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Lu HA, Wang YM, Chih Chen W, Wu CN, Lu YT, Wee Y, Wang CS, Dean Luo S. Post-irradiation dysbiosis in patients with nasopharyngeal carcinoma having received radiotherapy - A pilot study. Oral Oncol 2024; 154:106864. [PMID: 38824812 DOI: 10.1016/j.oraloncology.2024.106864] [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: 03/17/2024] [Revised: 05/02/2024] [Accepted: 05/19/2024] [Indexed: 06/04/2024]
Abstract
OBJECTIVE To compare the changes in the sinonasal mucosa microbiome in patients with nasopharyngeal carcinoma (NPC) before and after radiotherapy (RT), and to explore the pathogenesis of post-irradiation chronic rhinosinusitis (PI-CRS) and its association with dysbiosis. STUDY DESIGN Prospective cohort study. SETTING Unicenter, Tertiary referral hospital. METHODS Included patients newly diagnosed with NPC. Samples of ostiomeatal complex mucosa were collected before and after RT. Microbiome analysis was conducted using 16S rRNA sequencing, and statistical analysis was performed. Subgroup analyses based on RT modality (proton therapy or photon therapy) RESULTS: Total of 18 patients were enrolled in the study, with 62.1% receiving intensity-modulated proton therapy (IMPT). Corynebacterium was the most dominant genus identified in both the pre- and post-RT groups, with a visible increase in Staphylococcus and a decrease in Fusobacterium genus in post-RT group. Alpha-diversity did not significantly differ between groups, although the beta-diversity analysis revealed a dispersed microbiota in the post-RT group. The functional prediction indicated a higher relative abundance of taxonomies associated with biofilm formation in the post-RT group. The subgroup analysis revealed the above changes to be more significant in patients who received photon therapy (Intensity modulated radiation therapy, IMRT). CONCLUSIONS This is the first study to analyze the microbiome of patients with NPC after IMPT. We identified similarities between the post-RT microenvironment and that reported in patients with CRS, with a more apparent change noted in patients treated with IMRT. Further investigation is required to further elucidate the pathogenesis of PI-CRS and its relationship to post-RT dysbiosis, particularly IMPT.
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Affiliation(s)
- Heng-An Lu
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yu-Ming Wang
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Proton and Radiation Therapy Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Wei Chih Chen
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ching-Nung Wu
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ting Lu
- Department of Otolaryngology, St. Martin De Porres Hospital, Chiayi, Taiwan; Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yinshen Wee
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ching-Shuen Wang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Sheng Dean Luo
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; School of Traditional Chinese Medicine, Chang Gung University College of Medicine, Taoyuan 33302, Taiwan; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.
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Uzunoğlu E, Kalkancı A, Kılıç E, Kızıl Y, Aydil U, Diker KS, Uslu SS. Bacterial and fungal communities in chronic rhinosinusitis with nasal polyps. PLoS One 2024; 19:e0304634. [PMID: 38820284 PMCID: PMC11142431 DOI: 10.1371/journal.pone.0304634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/15/2024] [Indexed: 06/02/2024] Open
Abstract
OBJECTIVE Multiple inflammatory mechanisms dynamically interact in the development of chronic rhinosinusitis with nasal polyps (CRSwNP). Disruption of the relationship between host and environmental factors on the mucosal surface leads to the development of inflammation. Microorganisms constitute the most important part of environmental factors. METHODS 28 volunteers (18 CRSwNP patients and 10 healthy individuals) were included in the study. Eight patients were recurrent nasal polyposis cases, and the remaining were primary cases. Swab samples were taken from the middle meatus under endoscopic examination from all participants. After DNA extraction, a library was created with the Swift Amplicon 16S + ITS kit and sequenced with Illumina Miseq. Sequence analysis was performed using QIIME, UNITE v8.2 database for ITS and Silva v138 for 16S rRNA. RESULTS The predominant bacteria in all groups were Firmicutes, Proteobacteria, Actinobacteria as phyla and Staphylococcus, Corynebacterium, Sphingomonas as genera. Comparison of bacterial communities of CRSwNP patients and control group highlighted Corynebacterium, as the differentiating taxa for control group and Streptococcus, Moraxella, Rothia, Micrococcus, Gemella, and Prevotella for CRSwNP patients. The predominant fungal genus in all groups was Malassezia. Staphylococcus; showed a statistically significant negative correlation with Dolosigranulum. Corynebacterium had a positive correlation with Anaerococcus, and a negative correlation with Neisseria, Prevotella, Fusobacterium and Peptostreptococcus. CONCLUSION Nasal microbiome of CRSwNP patients shows greater inter-individual variation than the control group. Corynebacterium is less abundant in patients with CRSwNP compared to the control group. Malassezia is the predominant fungus in the nasal cavity and paranasal sinuses and correlates positively with the abundance of Corynebacterium.
