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Atencio LA, Quintero IJ, Almanza A, Eskildsen G, Sánchez-Gallego J, Herrera M, Fernández-Marín H, Loaiza JR, Mejía LC. Insights into the Naso-Oropharyngeal Bacterial Composition in Suspected SARS-CoV-2 Cases. Pathogens 2024; 13:615. [PMID: 39204216 PMCID: PMC11357247 DOI: 10.3390/pathogens13080615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 09/03/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. While research on COVID-19 has mainly focused on its epidemiology, pathogenesis, and treatment, studies on the naso-oropharyngeal microbiota have emerged in the last few years as an overlooked area of research. Here, we analyzed the bacterial community composition of the naso-oropharynx in 50 suspected SARS-CoV-2 cases (43 detected, 7 not detected) from Veraguas province (Panama) distributed across five age categories. Statistical analysis revealed no significant differences (p < 0.05) in bacterial alpha and beta diversities between the groups categorized by SARS-CoV-2 test results, age, or patient status. The genera Corynebacterium, Staphylococcus, Prevotella, Streptococcus, and Tepidiphilus were the most abundant in both detected and not-detected SARS-CoV-2 group. The linear discriminant analysis effect size (LEfSe) for biomarker exploration indicated that Veillonella and Prevotella were enriched in detected and hospitalized patients with SARS-CoV-2 relative to non-detected patients, while Thermoanaerobacterium and Haemophilus were enriched in non-detected patients with SARS-CoV-2. The results also indicated that the genus Corynebacterium was found to decrease in patients with detected SARS-CoV-2 relative to those with non-detected SARS-CoV-2. Understanding the naso-oropharyngeal microbiota provides insights into the diversity, composition, and resilience of the microbial community in patients with SARS-CoV-2.
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Affiliation(s)
- Librada A. Atencio
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
| | - Indira J. Quintero
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
| | - Alejandro Almanza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
| | - Gilberto Eskildsen
- Departamento de Microbiología Humana, Facultad de Medicina, Universidad de Panamá, Panama City 0819-07289, Panama;
| | - Joel Sánchez-Gallego
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA;
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
| | | | - Hermógenes Fernández-Marín
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
- Sistema Nacional de Investigación (SNI), Secretaría Nacional de Ciencia, Tecnología, e Innovación (SENACYT), Panama City 0816-02852, Panama
| | - José R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
- Sistema Nacional de Investigación (SNI), Secretaría Nacional de Ciencia, Tecnología, e Innovación (SENACYT), Panama City 0816-02852, Panama
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (I.J.Q.); (A.A.); (H.F.-M.)
- Sistema Nacional de Investigación (SNI), Secretaría Nacional de Ciencia, Tecnología, e Innovación (SENACYT), Panama City 0816-02852, Panama
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- Departamento de Genética y Biología Molecular, Universidad de Panamá, Estafeta Universitaria Apartado 3366, Zona 4, Panama City 0819-07289, Panama
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Galeana-Cadena D, Ramirez-Martínez G, Alberto Choreño-Parra J, Silva-Herzog E, Margarita Hernández-Cárdenas C, Soberón X, Zúñiga J. Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity. Heliyon 2024; 10:e31562. [PMID: 38826746 PMCID: PMC11141365 DOI: 10.1016/j.heliyon.2024.e31562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024] Open
Abstract
Background The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome. Methods We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages. Results The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of Lawsonella and Cutibacterium genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of Streptococcus, Actinomyces, Peptostreptococcus, Atopobium, Granulicatella, Mogibacterium, Veillonella, Prevotella_7, Rothia, Gemella, Alloprevotella, and Solobacterium genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of Staphylococcus, Corynebacterium, and Streptococcus. Conclusions Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.
