Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients
ABSTRACT Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease responsible for many infections worldwide. Differences in respiratory microbiota may correlate with disease severity. Samples were collected from 20 severe and 51 mild COVID-19 patients. High-throughput sequencing of th...
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-06-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01956-21 |
| _version_ | 1811333529762529280 |
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| author | Tian Qin Yajie Wang Jianping Deng BaoHong Xu Xiong Zhu Jitao Wang Haijian Zhou Na Zhao Fangfang Jin Hongyu Ren Huizhu Wang Qun Li Xinmin Xu Yumei Guo Ruihong Li Yanwen Xiong XiaoXia Wang Jiane Guo Han Zheng Xuexin Hou Kanglin Wan Jianzhong Zhang Jinxing Lu Biao Kan Jianguo Xu |
| author_facet | Tian Qin Yajie Wang Jianping Deng BaoHong Xu Xiong Zhu Jitao Wang Haijian Zhou Na Zhao Fangfang Jin Hongyu Ren Huizhu Wang Qun Li Xinmin Xu Yumei Guo Ruihong Li Yanwen Xiong XiaoXia Wang Jiane Guo Han Zheng Xuexin Hou Kanglin Wan Jianzhong Zhang Jinxing Lu Biao Kan Jianguo Xu |
| author_sort | Tian Qin |
| collection | DOAJ |
| description | ABSTRACT Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease responsible for many infections worldwide. Differences in respiratory microbiota may correlate with disease severity. Samples were collected from 20 severe and 51 mild COVID-19 patients. High-throughput sequencing of the 16S rRNA gene was used to analyze the bacterial community composition of the upper and lower respiratory tracts. The indices of diversity were analyzed. When one genus accounted for >50% of reads from a sample, it was defined as a super dominant pathobiontic bacterial genus (SDPG). In the upper respiratory tract, uniformity indices were significantly higher in the mild group than in the severe group (P < 0.001). In the lower respiratory tract, uniformity indices, richness indices, and the abundance-based coverage estimator were significantly higher in the mild group than in the severe group (P < 0.001). In patients with severe COVID-19, SDPGs were detected in 40.7% of upper and 63.2% of lower respiratory tract samples. In patients with mild COVID-19, only 10.8% of upper and 8.5% of lower respiratory tract samples yielded SDPGs. SDPGs were present in both upper and lower tracts in seven patients (35.0%), among which six (30.0%) patients possessed the same SDPG in the upper and lower tracts. However, no patients with mild infections had an SDPG in both tracts. Staphylococcus, Corynebacterium, and Acinetobacter were the main SDPGs. The number of SDPGs identified differed significantly between patients with mild and severe COVID-19 (P < 0.001). SDPGs in nasopharyngeal microbiota cause secondary bacterial infection in COVID-19 patients and aggravate pneumonia. IMPORTANCE The nasopharyngeal microbiota is composed of a variety of not only the true commensal bacterial species but also the two-face pathobionts, which are one a harmless commensal bacterial species and the other a highly invasive and deadly pathogen. In a previous study, we found that the diversity of nasopharyngeal microbiota was lost in severe influenza patients. We named the genus that accounted for over 50% of microbiota abundance as super dominant pathobiontic genus, which could invade to cause severe pneumonia, leading to high fatality. Similar phenomena were found here for SARS-CoV-2 infection. The diversity of nasopharyngeal microbiota was lost in severe COVID-19 infection patients. SDPGs in nasopharyngeal microbiota were frequently detected in severe COVID-19 patients. Therefore, the SDPGs in nasopharynx microbiota might invade into low respiratory and be responsible for secondary bacterial pneumonia in patients with SARS-CoV-2 infection. |
| first_indexed | 2024-04-13T16:54:03Z |
| format | Article |
| id | doaj.art-a0789bb8bdac4b72abe89c9919abdae7 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-13T16:54:03Z |
| publishDate | 2022-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-a0789bb8bdac4b72abe89c9919abdae72022-12-22T02:38:52ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-06-0110310.1128/spectrum.01956-21Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 PatientsTian Qin0Yajie Wang1Jianping Deng2BaoHong Xu3Xiong Zhu4Jitao Wang5Haijian Zhou6Na Zhao7Fangfang Jin8Hongyu Ren9Huizhu Wang10Qun Li11Xinmin Xu12Yumei Guo13Ruihong Li14Yanwen Xiong15XiaoXia Wang16Jiane Guo17Han Zheng18Xuexin Hou19Kanglin Wan20Jianzhong Zhang21Jinxing Lu22Biao Kan23Jianguo Xu24State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaBeijing Ditan Hospital, Capital Medical University, Beijing, ChinaCenters for Disease Control and Prevention of Zigong City, Zigong, ChinaCenters for Disease Control and Prevention of Shijiazhuang City, Shijiazhuang, ChinaCentral and Clinical Laboratory of Sanya People’s