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Xie L, Luo G, Yang Z, Wu WC, Chen J, Ren Y, Zeng Z, Ye G, Pan Y, Zhao WJ, Chen YQ, Hou W, Sun Y, Guo D, Yang Z, Li J, Holmes EC, Li Y, Chen L, Shi M. The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. J Infect 2024; 88:106118. [PMID: 38342382 DOI: 10.1016/j.jinf.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVES The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain. METHODS We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): "Healthy" (pseudotime 0), "Incremental" (pseudotime 1), "Critical" (pseudotime 2), "Complicated" (pseudotime 3), "Convalescent" (pseudotime 4), and "Long-term follow-up" (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes. RESULTS Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality. CONCLUSION This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.
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Affiliation(s)
- Linlin Xie
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gengyan Luo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhongzhou Yang
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei-Chen Wu
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jintao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yuting Ren
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhikun Zeng
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guangming Ye
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunbao Pan
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Jing Zhao
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Deying Guo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yirong Li
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Liangjun Chen
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Mang Shi
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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Tchoupou Saha OLF, Dubourg G, Yacouba A, Tola R, Raoult D, Lagier JC. Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants. Microb Pathog 2024; 188:106561. [PMID: 38307371 DOI: 10.1016/j.micpath.2024.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.
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Affiliation(s)
- Ornella La Fortune Tchoupou Saha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
| | - Abdourahamane Yacouba
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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3
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Nath S, Sarkar M, Maddheshiya A, De D, Paul S, Dey S, Pal K, Roy SK, Ghosh A, Sengupta S, Paine SK, Biswas NK, Basu A, Mukherjee S. Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups. Microbiol Spectr 2023; 11:e0236823. [PMID: 37905804 PMCID: PMC10715160 DOI: 10.1128/spectrum.02368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies. The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. However, although it has been known that different SARS-CoV-2 variants manifest distinct transmissibility and mortality rates in human populations, their effect on the composition and diversity of the URT microbiome has not been studied to date. Unlike the older variant (Delta), the newer variant (Omicron) have become more transmissible with lesser mortality and the symptoms have also changed significantly. Hence, in the present study, we have investigated the change in the URT microbiome associated with Delta and Omicron variants and identified variant-specific signatures that will be useful in the assessment of lung health and can be utilized for nasal probiotic therapy in the future.
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Affiliation(s)
- Shankha Nath
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Mousumi Sarkar
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Debjit De
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Shouvik Paul
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Souradeep Dey
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Kuhu Pal
- Department of Microbiology, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Suman Kr. Roy
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Ayan Ghosh
- Department of Community Medicine, College of Medicine and JNM Hospital, Kalyani, West Bengal, India
| | - Sharmila Sengupta
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Nidhan K. Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Souvik Mukherjee
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
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Abstract
The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.
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Affiliation(s)
- Sergio Candel
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Sylwia D. Tyrkalska
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Victoriano Mulero
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, Murcia, Spain,Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, Murcia, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain, Victoriano Mulero ; Sergio Candel ; Sylwia D. Tyrkalska Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB)-Pascual Parrilla, 30120, Murcia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
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5
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Li H, Wu X, Zeng H, Chang B, Cui Y, Zhang J, Wang R, Ding T. Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections. MICROBIOME 2023; 11:157. [PMID: 37482605 PMCID: PMC10364384 DOI: 10.1186/s40168-023-01597-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear. RESULTS Here, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens. CONCLUSIONS We found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections. Video Abstract.