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Affiliation(s)
- David Galeana-Cadena
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gustavo Ramirez-Martínez
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - José Alberto Choreño-Parra
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
| | - Eugenia Silva-Herzog
- Unidad de Vinculación Científica Facultad de Medicina UNAM-INMEGEN, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Carmen Margarita Hernández-Cárdenas
- Unidad de Cuidados Intensivos y Dirección General, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Ciudad de México, Mexico
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Joaquín Zúñiga
- Laboratorio de Inmunobiología y Genética, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas (INER), Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
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Aljabr W, Dandachi I, Abbas B, Karkashan A, Al-Amari A, AlShahrani D. Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities. Microbiol Spectr 2024; 12:e0416623. [PMID: 38557102 PMCID: PMC11237758 DOI: 10.1128/spectrum.04166-23] [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: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.
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Affiliation(s)
- Waleed Aljabr
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iman Dandachi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Basma Abbas
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Alaa Karkashan
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Ahod Al-Amari
- Department of Basic Medical Sciences, College of Medicine, Dar Al-Uloom University, Riyadh, Saudi Arabia
| | - Dayel AlShahrani
- Pediatric infectious diseases, King Fahad Medical City, Riyadh, Saudi Arabia
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Quinn-Bohmann N, Freixas-Coutin JA, Seo J, Simmons R, Diener C, Gibbons SM. Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC Biol 2024; 22:93. [PMID: 38654335 PMCID: PMC11040984 DOI: 10.1186/s12915-024-01887-0] [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: 09/02/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult. RESULTS In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex, and geographic location, in order to isolate these associations from health and disease states. CONCLUSIONS We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.
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Affiliation(s)
- Nick Quinn-Bohmann
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, 98195, USA.
| | | | - Jin Seo
- Reckitt Health US LLC, 1 Philips Pkwy, Montvale, NJ, 07645, USA
| | - Ruth Simmons
- Reckitt Benckiser Healthcare Ltd, 105 Bath Road, Slough, Berkshire, SL1 3UH, UK
| | | | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, 98195, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- eScience Institute, University of Washington, Seattle, WA, 98195, USA.
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Žuštra A, Leonard VR, Holland LA, Hu JC, Mu T, Holland SC, Wu LI, Begnel ER, Ojee E, Chohan BH, Richardson BA, Kinuthia J, Wamalwa D, Slyker J, Lehman DA, Gantt S, Lim ES. Longitudinal dynamics of the nasopharyngal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their infants. RESEARCH SQUARE 2024:rs.3.rs-4257641. [PMID: 38699359 PMCID: PMC11065085 DOI: 10.21203/rs.3.rs-4257641/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest and of clinical relevance. The impact of SARS-CoV-2, the etiological agent of the Coronavirus Disease 2019 (COVID-19) pandemic, on the nasopharyngeal microbiome, particularly among individuals living with HIV, is not fully characterized. Here we describe the nasopharyngeal microbiome before, during and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their infants (18 HIV-exposed, uninfected and 18 HIV-unexposed, uninfected), followed between September 2021 through March 2022. We show using genomic epidemiology that mother and infant dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. Additionally, we used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and infants infected with SARS-CoV-2, 6 infants negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint matched SARS-CoV-2 negative mothers and infants. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- and long-term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and infants had significantly different microbiome composition and bacterial load (p-values <.0001). However, in both mothers and infants, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV-exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.
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6
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Song HH, Choi JC, Lee R, Yoon SK, Park HJ, Shin YH, Shin JW, Kim J. Quality and composition of archived nucleic acids after use in SARS-CoV-2 molecular testing. Clin Chim Acta 2024; 554:117755. [PMID: 38182077 DOI: 10.1016/j.cca.2023.117755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 11/27/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Reverse transcription real-time PCR (rRT-PCR) has been a gold-standard method to detect SARS-CoV-2, for which quality assessment of nucleic acids (NAs) is not needed. In order to prepare for future use, we evaluated NA quality from archived SARS-CoV-2 rRT-PCR samples. METHODS NA samples were collected in February 2021 and extracted using the QIAamp DSP Virus Spin Kit, (53 SARS-CoV-2-positive and 100 SARS-CoV-2-negative). Quality, quantity, and purity of NA were measured spectrophotometrically or fluorescently. Droplet digital PCR was used to characterize the double strand DNA (dsDNA) origin and composition by quantifying 16S rDNA and RPP30. RESULTS The RIN and purity were not significantly different between groups (p = 0.3828). RNA quantity was significantly higher than dsDNA in both groups (p < 0.0001); both dsDNA and RNA quantity were significantly higher in positive samples (dsDNA, RNA p = 0.021). For dsDNA, 16S rDNA copies were significantly greater than RPP30 in both groups (p < 0.0001), and RPP30 were significantly higher in positive samples (p < 0.0001). CONCLUSIONS Archived NA quality after SARS-CoV-2 rRT-PCR was guaranteed for subsequent molecular research using human or bacterial DNA, especially for short targets.
