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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" article-type="other" dtd-version="1.2" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">Russian Journal of Infection and Immunity</journal-id><journal-title-group><journal-title xml:lang="en">Russian Journal of Infection and Immunity</journal-title><trans-title-group xml:lang="ru"><trans-title>Инфекция и иммунитет</trans-title></trans-title-group></journal-title-group><issn publication-format="print">2220-7619</issn><issn publication-format="electronic">2313-7398</issn><publisher><publisher-name xml:lang="en">SPb RAACI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">17946</article-id><article-id pub-id-type="doi">10.15789/2220-7619-IMC-17946</article-id><article-categories><subj-group subj-group-type="toc-heading" xml:lang="en"><subject>ORIGINAL ARTICLES</subject></subj-group><subj-group subj-group-type="toc-heading" xml:lang="ru"><subject>ОРИГИНАЛЬНЫЕ СТАТЬИ</subject></subj-group><subj-group subj-group-type="article-type"><subject>Unknown</subject></subj-group></article-categories><title-group><article-title xml:lang="en">IMMUNO-MICROBIOLOGICAL CHARACTERISATION OF THE SPECIES COMPOSITION OF THE BACTERIAL MICROFLORA OF THE RESPIRATORY TRACT IN COVID-19 PATIENTS WITH COMORBIDITIES</article-title><trans-title-group xml:lang="ru"><trans-title>ИММУНО-МИКРОБИОЛОГИЧЕСКАЯ ХАРАКТЕРИСТИКА ВИДОВОГО СОСТАВА БАКТЕРИАЛЬНОЙ МИКРОФЛОРЫ ДЫХАТЕЛЬНЫХ ПУТЕЙ У ПАЦИЕНТОВ С COVID-19 И КОМОРБИДНОСТЬЮ</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-4221-9911</contrib-id><name-alternatives><name xml:lang="en"><surname>Ashirova</surname><given-names>Mayra Zangarovna</given-names></name><name xml:lang="ru"><surname>Аширова</surname><given-names>Майра Зангаровна</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>PhD candidate</p></bio><bio xml:lang="ru"><p>Докторант</p></bio><email>mayra.ashirova@list.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-1210-2018</contrib-id><name-alternatives><name xml:lang="en"><surname>Abuova</surname><given-names>Gulzhan Narkenovna</given-names></name><name xml:lang="ru"><surname>Абуова</surname><given-names>Гульжан Наркеновна</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>Head of the Department of Infectious Diseases and Dermatovenereology, PhD, Professor</p></bio><bio xml:lang="ru"><p>Кандидат медицинских наук, профессор, заведующий кафедры инфекционных болезней и дерматовенерологии</p></bio><email>dr.abuova@gmail.com</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0008-7907-5246</contrib-id><name-alternatives><name xml:lang="en"><surname>Taukebayeva</surname><given-names>Gulnara Zamanbekovna</given-names></name><name xml:lang="ru"><surname>Таукебаевна</surname><given-names>Гульнара Заманбековна</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>Assistant at the Department of Infectious Diseases and Dermatovenereology, Shymkent, Kazakhstan</p></bio><email>taukebayevag2020@mail.ru</email><xref ref-type="aff" rid="aff2"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-5656-0918</contrib-id><name-alternatives><name xml:lang="en"><surname>Shaimerdenova</surname><given-names>Gulbanu Ganikyzy</given-names></name><name xml:lang="ru"><surname>Шаймерденова</surname><given-names>Гульбану Ганиевна</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>PhD candidate, аssistant at the Department of Infectious Diseases and Dermatovenereology. </p></bio><bio xml:lang="ru"><p>Авторы заявляют об отсутствии конфликта интересов относительно публикации данной статьи.</p></bio><email>gulbanu1008@mail.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-1064-7081</contrib-id><name-alternatives><name xml:lang="en"><surname>Timur</surname><given-names>Davlyatshin</given-names></name><name xml:lang="ru"><surname>Тимур</surname><given-names>Давлятшин</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>Lab assistant, Candidate of Medical Sciences</p></bio><bio xml:lang="ru"><p>Лаборант</p></bio><email>avegadti@mail.ru</email><xref ref-type="aff" rid="aff3"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0004-7780-7897</contrib-id><name-alternatives><name xml:lang="en"><surname>Isakhan</surname><given-names>Shahzad Shaukatuly</given-names></name><name xml:lang="ru"><surname>Шавкатулы</surname><given-names>Исахан Шахзад</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>Infectious disease doctor</p></bio><bio xml:lang="ru"><p>Врач