and Breeding, 2013, vol. 17, no. 4/2, pp. 972–984. (In. Russ.)]
- Романцев М.Г., Ершов Ф.И. Часто болеющие дети: современная фармакотерапия. М.: ГЭОТАР-Медиа, 2006. 192 с. [Romantsev M.G., Ershov F.I. Chasto boleyushchie deti: sovremennaya farmakoterapiya [Frequently ill children: modern pharmacotherapy]. Moscow: GEOTAR-Media, 2006. 192 p.]
- Романцов М.Г., Мельникова И.Ю. Часто болеющие дети: вопросы фармакотерапии (научный обзор) // Terra medica. 2014. № 1. С. 55–69. [Romantsov M.G., Melnikova I.Yu. Sickly children: issues of pharmacotherapy (scientific review). Terra Medica, 2014, no. 1, pp. 55–69. (In. Russ.)]
- Патент 2576839 Российская Федерация. Способ диагностики дисбиотических нарушений в биоптатах слизистой носа и глотки у детей раннего и дошкольного возраста с постоянно рецидивирующими острыми респираторными инфекциями / Тюменев А.В., Шабалдина Е.В., Шабалдин А.В., Рязанцев С.В., Симбирцев А.С. Заявители и патенто-обладатели: Тюменев А.В., Шабалдина Е.В., Шабалдин А.В., Рязанцев С.В., Симбирцев А.С.; завл. 16.10.2013; опубл. 10.03.2016 [Patent 2576839 Russian Federation. A method for diagnosing dysbiotic disorders in biopsies of nasal mucosa and pharynx in children of early and preschool age with recurring acute respiratory infections / Tyumenev A.V., Shabaldina E.V., Shabaldin A.V., Ryazantsev S.V., Simbirtsev A.S. Applicants and patent holders: Tyumenev A.V., Shabaldina E.V., Shabaldin A.V., Ryazantsev S.V., Simbirtsev A.S.; stat. 10.16.2013; publ. 03.10.2016]
- Патент 2569054 Российская Федерация. Способ определение провоспалительных и проаллергических интерлей-кинов в назальном секрете у детей раннего и дошкольного возраста для диагностики этиологии рецидивирующих острых ринофарингитов и аденоидитов / Тюменев А.В., Шабалдина Е.В., Шабалдин А.В., Симбирцев А.С., Рязан-цев С.В. Заявитель и патентообладатель ГБОУ ВПО Кемеровская государственная медицинская академия МЗ РФ; заявл. 24.09.2013; опубл. 20.11.2014 [Patent 2569054 Russian Federation. Method for the determination of proinflammatory and proallergic interleukins in nasal secretion in children of early and preschool age for diagnosis of the etiology of recurrent acute rhinopharyngitis and adenoiditis / Tyumenev A.V., Shabaldina E.V., Shabaldin A.V., Simbirtsev A.S., Ryazantsev S.V. Applicant and patent holder: Kemerovo State Medical Academy, Ministry of Health of the Russian Federation; stat. 24.09.2013; publ. 20.11.2014]
- Шабалдина Е.В., Кутенкова Н.Е, Шабалдин А.В., Лисаченко Г.В. Особенности иммунного и цитокинового статусов у детей с гипертрофией лимфоидного глоточного кольца и сопутствующей аллергией к инфекционным антигенам // Российская оториноларингология. 2012. № 2. С. 118–123. [Shabalina E.V., Kutenkova N.E., Shabaldin A.V., Tikhonuk V.P., Lisachenko G.V. Characteristics of immune and cytokine status in children with hypertrophy of lymphoid pharyngeal ring and concomitant allergies to infectious antigens. Rossiiskaya otorinolaringologiya = Russian Otorhinolaryngology, 2012, no. 2, pp. 118– 123. (In. Russ.)]