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Affiliation(s)
- Ho Hyun Song
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Asan, Chungcheongnam-do, Republic of Korea
| | - Jong Cheul Choi
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Ran Lee
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Sook Kyung Yoon
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Hye Jeong Park
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Young Hee Shin
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Jeong Won Shin
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea.
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea.
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7
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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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9
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Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I, Di Camillo B. Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + . Sci Rep 2023; 13:16867. [PMID: 37803040 PMCID: PMC10558486 DOI: 10.1038/s41598-023-43040-x] [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: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023] Open
Abstract
The outbreak of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, forced us to face a pandemic with unprecedented social, economic, and public health consequences. Several nations have launched campaigns to immunize millions of people using various vaccines to prevent infections. Meanwhile, therapeutic approaches and discoveries continuously arise; however, identifying infected patients that are going to experience the more severe outcomes of COVID-19 is still a major need, to focus therapeutic efforts, reducing hospitalization and mitigating drug adverse effects. Microbial communities colonizing the respiratory tract exert significant effects on host immune responses, influencing the susceptibility to infectious agents. Through 16S rDNAseq we characterized the upper airways' microbiota of 192 subjects with nasopharyngeal swab positive for SARS-CoV-2. Patients were divided into groups based on the presence of symptoms, pneumonia severity, and need for oxygen therapy or intubation. Indeed, unlike most of the literature, our study focuses on identifying microbial signatures predictive of disease progression rather than on the probability of infection itself, for which a consensus is lacking. Diversity, differential abundance, and network analysis at different taxonomic levels were synergistically adopted, in a robust bioinformatic pipeline, highlighting novel possible taxa correlated with patients' disease progression to intubation.
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Affiliation(s)
- Massimo Bellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Marco Cappellato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Francesca Longhin
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Giuseppina Brancaccio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Anna Maria Cattelan
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Infectious Diseases Unit, University Hospital Padova, 35128, Padova, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Claudio Salaris
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Microbiology and Virology Unit, University Hospital Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (PD), Italy.
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Reuben RC, Beugnon R, Jurburg SD. COVID-19 alters human microbiomes: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1211348. [PMID: 37600938 PMCID: PMC10433767 DOI: 10.3389/fcimb.2023.1211348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential. Methods We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries. Results Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma. Discussion Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Rémy Beugnon
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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11
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Kim JG, Zhang A, Rauseo AM, Goss CW, Mudd PA, O'Halloran JA, Wang L. The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity. J Med Virol 2023; 95:e28445. [PMID: 36583481 PMCID: PMC9880756 DOI: 10.1002/jmv.28445] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID-19), we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.
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Affiliation(s)
- Josh G. Kim
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Ai Zhang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Adriana M. Rauseo
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Charles W. Goss
- Division of BiostatisticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Philip A. Mudd
- Department of Emergency MedicineWashington University School of MedicineSt. LouisMissouriUSA
| | - Jane A. O'Halloran
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Leyao Wang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
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12
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SeyedAlinaghi S, Afzalian A, Pashaei Z, Varshochi S, Karimi A, Mojdeganlou H, Mojdeganlou P, Razi A, Ghanadinezhad F, Shojaei A, Amiri A, Dashti M, Ghasemzadeh A, Dadras O, Mehraeen E, Afsahi AM. Gut microbiota and COVID-19: A systematic review. Health Sci Rep 2023; 6:e1080. [PMID: 36721396 PMCID: PMC9881458 DOI: 10.1002/hsr2.1080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/24/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Background and Aims Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS-CoV-2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS-CoV-2 infection and its severity and the impact that SARS-CoV-2 could have on the gut microbiota. Methods We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full-text screening. The data of the eligible studies were extracted into a pre-designed word table. This study adhered to the PRISMA checklist and Newcastle-Ottawa Scale Bias Assessment tool. Results Sixty-three publications were included in this review. Our study shows that among COVID-19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID-19 disease would probably also be influenced by the gut, and lung microbiota's composition. Conclusion Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID-19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID-19 and human microbiome.