инфнекционист</p></bio><email>shahzod.isahan@mail.ru</email><xref ref-type="aff" rid="aff4"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0006-3456-6266</contrib-id><name-alternatives><name xml:lang="en"><surname>Nigmatov</surname><given-names>Farrukh Farkhodovich</given-names></name><name xml:lang="ru"><surname>Нигматов</surname><given-names>Фаррух Фарходович</given-names></name></name-alternatives><address><country country="KZ">Kazakhstan</country></address><bio xml:lang="en"><p>Infectious disease doctor</p></bio><bio xml:lang="ru"><p>Врач инфекционист</p></bio><email>farid250892@mail.ru</email><xref ref-type="aff" rid="aff5"/></contrib></contrib-group><aff-alternatives id="aff1"><aff><institution xml:lang="en">South Kazakhstan Medical Academy, Shymkent, Kazakhstan</institution></aff><aff><institution xml:lang="ru">Южно-Казахстанская медицинская академия, Шымкент, Казахстан</institution></aff></aff-alternatives><aff-alternatives id="aff2"><aff><institution xml:lang="en">Khoja Akhmet Yassawi International Kazakh-Turkish University, Shymkent, Kazakhstan</institution></aff><aff><institution xml:lang="ru">Международный казахско-турецкий университет имени Ходжи Ахмета Яссави, Шымкент, Казахстан</institution></aff></aff-alternatives><aff-alternatives id="aff3"><aff><institution xml:lang="en">Clinical diagnostic laboratory "Omikron 3D", Almaty, Kazakhstan</institution></aff><aff><institution xml:lang="ru">Клинико-диагностическая лаборатория «Омикрон 3D», Алматы, Казахстан</institution></aff></aff-alternatives><aff-alternatives id="aff4"><aff><institution xml:lang="en">Medical and health center "SANITAS", Turkestan, Kazakhstan</institution></aff><aff><institution xml:lang="ru">Медицинский оздоровительный центр «САНИТАС», Туркестан, Казахстан</institution></aff></aff-alternatives><aff-alternatives id="aff5"><aff><institution xml:lang="en">City Infectious Diseases Hospital, Shymkent, Kazakhstan</institution></aff><aff><institution xml:lang="ru">Городская инфекционная больница, Шымкент, Казахстан</institution></aff></aff-alternatives><pub-date date-type="preprint" iso-8601-date="2025-10-31" publication-format="electronic"><day>31</day><month>10</month><year>2025</year></pub-date><history><date date-type="received" iso-8601-date="2025-06-17"><day>17</day><month>06</month><year>2025</year></date><date date-type="accepted" iso-8601-date="2025-10-23"><day>23</day><month>10</month><year>2025</year></date></history><permissions><copyright-statement xml:lang="en">Copyright ©; , Ashirova M.Z., Abuova G.N., Taukebayeva G.Z., Shaimerdenova 4.G., Timur D., Isakhan S.S., Nigmatov F.F.</copyright-statement><copyright-statement xml:lang="ru">Copyright ©; , Ashirova M., Абуова Г.Н., Таукебаевна Г.З., Шаймерденова Г.Г., Тимур Д., Шавкатулы И.Ш., Нигматов Ф.Ф.</copyright-statement><copyright-holder xml:lang="en">Ashirova M.Z., Abuova G.N., Taukebayeva G.Z., Shaimerdenova 4.G., Timur D., Isakhan S.S., Nigmatov F.F.</copyright-holder><copyright-holder xml:lang="ru">Ashirova M., Абуова Г.Н., Таукебаевна Г.З., Шаймерденова Г.Г., Тимур Д., Шавкатулы И.Ш., Нигматов Ф.Ф.</copyright-holder><ali:free_to_read xmlns:ali="http://www.niso.org/schemas/ali/1.0/"/><license><ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/">https://creativecommons.org/licenses/by/4.0</ali:license_ref></license></permissions><self-uri xlink:href="https://iimmun.ru/iimm/article/view/17946">https://iimmun.ru/iimm/article/view/17946</self-uri><abstract xml:lang="en"><p>A significant proportion of COVID-19 cases are linked to recurrent respiratory infections, such as chronic and acute bronchitis, pneumonia, and various upper and lower respiratory tract diseases. This highlights the need to investigate the mechanisms contributing to airway dysfunction and immune suppression, especially regarding the long-term effects of SARS-CoV-2 infection. The development of these complications likely depends on factors like immune dysregulation, microbiome imbalance, and viral damage to airway epithelial cells. Understanding how these factors influence prolonged symptoms and recovery challenges is crucial. The role of the microbiome in the pathogenesis of respiratory infections has gained increasing attention. Disruption of the normal microbiota can lead to immune hyperreactivity and promote infections. In COVID-19, it is believed that SARS-CoV-2 infection may alter the microbiome, leading to secondary bacterial infections, such as pneumonia, and exacerbating chronic