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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 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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Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P, Putignani L. Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection. Microbiol Spectr 2024; 12:e0300923. [PMID: 38289047 PMCID: PMC10913489 DOI: 10.1128/spectrum.03009-23] [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: 08/02/2023] [Accepted: 12/12/2023] [Indexed: 03/06/2024] Open
Abstract
The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (T0), 72 h to 7 days (T1), and at the discharge (T2) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (N = 71) was characterized by reduction of α-diversity compared to CTRLs (N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus, Haemophilus, Staphylococcus, Veillonella, Enterococcus, Neisseria, Moraxella, Enterobacteriaceae, Gemella, Bacillus, and reduced in Faecalibacterium, Akkermansia, Blautia, Bifidobacterium, Ruminococcus, and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus, and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL. IMPORTANCE Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.
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Affiliation(s)
- L. Romani
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - F. Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - S. Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - M. V. Ristori
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - I. Pirona
- GenomeUp SRL, Viale Pasteur, Rome, Italy
| | | | - N. Cotugno
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - S. Bernardi
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - L. Lancella
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - C. F. Perno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - P. Rossi
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - A. Villani
- Pediatric Emergency Department and General Pediatrics, Bambino Gesù Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - A. Campana
- Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - P. Palma
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - L. Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - the CACTUS Study TeamCarducciFrancesca CalòCancriniCaterinaChiurchiùSaradegli AttiMarta CiofiCursiLauraCutreraRenatoD’AmoreCarmenD’ArgenioPatriziaDe IorisMaria A.De LucaMaiaFinocchiAndreaMannoEmma ConcettaMorrocchiElenaPansaPaolaSessaLiberaZangariPaola
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- GenomeUp SRL, Viale Pasteur, Rome, Italy
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Pediatric Emergency Department and General Pediatrics, Bambino Gesù Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
- Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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3
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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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Adzdzakiy MM, Sutarno S, Asyifa IZ, Sativa AR, Fiqri AR, Fibriani A, Ristandi RB, Ningrum RA, Iryanto SB, Prasetyoputri A, Dharmayanthi AB, Saputra S. SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia. J Taibah Univ Med Sci 2024; 19:70-81. [PMID: 37868100 PMCID: PMC10589881 DOI: 10.1016/j.jtumed.2023.09.001] [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: 02/24/2023] [Revised: 07/21/2023] [Accepted: 09/01/2023] [Indexed: 10/24/2023] Open
Abstract
Objective The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients. Methods We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021. Results The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Pseudomonas aeruginosa and Haemophilus parainfluenzae. Conclusions The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.
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Affiliation(s)
- Muhammad M. Adzdzakiy
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Sutarno Sutarno
- Graduate School of Bioscience, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Jl. Ir. Sutami 36A Surakarta, Central Java, Indonesia
| | - Isnaini Z. Asyifa
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Alvira R. Sativa
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ahmad R.A. Fiqri
- Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No.6, Jakarta, Indonesia
| | - Azzania Fibriani
- School of Life Science and Technology, Institut Teknologi Bandung, Jl. Ganesa 10, Bandung, West Java, Indonesia
| | - Ryan B. Ristandi
- West Java Health Laboratory, Jl. Sederhana No. 3-5, Pasteur, Sukajadi, Bandung, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Computation, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anggia Prasetyoputri
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor Km 46, Bogor, West Java, Indonesia
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5
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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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6
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Bourumeau W, Tremblay K, Jourdan G, Girard C, Laprise C. Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection. Microorganisms 2023; 11:2703. [PMID: 38004715 PMCID: PMC10673573 DOI: 10.3390/microorganisms11112703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.