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Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Arian Afzalian
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Zahra Pashaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Sanaz Varshochi
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | | | - Armin Razi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | - Alireza Shojaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Ava Amiri
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Mohsen Dashti
- Department of RadiologyTabriz University of Medical SciencesTabrizIran
| | | | - Omid Dadras
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
- Department of Global Public Health and Primary CareUniversity of BergenBergenNorway
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyKhalkhal University of Medical SciencesKhalkhalIran
| | - Amir Masoud Afsahi
- Department of RadiologyUniversity of California, San Diego (UCSD)CaliforniaUSA
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13
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Hoque MN, Rahman MS, Sarkar MMH, Habib MA, Akter S, Banu TA, Goswami B, Jahan I, Hossain MA, Khan MS, Islam T. Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients. PLoS One 2023; 18:e0278134. [PMID: 36656835 PMCID: PMC9851516 DOI: 10.1371/journal.pone.0278134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/09/2022] [Indexed: 01/20/2023] Open
Abstract
We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - M. Anwar Hossain
- Jashore Unive rsity of Science and Technology, Jashore, Bangladesh
| | - M. Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhanmondi, Dhaka, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur, Bangladesh
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14
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Crovetto F, Selma-Royo M, Crispi F, Carbonetto B, Pascal R, Larroya M, Casas I, Tortajada M, Escudero N, Muñoz-Almagro C, Gomez-Roig MD, González-Torres P, Collado MC, Gratacos E. Nasopharyngeal microbiota profiling of pregnant women with SARS-CoV-2 infection. Sci Rep 2022; 12:13404. [PMID: 35927569 PMCID: PMC9352760 DOI: 10.1038/s41598-022-17542-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/27/2022] [Indexed: 12/18/2022] Open
Abstract
We aimed to analyze the nasopharyngeal microbiota profiles in pregnant women with and without SARS-CoV-2 infection, considered a vulnerable population during COVID-19 pandemic. Pregnant women were enrolled from a multicenter prospective population-based cohort during the first SARS-CoV-2 wave in Spain (March-June 2020 in Barcelona, Spain) in which the status of SARS-CoV-2 infection was determined by nasopharyngeal RT–PCR and antibodies in peripheral blood. Women were randomly selected for this cross-sectional study on microbiota. DNA was extracted from nasopharyngeal swab samples, and the V3-V4 region of the 16S rRNA of bacteria was amplified using region-specific primers. The differential abundance of taxa was tested, and alpha/beta diversity was evaluated. Among 76 women, 38 were classified as positive and 38 as negative for SARS-CoV-2 infection. All positive women were diagnosed by SARS-CoV-2 IgG and IgM/IgA antibodies, and 14 (37%) also had a positive RT–PCR. The overall composition of the nasopharyngeal microbiota differ in pregnant women with SARS-CoV-2 infection (positive SARS-CoV-2 antibodies), compared to those without the infection (negative SARS-CoV-2 antibodies) (p = 0.001), with a higher relative abundance of the Tenericutes and Bacteroidetes phyla and a higher abundance of the Prevotellaceae family. Infected women presented a different pattern of microbiota profiling due to beta diversity and higher richness (observed ASV < 0.001) and evenness (Shannon index < 0.001) at alpha diversity. These changes were also present in women after acute infection, as revealed by negative RT–PCR but positive SARS-CoV-2 antibodies, suggesting a potential association between SARS-CoV-2 infection and long-lasting shift in the nasopharyngeal microbiota. No significant differences were reported in mild vs. severe cases. This is the first study on nasopharyngeal microbiota during pregnancy. Pregnant women with SARS-CoV-2 infection had a different nasopharyngeal microbiota profile compared to negative cases.