- Шабалдина Е.В., Кутенкова Н.Е., Шабалдин А.В., Тихонюк В.П., Лисаченко Г.В. Роль сенсибилизации к инфек-ционным антигенам в патогенезе рецидивирования острых респираторных инфекций у детей // Педиатрия. 2013. № 1. С. 24–33. [Shabalina E.V., Kutenkova N.E., Shabaldin A.V., Tikhonuk V.P., Lisachenko G.V. The role of sensitization to infectious antigens in the pathogenesis of recurrence of acute respiratory infections in children. Pediatriya = Pediatrics, 2013, no. 1, pp. 24–33. (In. Russ.)]
- Шестаков С.В. Как происходит и чем лимитируется горизонтальный перенос генов у бактерий // Экологическая генетика. 2007. Т. 2, № 5. С. 12–24. [Shestakov S.V. How is and then is limited by horizontal gene transfer in bacteria. Ekologicheskaya genetika = Ecological Genetics, 2007, vol. 2, no. 5, pp. 12–24. (In. Russ.)]
- Шестаков С.В. Метагеномика микробиома человека // Успехи современной биологии. 2010. Т. 130, № 6. С. 531–543. [Shestakov S.V. Metagenomics of the human microbiome. Uspekhi sovremennoi biologii = Advances in Current Biology, 2010, vol. 130, no. 6, pp. 531–543. (In. Russ.)]
- Щеплягина Л.А. Секреторный иммунитет кишечника у детей раннего возраста // Педиатрия. 2011. № 3. С. 48–50. [Schepljagina L.A. Secretory immune system of the intestine at children of early age. Pediatriya = Pediatrics, 2011, no. 3, pp. 48–50. (In. Russ.)]
- Bassis C.M., Erb-Downward J.R., Dickson R.P., Freeman C.M., Schmidt T.M., Yong V.B., Beck J.M., Curtis J.L., Huffnagle G.B., Ravel J. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio, 2015, vol. 6, no. 2: e00037-15. doi: 10.1128/mBio.00037-15
- Benninger M., Brook I., Bernstein J.M., Casey J.R., Roos K., Marple B., Farrar J.R. Bacterial interference in upper respiratory tract infections: a systematic review. Am. J. Rhinolm. Allergy, 2011, vol. 25, no. 2, pp. 82–88. doi: 10.2500/ajra.2011.25.3594
- Biesbroek G., Tsivtsivadze E., Sanders E.A., Montijn R., Veenhoven R.H., Keijser B.J. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am. J. Respir. Crit. Care Med., 2014, vol. 190, no. 11, pp. 1283–1292. doi: 10.1164/rccm.201407-1240OC
- Bochkov Y.A., Grindle K., Vang F., Evans M.D., Gern J.E. Improved molecular typing assay for rhinovirus species A, B, and C. J. Clin. Microbiol., 2014, vol. 52, no. 7, pp. 2461–2471. doi: 10.1128/JCM.00075-14
- Bogaert D., Keijser B., Huse S., Rossen J., Veenhoven R., Van Gils E., Bruin J., Montijn R., Bonten M., Sanders E. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS One, 2011, vol. 6, no. 2, pp. 17035–17043. doi: 10.1371/journal.pone.0017035
- Bogaert D., van Belkum A., Sluijter M., Luijendijk A., de Groot R., Rumke H.C. Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children. Lancet, 2004, vol. 363, iss. 9424, pp. 1871–1872. doi: 10.1016/S0140-6736(04)16357-5
- Costello E.K., Lauber C.L., Hamady M., Fierer N., Gordon J.I., Knight R. Bacterial community variation in human body habitats across space and time. Science, 2009, vol. 326, iss. 5960, pp. 1694–1697. doi: 10.1126/science.1177486
- Dickson R.P., Erb-Downward J.R., Huffnagle G.B. The role of the bacterial microbiome in lung disease. Expert Rev. Respir. Med., 2013, vol. 7, iss. 3, pp. 245–257. doi: 10.1586/ers.13.24