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Affiliation(s)
- Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan, 528200, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Jingxiang Zhang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ruixia Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
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Zhang N, Mou D, Li T, Chen Z, Ma C, Liang L, He Q. Integrated analysis reveals important differences in the gut and oropharyngeal microbiota between children with mild and severe hand, foot and mouth disease. Emerg Microbes Infect 2023; 12:2192819. [PMID: 36927539 PMCID: PMC10071984 DOI: 10.1080/22221751.2023.2192819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Little is known about alternation and difference in gut microbiota between patients with mild and severe hand, foot and mouth disease (HFMD). We investigated the differences in gut and oropharynx microbiotas between mild and severe HFMD in young children and changes in bacterial profiles as the disease progresses from acute to convalescent phase. Forty-two patients with confirmed HFMD were studied, among which thirty-two had severe HFMD and ten had mild HFMD. First rectal swabs were collected from all patients at an average of 2 days (acute phase) after the onset of symptoms, and second rectal swabs were collected from 8 severe patients at day 9 (convalescent phase) after the onset. Oropharyngeal swabs were obtained from 10 patients in the acute phase and 6 in the convalescent phase. 16S rRNA sequencing was performed for all 70 samples. Compared with mild HFMD, severe HFMD exhibited significantly decreased diversity and richness of gut microbiota. Gut microbiota bacterial profiles observed in the acute and convalescent phases resembled each other, but differed from those in mild cases. Additionally, 50% of patients with severe HFMD in the acute phase harbored a dominant pathobiontic bacterial genus. However, none of patients with mild HFMD had such bacteria. Similar bacterial compositions in oropharynx microbiota were detected between mild and severe cases. Our findings indicate that severe HFMD exhibits significantly impaired diversity of gut microbiota and frequent gut and oropharyngeal inflammation-inducing bacteria. However, the results should be interpreted with caution as the number of the subjects was limited.
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Affiliation(s)
- Nan Zhang
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: )
| | - Danlei Mou
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Tongzeng Li
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Zhiyun Chen
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: )
| | - Chunhua Ma
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Lianchun Liang
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, No. 8 Xi TouTiao, You'an Men Wai, Feng Tai District, Beijing 100069, China (D.M.: ; T.L.: ; C.M.: ; L.L.: )
| | - Qiushui He
- Department of Medical Microbiology, Capital Medical University. No. 10 Xi Tou Tiao, You'an Meng Wai, Feng Tai District, Beijing 100069, China (N.Z.: ; Z.C.: ).,Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, Turku 20520, Finland (Q.H.: )
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7
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Xu X, Yang M, Jiang Y, Tao N, Fu Y, Fan J, Xu X, Shi H, Lu Z, Shen C. A new acridine-based photosensitizer with ultra-low light requirement efficiently inactivates carbapenem-resistant Acinetobacter baumannii and methicillin-resistant Staphylococcus aureus and degrades their antibiotic resistance genes. ENVIRONMENT INTERNATIONAL 2023; 173:107839. [PMID: 36822004 DOI: 10.1016/j.envint.2023.107839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
The spread of antibiotic resistant pathogens and antibiotic resistance genes (ARGs) in the environment poses a serious threat to public health. However, existing methods are difficult to effectively remove antibiotic resistant pathogens and ARGs from the environment. In this study, we synthesized a new acridine-based photosensitizer, 2,7-dibromo-9-mesityl-10-methylacridinium perchlorate (YM-3), by the heavy atom effect, which could photodynamically inactivate antibiotic resistant pathogens and reduce ARGs by generating singlet oxygen (1O2) in an aqueous environment. The 1O2 yield of YM-3 was 4.9 times that of its modified precursor. YM-3 could reduce the culturable number and even the viable counts of methicillin-resistant Staphylococcus aureus and carbapenem-resistant Acinetobacter baumannii to 0 (inactivation rate > 99.99999%) after 2 and 8 h of low-intensity blue light (15 W/m2) irradiation, respectively. After 20 h of light exposure, the copy numbers of ARGs in both bacteria were reduced by 5.80 and 4.48 log, respectively, which might indicate that ARGs had been degraded. In addition, YM-3 still had an efficient bactericidal effect after five inactivation cycle. These characteristics of ultra-low light intensity requirement and efficient bactericidal ability make YM-3 have good application prospects for disinfection in indoor and sunlight environment.