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Affiliation(s)
- Francesca Crovetto
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain. .,Institut de Recerca Sant Joan de Deu, Barcelona, Spain. .,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain.
| | - Marta Selma-Royo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Fàtima Crispi
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca August Pi Sunyer, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases, Barcelona, Spain
| | | | - Rosalia Pascal
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Larroya
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Irene Casas
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Marta Tortajada
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | | | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Ciber of Epidemiology and Public Health (CIBERESP), Madrid, Spain.,Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Maria Dolores Gomez-Roig
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin (RICORS), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Eduard Gratacos
- Department of Maternal-Fetal Medicine, BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, Universitat de Barcelona, Passeig de Sant Joan de Déu 2, 08950, Esplugues de Llobregat, Barcelona, Spain.,Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Institut de Recerca August Pi Sunyer, Barcelona, Spain.,Center for Biomedical Network Research on Rare Diseases, Barcelona, Spain
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15
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Rocafort M, Henares D, Brotons P, Launes C, Fernandez de Sevilla M, Fumado V, Barrabeig I, Arias S, Redin A, Ponomarenko J, Mele M, Millat-Martinez P, Claverol J, Balanza N, Mira A, Garcia-Garcia JJ, Bassat Q, Jordan I, Muñoz-Almagro C. Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home. Viruses 2022; 14:v14071521. [PMID: 35891502 PMCID: PMC9315980 DOI: 10.3390/v14071521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023] Open
Abstract
The increased incidence of COVID-19 cases and deaths in Spain in March 2020 led to the declaration by the Spanish government of a state of emergency imposing strict confinement measures on the population. The objective of this study was to characterize the nasopharyngeal microbiota of children and adults and its relation to SARS-CoV-2 infection and COVID-19 severity during the pandemic lockdown in Spain. This cross-sectional study included family households located in metropolitan Barcelona, Spain, with one adult with a previous confirmed COVID-19 episode and one or more exposed co-habiting child contacts. Nasopharyngeal swabs were used to determine SARS-CoV-2 infection status, characterize the nasopharyngeal microbiota and determine common respiratory DNA/RNA viral co-infections. A total of 173 adult cases and 470 exposed children were included. Overall, a predominance of Corynebacterium and Dolosigranulum and a limited abundance of common pathobionts including Haemophilus and Streptococcus were found both among adults and children. Children with current SARS-CoV-2 infection presented higher bacterial richness and increased Fusobacterium, Streptococcus and Prevotella abundance than non-infected children. Among adults, persistent SARS-CoV-2 RNA was associated with an increased abundance of an unclassified member of the Actinomycetales order. COVID-19 severity was associated with increased Staphylococcus and reduced Dolosigranulum abundance. The stringent COVID-19 lockdown in Spain had a significant impact on the nasopharyngeal microbiota of children, reflected in the limited abundance of common respiratory pathobionts and the predominance of Corynebacterium, regardless of SARS-CoV-2 detection. COVID-19 severity in adults was associated with decreased nasopharynx levels of healthy commensal bacteria.
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Affiliation(s)
- Muntsa Rocafort
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Desiree Henares
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Mariona Fernandez de Sevilla
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Victoria Fumado
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Irene Barrabeig
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Epidemiological Surveillance Unit, Department of Health, Generalitat de Catalunya, 08907 Barcelona, Spain
| | - Sara Arias
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alba Redin
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Maria Mele
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Pere Millat-Martinez
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Joana Claverol
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
| | - Nuria Balanza
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain
| | - Juan J. Garcia-Garcia
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Quique Bassat
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain; (S.A.); (P.M.-M.); (N.B.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça Maputo 1929, Mozambique
| | - Iolanda Jordan
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Pediatrics Department, Hospital Sant Joan de Déu, Universitat de Barcelona, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Déu (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain; (M.R.); (D.H.); (P.B.); (C.L.); (M.F.d.S.); (V.F.); (A.R.); (M.M.); (J.C.); (J.J.G.-G.); (I.J.)