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Affiliation(s)
- William Bourumeau
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Karine Tremblay
- Pharmacology-Physiology Department, Université de Sherbrooke, Saguenay, QC J1K 2R1, Canada;
- Research Centre of Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay–Lac-Saint-Jean (CIUSSS-SLSJ), Saguenay, QC G7H 7K9, Canada
| | - Guillaume Jourdan
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Girard
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
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7
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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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8
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Mancabelli L, Taurino G, Ticinesi A, Ciociola T, Vacondio F, Milani C, Fontana F, Lugli GA, Tarracchini C, Alessandri G, Viappiani A, Bianchi M, Nouvenne A, Chetta AA, Turroni F, Meschi T, Mor M, Bussolati O, Ventura M. Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection. Microbiol Spectr 2023; 11:e0219423. [PMID: 37728335 PMCID: PMC10581039 DOI: 10.1128/spectrum.02194-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/01/2023] [Indexed: 09/21/2023] Open
Abstract
The human organism is inhabited by trillions of microorganisms, known as microbiota, which are considered to exploit a pivotal role in the regulation of host health and immunity. Recent investigations have suggested a relationship between the composition of the human microbiota and COVID-19 infection, highlighting a possible role of bacterial communities in the modulation of the disease severity. In this study, we performed a shotgun metagenomics analysis to explore and compare the nasopharyngeal microbiota of 38 hospitalized Italian patients with and without COVID-19 infection during the third and fourth pandemic waves. In detail, the metagenomic analysis combined with specific correlation analyses suggested a positive association of several microbial species, such as S. parasanguinis and P. melaninogenica, with the severity of COVID-19 infection. Furthermore, the comparison of the microbiota composition between the nasopharyngeal and their respective fecal samples highlighted an association between these different compartments represented by a sharing of several bacterial species. Additionally, lipidomic and deep-shotgun functional analyses of the fecal samples suggested a metabolic impact of the microbiome on the host's immune response, indicating the presence of key metabolic compounds in COVID-19 patients, such as lipid oxidation end products, potentially related to the inflammatory state. Conversely, the patients without COVID-19 displayed enzymatic patterns associated with the biosynthesis and degradation of specific compounds like lysine (synthesis) and phenylalanine (degradation) that could positively impact disease severity and contribute to modulating COVID-19 infection. IMPORTANCE The human microbiota is reported to play a major role in the regulation of host health and immunity, suggesting a possible impact on the severity of COVID-19 disease. This preliminary study investigated the possible correlation between nasopharyngeal microbiota and COVID-19 infection. In detail, the analysis of the nasopharyngeal microbiota of hospitalized Italian patients with and without COVID-19 infection suggested a positive association of several microbial species with the severity of the disease and highlighted a sharing of several bacteria species with the respective fecal samples. Moreover, the metabolic analyses suggested a possible impact of the microbiome on the host's immune response and the disease severity.
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Affiliation(s)
- Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Department of Geriatric-Rehabilitation, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tecla Ciociola
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Federica Vacondio
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Christian Milani
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Massimiliano Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Antonio Nouvenne
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Department of Geriatric-Rehabilitation, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Alfredo Antonio Chetta
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Francesca Turroni
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Department of Geriatric-Rehabilitation, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Marco Mor
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Marco Ventura
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Bose T, Wasimuddin, Acharya V, Pinna NK, Kaur H, Ranjan M, SaiKrishna J, Nagabandi T, Varma B, Tallapaka KB, Sowpati DT, Haque MM, Dutta A, Siva AB, Mande SS. A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India. Front Microbiol 2023; 14:1238829. [PMID: 37744900 PMCID: PMC10511876 DOI: 10.3389/fmicb.2023.1238829] [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: 06/12/2023] [Accepted: 08/09/2023] [Indexed: 09/26/2023] Open
Abstract