respiratory conditions. This study aimed to explore the microbiome of the upper and lower respiratory tracts and its association with clinical outcomes in patients with SARS-CoV-2 infection. It included 159 patients from Shymkent, Kazakhstan, confirmed positive for SARS-CoV-2 by PCR. Specific IgG antibodies were measured to assess immune responses to coinfections. Among patients with comorbidities, the most common antibodies were to Mycoplasma pneumoniae (41.41%), Staphylococcus aureus (35.35%), and Klebsiella pneumoniae (23%). In contrast, antibodies to Streptococcus pyogenes (23%) were more common in patients without comorbidities. Statistically significant differences in antibody avidity were observed for Klebsiella pneumoniae (p = 0.036) and Mycoplasma pneumoniae (p = 0.028), suggesting a role for these pathogens in post-COVID complications. These results support the hypothesis that coinfections play a significant role in post-COVID respiratory diseases. The higher frequency of bacterial antibodies in patients with comorbidities indicates that chronic infections or microbiome imbalances may contribute to more severe COVID-19 outcomes and increase the risk of long-term symptoms, underscoring the need for further microbiological research and rehabilitation strategies. </p></abstract><trans-abstract xml:lang="ru"><p>Значительная часть случаев COVID-19 связана с рецидивирующими респираторными инфекциями, такими как хронический и острый бронхит, пневмония и различные заболевания верхних и нижних дыхательных путей. Это подчеркивает необходимость изучения механизмов, способствующих дисфункции дыхательных путей и подавлению иммунитета, особенно в отношении долгосрочных последствий инфекции SARS-CoV-2. Развитие таких осложнений, вероятно, зависит от ряда факторов, например, нарушения регуляции иммунитета, дисбаланса микробиома и вирусного повреждения эпителиальных клеток дыхательных путей. Понимание того, как указанные факторы влияют на продолжительность симптомов и препятствуют выздоровлению, имеет решающее значение. Роль микробиома в патогенезе респираторных инфекций привлекает все большее внимание. Нарушение нормальной микробиоты может привести к иммунной гиперреактивности и способствовать развитию инфекций. При COVID-19 считается, что инфекция SARS-CoV-2 может модифицировать микробиом, приводя к вторичным бактериальным инфекциям, таким как пневмония, и обострению хронических респираторных заболеваний. Целью настоящего исследования было изучение микробиома верхних и нижних дыхательных путей и его связи с клиническими исходами у пациентов с инфекцией SARS-CoV-2. В исследование было включено 159 пациентов из Шымкента, Казахстан, у которых был подтвержден положительный результат теста на SARS-CoV-2 методом ПЦР. Для оценки иммунного ответа на коинфекции измеряли специфические IgG антитела. Среди пациентов с сопутствующими заболеваниями наиболее распространенными были IgG антитела к Mycoplasma pneumoniae (41,41%), Staphylococcus aureus (35,35%) и Klebsiella pneumoniae (23%). Напротив, антитела к Streptococcus pyogenes (23%) чаще встречались у пациентов без сопутствующих заболеваний. Статистически значимые различия отмечены в авидности антител к Klebsiella pneumoniae (p = 0,036) и Mycoplasma pneumoniae (p = 0,028), что указывает на роль этих патогенов в развитии осложнений после COVID. Полученные результаты подтверждают гипотезу о том, что коинфекции играют важную роль в развитии респираторных заболеваний после COVID-19. Более высокая частота антител против бактериальных возбудителей у пациентов с сопутствующими заболеваниями указывает на то, что хронические инфекции или дисбаланс микробиома могут способствовать более тяжёлому исходу COVID-19 и повышать риск развития отдаленных симптомов, что подчёркивает необходимость проведения дальнейших микробиологических исследований и развития стратегий реабилитации.</p></trans-abstract><kwd-group xml:lang="en"><kwd>comorbid conditions</kwd><kwd>COVID-19</kwd><kwd>microbial landscape</kwd><kwd>microflora</kwd><kwd>respiratory tract.</kwd></kwd-group><kwd-group xml:lang="ru"><kwd>коморбидные состояния</kwd><kwd>COVID-19</kwd><kwd>микробный профиль</kwd><kwd>микрофлора</kwd><kwd>дыхательные пути.</kwd></kwd-group><funding-group/></article-meta></front><body></body><back><ref-list><ref id="B1"><label>1.</label><mixed-citation>The World Health Organization. New navigator (2019-nCoV). Learn more about the situation. 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