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain; (I.B.); (A.M.); (Q.B.)
- Medicine Department, Universitat Internacional de Catalunya, Sant Cugat, 08195 Barcelona, Spain
- Correspondence: ; Tel.: +34-673302405; Fax: +34-932803626
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16
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Rovito R, Augello M, Ben-Haim A, Bono V, d'Arminio Monforte A, Marchetti G. Hallmarks of Severe COVID-19 Pathogenesis: A Pas de Deux Between Viral and Host Factors. Front Immunol 2022; 13:912336. [PMID: 35757770 PMCID: PMC9231592 DOI: 10.3389/fimmu.2022.912336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
Two years into Coronavirus Disease 2019 (COVID-19) pandemic, a comprehensive characterization of the pathogenesis of severe and critical forms of COVID-19 is still missing. While a deep dysregulation of both the magnitude and functionality of innate and adaptive immune responses have been described in severe COVID-19, the mechanisms underlying such dysregulations are still a matter of scientific debate, in turn hampering the identification of new therapies and of subgroups of patients that would most benefit from individual clinical interventions. Here we review the current understanding of viral and host factors that contribute to immune dysregulation associated with COVID-19 severity in the attempt to unfold and broaden the comprehension of COVID-19 pathogenesis and to define correlates of protection to further inform strategies of targeted therapeutic interventions.
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Affiliation(s)
- Roberta Rovito
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Matteo Augello
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Assaf Ben-Haim
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Antonella d'Arminio Monforte
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
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17
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Prasad P, Mahapatra S, Mishra R, Murmu KC, Aggarwal S, Sethi M, Mohapatra P, Ghosh A, Yadav R, Dodia H, Ansari SA, De S, Singh D, Suryawanshi A, Dash R, Senapati S, Beuria TK, Chattopadhyay S, Syed GH, Swain R, Raghav SK, Parida A. Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: a potential source of co-infection. Mol Omics 2022; 18:490-505. [PMID: 35506682 DOI: 10.1039/d2mo00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown alterations in nasopharyngeal (NP) microbial diversity, enrichment of opportunistic pathogens and their role in co-infections during respiratory infections. Therefore, we hypothesized that microbial diversity changes, with increase in the population of opportunistic pathogens, during SARS-CoV2 infection in the nasopharynx, which may be involved in co-infection in COVID-19 patients. The 16S rRNA variable regions, V1-V9, of NP samples of control and COVID-19 (symptomatic and asymptomatic) patients were sequenced using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis for determining alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index were used to analyze the control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in the COVID-19 NP microbiome with an increase in the abundance of opportunistic pathogens at genus and species levels in asymptomatic/symptomatic patients. The significant abundance of Mycobacteria spp. and Mycoplasma spp. in symptomatic patients suggests their association and role in co-infections in COVID-19 patients. Furthermore, we found strong correlation of enrichment of Mycobacteria and Mycoplasma with the occurrences of chest pain and fever in symptomatic COVID-19 patients. This is the first study from India to show the abundance of Mycobacteria and Mycoplasma opportunistic pathogens in non-hospitalized COVID-19 patients and their relationship with symptoms, indicating the possibility of co-infections.
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Affiliation(s)
- Punit Prasad
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Soumendu Mahapatra
- Institute of Life Sciences, Bhubaneswar, Odisha, India. .,Kalinga Institute of Industrial Technology (KIIT), School of Biotechnology, Bhubaneswar, Odisha, India
| | | | | | | | - Manisha Sethi
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Arup Ghosh
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Rina Yadav
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Hiren Dodia
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Saikat De
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Deepak Singh
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Rupesh Dash
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | | | | | | | - Rajeeb Swain
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | | | - Ajay Parida
- Institute of Life Sciences, Bhubaneswar, Odisha, India.