- Dickson R.P., Erb-Downward J.R., Martinez F.J., Huffnagle G.B. The microbiome and the respiratory tract. Annu. Rev. Physiol., 2016, vol. 78, pp. 481–504. doi: 10.1146/annurev-physiol-021115-105238
- Dickson R.P., Martinez F.J., Huffnagle G.B. The role of the microbiome in exacerbations of chronic lung diseases. Lancet, 2014, vol. 384, iss. 9944, pp. 691–702. doi: 10.1016/S0140-6736(14)61136-3
- Edwards R.A., Rohwer F. Viral metagenomics. Nat. Rev. Microbiol., 2005, vol. 3, pp. 504–510. doi: 10.1038/nrmicro1163
- Gao Z., Kang Y., Jun Y., Ren L. Human pharyngeal microbiome may play a protective role in respiratory tract infections. Genom. Proteom. Bioinformat., 2014, vol. 12, iss. 3, pp. 144–150. doi: 10.1016/j.gpb.2014.06.001
- Hilty M., Burke C., Pedro H., Cardenas P., Bush A., Bossley C., Davies J., Ervine A., Poulter L., Pachter L., Moffatt M.F., Cookson W.O. Disordered microbial communities in asthmatic airways. PLoS One, 2010, vol. 5, iss. 1, e:8578. doi: 10.1371/journal.pone.0008578
- Jensen A., Fago-Olsen H., Sorensen C.H., Kilian M. Molecular mapping to species level of the tonsillar crypt microbiota associated with health and recurrent tonsillitis. PLoS One, 2013, vol. 8, iss. 2: e56418. doi: 10.1371/journal.pone.0056418
- Kononen E. Development of oral bacterial flora in young children. Ann. Med, 2000, vol. 32, iss. 2, pp. 107–112. doi: 10.3109/ 07853890009011759
- Kumar H., Lund R., Laiho A., Lundelin K., Ley R.E., Isolauri E., Salminen S. Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. MBio, 2014, vol. 5, no. 6: e02113-14. doi: 10.1128/mBio.02113-14
- Lebon A., Labout J.A., Verbrugh H.A., Jaddoe V.W., Hofman A., van Wamel W., Moll H.A., van Belkam A. Dynamics and determinants of Staphylococcus aureus carriage in infancy: the Generation R Study. J. Clin. Microbiol., 2008, vol. 46, no. 10, pp. 3517–3521. doi: 10.1128/JCM.00641-08
- Lee W.-M., Grindle K., Pappas T., Marshall D.J., Moser M.J., Beaty E.L., Shult P.A., Prudent J.R., Gern J.E. High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses. J. Clin. Microbiol., 2007, vol. 45, no. 8, pp. 2626–2634. doi: 10.1128/JCM.02501-06
- Liu C.M., Cosetti M.K., Aziz M., Buchhagen J.L., Contente-Cuomo T.L., Price L.B., Keim P.S., Lalwani A.K. The otologic microbiome: a study of the bacterial microbiota in a pediatric patient with chronic serous otitis media using 16SrRNA gene-based pyrosequencing. Arch. Otolaryngol. Head Neck Surg., 2011, vol. 137, no. 7, pp. 664–668. doi: 10.1001/archoto.2011.116
- Lysholm F., Wetterbom A., Lindau C., Darban H., Bjerkner A., Fahlander K., Lindberg A.M., Persson B., Allander T., Anders-son B. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS One, 2012, vol. 7, no. 2: e30875. doi: 10.1371/journal.pone.0030875
- Malygina O.G., Bazhukova T.A. Influence of antibiotics on formation of microecology in premature children with low and extremely low body weight at birth. J. Microbiol. Epidemiol. Immunobiol., 2014, no. 1, pp. 61–65. PMID: 24738296