Hospital, Sanya, ChinaCenters for Disease Control and Prevention of Taiyuan City, Taiyuan, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaBeijing Ditan Hospital, Capital Medical University, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaBeijing Ditan Hospital, Capital Medical University, Beijing, ChinaCenters for Disease Control and Prevention of Zigong City, Zigong, ChinaBeijing Ditan Hospital, Capital Medical University, Beijing, ChinaCenters for Disease Control and Prevention of Shijiazhuang City, Shijiazhuang, ChinaBeijing Ditan Hospital, Capital Medical University, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaCentral and Clinical Laboratory of Sanya People’s Hospital, Sanya, ChinaCenters for Disease Control and Prevention of Taiyuan City, Taiyuan, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaState Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centers for Disease Control and Prevention, Beijing, ChinaABSTRACT Coronavirus disease 2019 (COVID-19) is a respiratory infectious disease responsible for many infections worldwide. Differences in respiratory microbiota may correlate with disease severity. Samples were collected from 20 severe and 51 mild COVID-19 patients. High-throughput sequencing of the 16S rRNA gene was used to analyze the bacterial community composition of the upper and lower respiratory tracts. The indices of diversity were analyzed. When one genus accounted for >50% of reads from a sample, it was defined as a super dominant pathobiontic bacterial genus (SDPG). In the upper respiratory tract, uniformity indices were significantly higher in the mild group than in the severe group (P < 0.001). In the lower respiratory tract, uniformity indices, richness indices, and the abundance-based coverage estimator were significantly higher in the mild group than in the severe group (P < 0.001). In patients with severe COVID-19, SDPGs were detected in 40.7% of upper and 63.2% of lower respiratory tract samples. In patients with mild COVID-19, only 10.8% of upper and 8.5% of lower respiratory tract samples yielded SDPGs. SDPGs were present in both upper and lower tracts in seven patients (35.0%), among which six (30.0%) patients possessed the same SDPG in the upper and lower tracts. However, no patients with mild infections had an SDPG in both tracts. Staphylococcus, Corynebacterium, and Acinetobacter were the main SDPGs. The number of SDPGs identified differed significantly between patients with mild and severe COVID-19 (P < 0.001). SDPGs in nasopharyngeal microbiota cause secondary bacterial infection in COVID-19 patients and aggravate pneumonia. IMPORTANCE The nasopharyngeal microbiota is composed of a variety of not only the true commensal bacterial species but also the two-face pathobionts, which are one a harmless commensal bacterial species and the other a highly invasive and deadly pathogen. In a previous study, we found that the diversity of nasopharyngeal microbiota was lost in severe influenza patients. We named the genus that accounted for over 50% of microbiota abundance as super dominant pathobiontic genus, which could invade to cause severe pneumonia, leading to high fatality. Similar phenomena were found here for SARS-CoV-2 infection. The diversity of nasopharyngeal microbiota was lost in severe COVID-19 infection patients. SDPGs in nasopharyngeal microbiota were frequently detected in severe COVID-19 patients. Therefore, the SDPGs in nasopharynx microbiota might invade into low respiratory and be responsible for secondary bacterial pneumonia in patients with SARS-CoV-2 infection.https://journals.asm.org/doi/10.1128/spectrum.01956-21pathobiontic bacterianasopharyngeal microbiotasecondary bacterial infectionCOVID-19 |
| spellingShingle | Tian Qin Yajie Wang Jianping Deng BaoHong Xu Xiong Zhu Jitao Wang Haijian Zhou Na Zhao Fangfang Jin Hongyu Ren Huizhu Wang Qun Li Xinmin Xu Yumei Guo Ruihong Li Yanwen Xiong XiaoXia Wang Jiane Guo Han Zheng Xuexin Hou Kanglin Wan Jianzhong Zhang Jinxing Lu Biao Kan Jianguo Xu Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients Microbiology Spectrum pathobiontic bacteria nasopharyngeal microbiota secondary bacterial infection COVID-19 |
| title | Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients |
| title_full | Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients |
| title_fullStr | Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients |
| title_full_unstemmed | Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients |
| title_short | Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients |
| title_sort | super dominant pathobiontic bacteria in the nasopharyngeal microbiota cause secondary bacterial infection in covid 19 patients |
| topic | pathobiontic bacteria nasopharyngeal microbiota secondary bacterial infection COVID-19 |
| url | https://journals.asm.org/doi/10.1128/spectrum.01956-21 |
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