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18
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Giugliano R, Sellitto A, Ferravante C, Rocco T, D'Agostino Y, Alexandrova E, Lamberti J, Palumbo D, Galdiero M, Vaccaro E, Pagliano P, Weisz A, Giurato G, Franci G, Rizzo F. NGS analysis of nasopharyngeal microbiota in SARS-CoV-2 positive patients during the first year of the pandemic in the Campania Region of Italy. Microb Pathog 2022; 165:105506. [PMID: 35358660 PMCID: PMC8958261 DOI: 10.1016/j.micpath.2022.105506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/26/2022] [Indexed: 11/27/2022]
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19
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Shilts MH, Rosas-Salazar C, Strickland BA, Kimura KS, Asad M, Sehanobish E, Freeman MH, Wessinger BC, Gupta V, Brown HM, Boone HH, Patel V, Barbi M, Bottalico D, O’Neill M, Akbar N, Rajagopala SV, Mallal S, Phillips E, Turner JH, Jerschow E, Das SR. Severe COVID-19 Is Associated With an Altered Upper Respiratory Tract Microbiome. Front Cell Infect Microbiol 2022; 11:781968. [PMID: 35141167 PMCID: PMC8819187 DOI: 10.3389/fcimb.2021.781968] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background The upper respiratory tract (URT) is the portal of entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-CoV-2 likely interacts with the URT microbiome. However, understanding of the associations between the URT microbiome and the severity of coronavirus disease 2019 (COVID-19) is still limited. Objective Our primary objective was to identify URT microbiome signature/s that consistently changed over a spectrum of COVID-19 severity. Methods Using data from 103 adult participants from two cities in the United States, we compared the bacterial load and the URT microbiome between five groups: 20 asymptomatic SARS-CoV-2-negative participants, 27 participants with mild COVID-19, 28 participants with moderate COVID-19, 15 hospitalized patients with severe COVID-19, and 13 hospitalized patients in the ICU with very severe COVID-19. Results URT bacterial load, bacterial richness, and within-group microbiome composition dissimilarity consistently increased as COVID-19 severity increased, while the relative abundance of an amplicon sequence variant (ASV), Corynebacterium_unclassified.ASV0002, consistently decreased as COVID-19 severity increased. Conclusions We observed that the URT microbiome composition significantly changed as COVID-19 severity increased. The URT microbiome could potentially predict which patients may be more likely to progress to severe disease or be modified to decrease severity. However, further research in additional longitudinal cohorts is needed to better understand how the microbiome affects COVID-19 severity.
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Affiliation(s)
- Meghan H. Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christian Rosas-Salazar
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Britton A. Strickland
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Kyle S. Kimura
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mohammad Asad
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Esha Sehanobish
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Michael H. Freeman
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bronson C. Wessinger
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Veerain Gupta
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Hunter M. Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Helen H. Boone
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Viraj Patel
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mali Barbi
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Danielle Bottalico
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meaghan O’Neill
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | - Nadeem Akbar
- Department of Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, United States
| | | | - Simon Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Justin H. Turner
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Elina Jerschow
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Suman R. Das
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
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20
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Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients: a retrospective cohort study in a Mediterranean area. J Infect 2021; 84:329-336. [PMID: 34963638 PMCID: PMC8709923 DOI: 10.1016/j.jinf.2021.12.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/08/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022]
Abstract
This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. To study the microbiota, we utilized 16S rRNA sequencing of 177 samples that came from a retrospective cohort of COVID-19 hospitalized patients. Raw sequences were processed by QIIME2. The associations between microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression, adjusted for age, gender, and comorbidity. The microbiota α diversity indexes were lower in patients with a fatal outcome, whereas the β diversity analysis showed a significant clustering in these patients. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduction of more than 90% of IMV. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalized COVID-19 patients.
