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Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lun...

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Autores principales: Paine, Suman Kalyan, Rout, Usha Kiran, Bhattacharyya, Chandrika, Parai, Debaprasad, Alam, Mahabub, Nanda, Rasmi Ranjan, Tripathi, Devashish, Choudhury, Parveena, Kundu, Chanakya Nath, Pati, Sanghamitra, Bhattacharya, Debdutta, Basu, Analabha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400563/
https://www.ncbi.nlm.nih.gov/pubmed/36002454
http://dx.doi.org/10.1038/s41522-022-00330-y
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author Paine, Suman Kalyan
Rout, Usha Kiran
Bhattacharyya, Chandrika
Parai, Debaprasad
Alam, Mahabub
Nanda, Rasmi Ranjan
Tripathi, Devashish
Choudhury, Parveena
Kundu, Chanakya Nath
Pati, Sanghamitra
Bhattacharya, Debdutta
Basu, Analabha
author_facet Paine, Suman Kalyan
Rout, Usha Kiran
Bhattacharyya, Chandrika
Parai, Debaprasad
Alam, Mahabub
Nanda, Rasmi Ranjan
Tripathi, Devashish
Choudhury, Parveena
Kundu, Chanakya Nath
Pati, Sanghamitra
Bhattacharya, Debdutta
Basu, Analabha
author_sort Paine, Suman Kalyan
collection PubMed
description The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lung infection. Post-hoc studies of previous SARS outbreaks postulate secondary bacterial infections with microbial dysbiosis. Oral microbial dysbiosis, particularly the altered proportion of Firmicutes and Proteobacteria, observed in other respiratory virus infection, like influenza, has shown to be associated with increased morbidity and mortality. Oropharynx and lung share similar kinds of bacterial species. We hypothesized that alteration in the Human Oropharyngeal Microbiome in SARS-CoV-2 patients can be a clinical indicator of bacterial infection related complications. We made a longitudinal comparison of oropharyngeal microbiome of 20 SARS-CoV-2 patients over a period of 30 days; at three time points, with a 15 days interval; contrasting them with a matched group of 10 healthy controls. Present observation indicates that posterior segment of the oropharyngeal microbiome is a key reservoir for bacteria causing pneumonia and chronic lung infection on SARS-CoV-2 infection. Oropharyngeal microbiome is indeed altered and its α-diversity decreases, indicating reduced stability, in all SARS-CoV-2 positive individuals right at Day-1; i.e. within ~24 h of post clinical diagnosis. The dysbiosis persists long-term (30 days) irrespective of viral clearance and/or administration of antibiotics. There is a severe depletion of commensal bacteria phyla like Firmicutes among the patients and that depletion is compensated by higher proportion of bacteria associated with sepsis and severe lung infection from phyla Proteobacteria. We also found elevated proportions of certain genus that have previously been shown to be causal for lung pneumonia in studies of model organisms and human autopsies’ including Stenotrophomonas, Acenetobactor, Enterobactor, Klebsiella and Chryseobacterium that were to be elevated among the cases. We also show that responses to the antibiotics (Azithromycin and Doxycycline) are not uniform for all individuals.
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spelling pubmed-94005632022-08-25 Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance Paine, Suman Kalyan Rout, Usha Kiran Bhattacharyya, Chandrika Parai, Debaprasad Alam, Mahabub Nanda, Rasmi Ranjan Tripathi, Devashish Choudhury, Parveena Kundu, Chanakya Nath Pati, Sanghamitra Bhattacharya, Debdutta Basu, Analabha NPJ Biofilms Microbiomes Article The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has posed multiple challenges to global public health. Clinical features and sequela of SARS-CoV-2 infection include long-term and short-term complications often clinically indistinguishable from bacterial sepsis and acute lung infection. Post-hoc studies of previous SARS outbreaks postulate secondary bacterial infections with microbial dysbiosis. Oral microbial dysbiosis, particularly the altered proportion of Firmicutes and Proteobacteria, observed in other respiratory virus infection, like influenza, has shown to be associated with increased morbidity and mortality. Oropharynx and lung share similar kinds of bacterial species. We hypothesized that alteration in the Human Oropharyngeal Microbiome in SARS-CoV-2 patients can be a clinical indicator of bacterial infection related complications. We made a longitudinal comparison of oropharyngeal microbiome of 20 SARS-CoV-2 patients over a period of 30 days; at three time points, with a 15 days interval; contrasting them with a matched group of 10 healthy controls. Present observation indicates that posterior segment of the oropharyngeal microbiome is a key reservoir for bacteria causing pneumonia and chronic lung infection on SARS-CoV-2 infection. Oropharyngeal microbiome is indeed altered and its α-diversity decreases, indicating reduced stability, in all SARS-CoV-2 positive individuals right at Day-1; i.e. within ~24 h of post clinical diagnosis. The dysbiosis persists long-term (30 days) irrespective of viral clearance and/or administration of antibiotics. There is a severe depletion of commensal bacteria phyla like Firmicutes among the patients and that depletion is compensated by higher proportion of bacteria associated with sepsis and severe lung infection from phyla Proteobacteria. We also found elevated proportions of certain genus that have previously been shown to be causal for lung pneumonia in studies of model organisms and human autopsies’ including Stenotrophomonas, Acenetobactor, Enterobactor, Klebsiella and Chryseobacterium that were to be elevated among the cases. We also show that responses to the antibiotics (Azithromycin and Doxycycline) are not uniform for all individuals. Nature Publishing Group UK 2022-08-24 /pmc/articles/PMC9400563/ /pubmed/36002454 http://dx.doi.org/10.1038/s41522-022-00330-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Paine, Suman Kalyan
Rout, Usha Kiran
Bhattacharyya, Chandrika
Parai, Debaprasad
Alam, Mahabub
Nanda, Rasmi Ranjan
Tripathi, Devashish
Choudhury, Parveena
Kundu, Chanakya Nath
Pati, Sanghamitra
Bhattacharya, Debdutta
Basu, Analabha
Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title_full Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title_fullStr Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title_full_unstemmed Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title_short Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance
title_sort temporal dynamics of oropharyngeal microbiome among sars-cov-2 patients reveals continued dysbiosis even after viral clearance
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9400563/
https://www.ncbi.nlm.nih.gov/pubmed/36002454
http://dx.doi.org/10.1038/s41522-022-00330-y
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