- Moore H.C., Jacoby P., Taylor A., Harnett G., Bowman J., Riley T.V., Smith D.W., Lehmann D. The interaction between respiratory viruses and pathogenic bacteria in the upper respiratory tract of asymptomatic aboriginal and non-aboriginal children. Pediatr. Infect. Dis. J., 2010, vol. 29, iss. 6, pp. 540–545. doi: 10.1097/inf.0b013e3181d067cb
- Peterson S.W., Knox N.C., Golding G.R., Tyler S.D., Tyler A.D., Mabon P., Embree J.E., Fleming F., Fanella S., van Domselaar G., Mulvey M.R., Graham M.R. A study of the infant nasal microbiome development over the first year of life and in relation to their primary adult caregivers using cpn60 universal target (UT) as a phylogenetic marker. PLoS One, 2016, vol. 11, no. 3: e0152493. doi: 10.1371/journal.pone.0152493
- Quintero B., Araque M., van der Gaast-de Jongh C., Escalona F., Correa M., Morillo-Puente S., Vielma S., Hermans P.W.M. Epidemiology of Streptococcus pneumoniae and Staphylococcus aureus colonization in healthy Venezuelan children. Eur. J. Clin. Microbiol. Infect. Dis., 2011, vol. 30, iss. 1, pp. 7–19. doi: 10.1007/s10096-010-1044-6
- Rajeschwary A., Rai S., Somayaji G., Pai V. Bacteriology of symptomatic adenoids in children. North Am. J. Med. Sci., 2013, vol. 5, no. 2, pp. 113–118. doi: 10.4103/1947-2714.107529
- Ren T., Ulrike D.G., Nguyen T.N., Kaitlynn E.A., Early S.V., Sale M., Winther B., Wu M. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids. Environ. Microbiol., 2012, vol. 15, no. 2, pp. 2–13. doi: 10.1111/1462-2920.12000
- Sakwinska O., Schmid V.B., Berger B., Bruttin A., Keitel K., Lepage M., Moine D., Bru C.N., Brüssow H., Gervaix A. Nasopharyngeal microbiota in healthy children and pneumonia patients. J. Clin. Microbiol., 2014, vol. 52, no. 5, pp. 1590–1594. doi: 10.1128/JCM.03280-13
- Santee C.A., Nagalingam N.A., Faruqi A.A., DeMuri G.P., Gern J.E., Wald E.R., Lynch S.V. Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis. Microbiome, 2016, vol. 4: 34. doi: 10.1186/s40168-016-0179-9
- Scholz C.F., Poulsen K., Kilian M. Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J. Clin. Microbiol., 2012, vol. 50, no. 6, pp. 1968–1973. doi: 10.1128/JCM.00365-12
- Shilts M.H., Rosas-Salazar C., Tovchigrechko A., Larkin E.K., Torralba M., Akopov A., Halpin R., Peebles R.S., Moore M.L., Anderson L.J., Nelson K.E., Hartert T.V., Das S.R. Minimally invasive sampling method identifies differences in taxonomic richness of nasal microbiomes in young infants associated with mode of delivery. Microb. Ecol., 2016, vol. 71, iss. 1, pp. 233–242. doi: 10.1007/s00248-015-0663-y
- Stearns J.C., Davidson C.J., McKeon S., Whelan F.J., Fontes M.E., Schryvers A.B., Bowdish D.M., Kellner J.D., Surette M.G. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J., 2015, no. 9, pp. 1246–1259. doi: 10.1038/ismej.2014.250
- Structure, function and diversity of the healthy human microbiome. The Human Microbiome Project Consortium. Nature, 2012, vol. 486, no. 7402, pp. 201–214. doi: 10.1038/nature11234
- Teo S.M., Mok D., Pham K., Kusel M., Serralha M., Troy N., Holt B.J., Hales B.J., Walker M.V., Hollams E., Bochkov Y.A., Grindle K., Johnston S.L., Gern J.E., Sly P.D., Holt P.G., Holt K.E., Inouye M. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host & Microbe, 2015, vol. 17, no. 5, pp. 704–715. doi: 10.1016/j.chom.2015.03.008