Background Multiple variants of the SARS-CoV-2 virus have plagued the world through successive waves of infection over the past three years. Independent research groups across geographies have shown that the microbiome composition in COVID-19 positive patients (CP) differs from that of COVID-19 negative individuals (CN). However, these observations were based on limited-sized sample-sets collected primarily from the early days of the pandemic. Here, we study the nasopharyngeal microbiota in COVID-19 patients, wherein the samples have been collected across the three COVID-19 waves witnessed in India, which were driven by different variants of concern. Methods The nasopharyngeal swabs were collected from 589 subjects providing samples for diagnostics purposes at the Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India and subjected to 16s rRNA gene amplicon - based sequencing. Findings We found variations in the microbiota of symptomatic vs. asymptomatic COVID-19 patients. CP showed a marked shift in the microbial diversity and composition compared to CN, in a wave-dependent manner. Rickettsiaceae was the only family that was noted to be consistently depleted in CP samples across the waves. The genera Staphylococcus, Anhydrobacter, Thermus, and Aerococcus were observed to be highly abundant in the symptomatic CP patients when compared to the asymptomatic group. In general, we observed a decrease in the burden of opportunistic pathogens in the host microbiota during the later waves of infection. Interpretation To our knowledge, this is the first analytical cross-sectional study of this scale, which was designed to understand the relation between the evolving nature of the virus and the changes in the human nasopharyngeal microbiota. Although no clear signatures were observed, this study shall pave the way for a better understanding of the disease pathophysiology and help gather preliminary evidence on whether interventions to the host microbiota can help in better protection or faster recovery.
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Affiliation(s)
- Tungadri Bose
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Wasimuddin
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Varnali Acharya
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Nishal Kumar Pinna
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Harrisham Kaur
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | - Manish Ranjan
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Jandhyala SaiKrishna
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Tulasi Nagabandi
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | - Binuja Varma
- TCS Genomics Lab, Tata Consultancy Services Limited, Noida, Uttar Pradesh, India
| | | | - Divya Tej Sowpati
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, Telangana, India
| | | | - Anirban Dutta
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
| | | | - Sharmila S. Mande
- TCS Research, Tata Consultancy Services Limited, Pune, Maharashtra, India
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10
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Toro-Ascuy D, Cárdenas JP, Zorondo-Rodríguez F, González D, Silva-Moreno E, Puebla C, Nunez-Parra A, Reyes-Cerpa S, Fuenzalida LF. Microbiota Profile of the Nasal Cavity According to Lifestyles in Healthy Adults in Santiago, Chile. Microorganisms 2023; 11:1635. [PMID: 37512807 PMCID: PMC10384449 DOI: 10.3390/microorganisms11071635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The respiratory microbiome is dynamic, varying between anatomical niches, and it is affected by various host and environmental factors, one of which is lifestyle. Few studies have characterized the upper respiratory tract microbiome profile according to lifestyle. We explored the association between lifestyles and microbiota profiles in the upper respiratory tract of healthy adults. METHODS We analyzed nasal samples from 110 healthy adults who were living in Santiago, Chile, using 16S ribosomal RNA gene-sequencing methods. Volunteers completed a structured questionnaire about lifestyle. RESULTS The composition and abundance of taxonomic groups varied across lifestyle attributes. Additionally, multivariate models suggested that alpha diversity varied in the function of physical activity, nutritional status, smoking, and the interaction between nutritional status and smoking, although the significant impact of those variables varied between women and men. Although physical activity and nutritional status were significantly associated with all indexes of alpha diversity among women, the diversity of microbiota among men was associated with smoking and the interaction between nutritional status and smoking. CONCLUSIONS The alpha diversity of nasal microbiota is associated with lifestyle attributes, but these associations depend on sex and nutritional status. Our results suggest that future studies of the airway microbiome may provide a better resolution if data are stratified for differences in sex and nutritional status.
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Affiliation(s)
- Daniela Toro-Ascuy
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Juan P Cárdenas
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Francisco Zorondo-Rodríguez
- Departamento de Gestión Agraria, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 8910060, Chile
| | - Damariz González
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Evelyn Silva-Moreno
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Carlos Puebla
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Alexia Nunez-Parra
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Loreto F Fuenzalida
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile
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11
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Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
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Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
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