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Affiliation(s)
- Xiaojie Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Min Yang
- Department of Chemistry, Zhejiang University, Hangzhou 310058, PR China
| | - Yunhan Jiang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Ningyao Tao
- Zhejiang Key Laboratory of Drinking Water Safety and Distribution Technology, Zhejiang University, Hangzhou 310058, PR China
| | - Yulong Fu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Jiahui Fan
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Xin Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Huixiang Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China
| | - Zhan Lu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, PR China.
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, PR China.
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8
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Chen J, Liu X, Liu W, Yang C, Jia R, Ke Y, Guo J, Jia L, Wang C, Chen Y. Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity. J Med Virol 2022; 94:5284-5293. [PMID: 35838111 PMCID: PMC9349541 DOI: 10.1002/jmv.28002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022]
Abstract
Little is known about the characteristics of respiratory tract microbiome in Coronavirus disease 2019 (COVID-19) inpatients with different severity. We conducted a study that expected to clarify these characteristics as much as possible. A cross-sectional study was conducted to characterize respiratory tract microbial communities of 69 COVID-19 inpatients from 64 nasopharyngeal swabs and 5 sputum specimens using 16S ribosomal RNA gene V3-V4 region sequencing. The bacterial profiles were analyzed to find potential biomarkers by the two-step method, the combination of random forest model and the linear discriminant analysis effect size, and explore the connections with clinical characteristics by Spearman's rank test. Compared with mild COVID-19 patients, severe patients had significantly decreased bacterial diversity (p-values were less than 0.05 in the alpha and beta diversity) and relative lower abundance of opportunistic pathogens, including Actinomyces, Prevotella, Rothia, Streptococcus, Veillonella. Eight potential biomarkers including Treponema, Leptotrichia, Lachnoanaerobaculum, Parvimonas, Alloprevotella, Porphyromonas, Gemella, and Streptococcus were found to distinguish the mild COVID-19 patients from the severe COVID-19 patients. The genera of Actinomyces and Prevotella were negatively correlated with age in two groups. Intensive care unit admission, neutrophil count, and lymphocyte count were significantly correlated with different genera in the two groups. In addition, there was a positive correlation between Klebsiella and white blood cell count in two groups. The respiratory tract microbiome had significant differences in COVID-19 patients with different severity. The value of the respiratory tract microbiome as predictive biomarkers for COVID-19 severity deserves further exploration.
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Affiliation(s)
- Jiali Chen
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
- School of Public HealthChina Medical UniversityShenyangChina
| | - Xiong Liu
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Wei Liu
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Chaojie Yang
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Ruizhong Jia
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Yuehua Ke
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Jinpeng Guo
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Leili Jia
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Changjun Wang
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Yong Chen
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
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9
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Xia X, Chen J, Cheng Y, Chen F, Lu H, Liu J, Wang L, Pu F, Wang Y, Liu H, Cao D, Zhang Z, Xia Z, Fan M, Ling Z, Zhao L. Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study. Front Cell Infect Microbiol 2022; 12:1024867. [PMID: 36389135 PMCID: PMC9663837 DOI: 10.3389/fcimb.2022.1024867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022] Open
Abstract
Recent evidence suggests that lung microbiota can be recognized as one of the ecological determinants of various respiratory diseases. However, alterations in the lung microbiota and associated lung immunity in these respiratory diseases remain unclear. To compare the lung microbiota and lung immune profiles in common respiratory diseases, a total of 78 patients were enrolled in the present study, including 21 patients with primary pulmonary tuberculosis (PTB), eight patients with newly diagnosed lung cancer (LC), and 49 patients with community-acquired pneumonia (CAP). Bronchoalveolar lavage fluid (BALF) was collected for microbiota and cytokine analyses. With MiSeq sequencing system, increased bacterial alpha-diversity and richness were observed in patients with LC than in those with PTB and CAP. Linear discriminant analysis effect size revealed that CAP-associated pulmonary microbiota were significantly different between the PTB and LC groups. More key functionally different genera were found in the PTB and LC groups than in the CAP group. The interaction network revealed stronger positive and negative correlations among these genera in the LC group than in the other two groups. However, increased BALF cytokine profiles were observed in the PTB group than in the other two groups, while BALF cytokines were correlated with key functional bacteria. This comparative study provides evidence for the associations among altered lung microbiota, BALF inflammation, and different respiratory disorders, which provides insight into the possible roles and mechanisms of pulmonary microbiota in the progression of respiratory disorders.