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21
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Hernández-Terán A, Mejía-Nepomuceno F, Herrera MT, Barreto O, García E, Castillejos M, Boukadida C, Matias-Florentino M, Rincón-Rubio A, Avila-Rios S, Mújica-Sánchez M, Serna-Muñoz R, Becerril-Vargas E, Guadarrama-Pérez C, Ahumada-Topete VH, Rodríguez-Llamazares S, Martínez-Orozco JA, Salas-Hernández J, Pérez-Padilla R, Vázquez-Pérez JA. Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes. Sci Rep 2021; 11:21297. [PMID: 34716394 PMCID: PMC8556282 DOI: 10.1038/s41598-021-00851-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/18/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 outbreak has caused over three million deaths worldwide. Understanding the pathology of the disease and the factors that drive severe and fatal clinical outcomes is of special relevance. Studying the role of the respiratory microbiota in COVID-19 is especially important as the respiratory microbiota is known to interact with the host immune system, contributing to clinical outcomes in chronic and acute respiratory diseases. Here, we characterized the microbiota in the respiratory tract of patients with mild, severe, or fatal COVID-19, and compared it to healthy controls and patients with non-COVID-19-pneumonia. We comparatively studied the microbial composition, diversity, and microbiota structure between the study groups and correlated the results with clinical data. We found differences in the microbial composition for COVID-19 patients, healthy controls, and non-COVID-19 pneumonia controls. In particular, we detected a high number of potentially opportunistic pathogens associated with severe and fatal levels of the disease. Also, we found higher levels of dysbiosis in the respiratory microbiota of patients with COVID-19 compared to the healthy controls. In addition, we detected differences in diversity structure between the microbiota of patients with mild, severe, and fatal COVID-19, as well as the presence of specific bacteria that correlated with clinical variables associated with increased risk of mortality. In summary, our results demonstrate that increased dysbiosis of the respiratory tract microbiota in patients with COVID-19 along with a continuous loss of microbial complexity structure found in mild to fatal COVID-19 cases may potentially alter clinical outcomes in patients. Taken together, our findings identify the respiratory microbiota as a factor potentially associated with the severity of COVID-19.
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Affiliation(s)
- Alejandra Hernández-Terán
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Fidencio Mejía-Nepomuceno
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - María Teresa Herrera
- Departamento de Investigación en Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Omar Barreto
- Coordinación de Atención Médica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Emma García
- Coordinación de Atención Médica, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Manuel Castillejos
- Departamento de Unidad de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, CIENI, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Margarita Matias-Florentino
- Centro de Investigación en Enfermedades Infecciosas, CIENI, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, CIENI, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, CIENI, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Mario Mújica-Sánchez
- Laboratorio de Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Ricardo Serna-Muñoz
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Eduardo Becerril-Vargas
- Laboratorio de Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Cristobal Guadarrama-Pérez
- Servicio de Urgencias Médicas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Víctor Hugo Ahumada-Topete
- Departamento de Unidad de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Sebastián Rodríguez-Llamazares
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - José Arturo Martínez-Orozco
- Laboratorio de Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Jorge Salas-Hernández
- Dirección General INER, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Rogelio Pérez-Padilla
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico
| | - Joel Armando Vázquez-Pérez
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Mexico, Mexico.
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22
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Nesbitt H, Burke C, Haghi M. Manipulation of the Upper Respiratory Microbiota to Reduce Incidence and Severity of Upper Respiratory Viral Infections: A Literature Review. Front Microbiol 2021; 12:713703. [PMID: 34512591 PMCID: PMC8432964 DOI: 10.3389/fmicb.2021.713703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
There is a high incidence of upper respiratory viral infections in the human population, with infection severity being unique to each individual. Upper respiratory viruses have been associated previously with secondary bacterial infection, however, several cross-sectional studies analyzed in the literature indicate that an inverse relationship can also occur. Pathobiont abundance and/or bacterial dysbiosis can impair epithelial integrity and predispose an individual to viral infection. In this review we describe common commensal microorganisms that have the capacity to reduce the abundance of pathobionts and maintain bacterial symbiosis in the upper respiratory tract and discuss the potential and limitations of localized probiotic formulations of commensal bacteria to reduce the incidence and severity of viral infections.
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Affiliation(s)
- Henry Nesbitt
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Catherine Burke
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Mehra Haghi
- Discipline of Pharmacy, Graduate School Health, University of Technology Sydney, Sydney, NSW, Australia
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23
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Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.
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