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Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections

This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COV...

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Autores principales: Zhou, Yongzhao, Lu, Sifen, Wei, Xiaozhen, Hu, Ya, Li, Honghao, Wang, Jing, Lin, Yifei, Li, Mengjiao, Wang, Minjin, Ma, Jinmin, Zhu, Zhongyi, Yang, Shengying, Ying, Binwu, Zhang, Wengeng, Chen, Bojiang, Li, Weimin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9856197/
https://www.ncbi.nlm.nih.gov/pubmed/36671391
http://dx.doi.org/10.3390/biom13010006
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author Zhou, Yongzhao
Lu, Sifen
Wei, Xiaozhen
Hu, Ya
Li, Honghao
Wang, Jing
Lin, Yifei
Li, Mengjiao
Wang, Minjin
Ma, Jinmin
Zhu, Zhongyi
Yang, Shengying
Ying, Binwu
Zhang, Wengeng
Chen, Bojiang
Li, Weimin
author_facet Zhou, Yongzhao
Lu, Sifen
Wei, Xiaozhen
Hu, Ya
Li, Honghao
Wang, Jing
Lin, Yifei
Li, Mengjiao
Wang, Minjin
Ma, Jinmin
Zhu, Zhongyi
Yang, Shengying
Ying, Binwu
Zhang, Wengeng
Chen, Bojiang
Li, Weimin
author_sort Zhou, Yongzhao
collection PubMed
description This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.
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spelling pubmed-98561972023-01-21 Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections Zhou, Yongzhao Lu, Sifen Wei, Xiaozhen Hu, Ya Li, Honghao Wang, Jing Lin, Yifei Li, Mengjiao Wang, Minjin Ma, Jinmin Zhu, Zhongyi Yang, Shengying Ying, Binwu Zhang, Wengeng Chen, Bojiang Li, Weimin Biomolecules Article This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19. MDPI 2022-12-20 /pmc/articles/PMC9856197/ /pubmed/36671391 http://dx.doi.org/10.3390/biom13010006 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhou, Yongzhao
Lu, Sifen
Wei, Xiaozhen
Hu, Ya
Li, Honghao
Wang, Jing
Lin, Yifei
Li, Mengjiao
Wang, Minjin
Ma, Jinmin
Zhu, Zhongyi
Yang, Shengying
Ying, Binwu
Zhang, Wengeng
Chen, Bojiang
Li, Weimin
Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title_full Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title_fullStr Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title_full_unstemmed Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title_short Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections
title_sort metatranscriptomic analysis reveals disordered alterations in oropharyngeal microbiome during the infection and clearance processes of sars-cov-2: a warning for secondary infections
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9856197/
https://www.ncbi.nlm.nih.gov/pubmed/36671391
http://dx.doi.org/10.3390/biom13010006
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