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Affiliation(s)
- Xiaoxue Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Jiang Chen
- Department of Neurosurgery, Changxing People’s Hospital, Huzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Feng Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huoquan Lu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Jianfeng Liu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Ling Wang
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Fengxia Pu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Ying Wang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Hua Liu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Daxing Cao
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zhengye Zhang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zeping Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Meili Fan
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
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10
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Zhu Q, Zhou J, Li F, Shi P, Lu Y, Lin X, Yuan L, Zhuo Z, Shen J. Nasopharyngeal aspirates in children with severe community-acquired pneumonia collected within 3 days before bronchoscopy can partially reflect the pathogens in bronchoalveolar lavage fluids. BMC Infect Dis 2022; 22:814. [PMID: 36319953 PMCID: PMC9623994 DOI: 10.1186/s12879-022-07749-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND There is little evidence about consistency between nasopharyngeal and pulmonary pathogens in children with severe pneumonia. This study aims to compare the difference of pathogens between nasopharyngeal aspirates (NPAs) collected before bronchoscopy and bronchoalveolar lavage fluids (BALFs) in children with severe community-acquired pneumonia (SCAP). METHODS NPAs and BALFs were collected form pediatric SCAP cases hospitalized from January 2018 to March 2019. NPAs were colleced within 3 days before bronchoscopy. Samples were detected by direct immunofluorescence assay (DFA) for seven respiratory viruses and by routine bacterial culture in the clinical microbiology laboratory. Respiratory syncytial virus (RSV), Adenovirus (ADV), Influenza virus types A, B (IV-A and IV-B), Parainfluenza virus 1-3 (PIV1-3) were detected with a commercial assay. The virological and bacteriological detention results of NPAs were compared with the results of BALFs. RESULTS In total 204 cases with mean age of 3.4 ± 2.8 years (IQR, 1 month-14 years) were included in the study. Both NPA and BALF were collected from those cases. The positive rates of pathogen in NPAs and BALFs were 25.0% (51/204) and 36.7% (75/204), respectively (x2 = 6.614, P = 0.010). Respiratory viruses were found in 16.1% (33/204) from NPAs and 32.3% (66/204) from BALFs (x2 = 14.524, P < 0.001). RSV and ADV were the two most frequent detected viruses in NPAs and BALFs. High consistentcy of pathogens between NPAs and BALFs was observed, and 96.9% (32/33) viruses detected in NPAs were also found in BALFs. While bacteria were isolated from 12.7% (26/204) and 10.7% (22/204) of the two kinds of samples, respectively (x2 = 0.378, P = 0.539). In addition, Haemophilus influenzae (HI) was the dominant germ in both samples. CONCLUSION The DFA method used to detect seven respiratory viruses from NPAs collected within 3 days before bronchoscopy can partially reflect the pathogens in the lungs in children with SCAP.
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Affiliation(s)
- Qiguo Zhu
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Junli Zhou
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Fei Li
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Peng Shi
- Statistics and data management center, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yi Lu
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Xiaoliang Lin
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Lin Yuan
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Zhiqiang Zhuo
- Xiamen Children's Hospital, Xiamen Branch of children's Hospital of Fudan University, 361006, Xia Men, China
| | - Jun Shen
- Infectious Disease Department, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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11
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Alterations in the nasopharyngeal microbiota associated with active and latent tuberculosis. Tuberculosis (Edinb) 2022; 136:102231. [DOI: 10.1016/j.tube.2022.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/24/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022]
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