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Affiliation(s)
- Eray Uzunoğlu
- Department of Otorhinolaryngology, Izmir Ekol Hospital, İzmir, Turkey
| | - Ayşe Kalkancı
- Department of Medical Microbiology, Gazi University Hospital, Ankara, Turkey
| | - Esra Kılıç
- Department of Medical Microbiology, Gazi University Hospital, Ankara, Turkey
| | - Yusuf Kızıl
- Department of Otorhinolaryngology, Gazi University Hospital, Ankara, Turkey
| | - Utku Aydil
- Department of Otorhinolaryngology, Gazi University Hospital, Ankara, Turkey
| | - Kadir Serdar Diker
- Department of Microbiology, Adnan Menderes University Faculty of Veterinary Medicine, Aydin, Turkey
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Zhu K, Jin Y, Zhao Y, He A, Wang R, Cao C. Proteomic scrutiny of nasal microbiomes: implications for the clinic. Expert Rev Proteomics 2024; 21:169-179. [PMID: 38420723 DOI: 10.1080/14789450.2024.2323983] [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: 06/20/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION The nasal cavity is the initial site of the human respiratory tract and is one of the habitats where microorganisms colonize. The findings from a growing number of studies have shown that the nasal microbiome is an important factor for human disease and health. 16S rRNA sequencing and metagenomic next-generation sequencing (mNGS) are the most commonly used means of microbiome evaluation. Among them, 16S rRNA sequencing is the primary method used in previous studies of nasal microbiomes. However, neither 16S rRNA sequencing nor mNGS can be used to analyze the genes specifically expressed by nasal microorganisms and their functions. This problem can be addressed by proteomic analysis of the nasal microbiome. AREAS COVERED In this review, we summarize current advances in research on the nasal microbiome, introduce the methods for proteomic evaluation of the nasal microbiome, and focus on the important roles of proteomic evaluation of the nasal microbiome in the diagnosis and treatment of related diseases. EXPERT OPINION The detection method for microbiome-expressed proteins is known as metaproteomics. Metaproteomic analysis can help us dig deeper into the nasal microbiomes and provide new targets and ideas for clinical diagnosis and treatment of many nasal dysbiosis-related diseases.
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Affiliation(s)
- Ke Zhu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yan Jin
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
- Department of Respiratory and Critical Care Medicine, Municipal Hospital Affiliated to Taizhou University, Taizhou, China
| | - Yun Zhao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Andong He
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chao Cao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Respiratory Disease of Ningbo, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Duff AF, Jurcisek JA, Kurbatfinski N, Chiang T, Goodman SD, Bakaletz LO, Bailey MT. Oral and middle ear delivery of otitis media standard of care antibiotics, but not biofilm-targeted antibodies, alter chinchilla nasopharyngeal and fecal microbiomes. NPJ Biofilms Microbiomes 2024; 10:10. [PMID: 38310144 PMCID: PMC10838340 DOI: 10.1038/s41522-024-00481-0] [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: 07/24/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Otitis media (OM) is one of the most globally pervasive pediatric conditions. Translocation of nasopharynx-resident opportunistic pathogens like nontypeable Haemophilus influenzae (NTHi) assimilates into polymicrobial middle ear biofilms, which promote OM pathogenesis and substantially diminish antibiotic efficacy. Oral or tympanostomy tube (TT)-delivered antibiotics remain the standard of care (SOC) despite consequences including secondary infection, dysbiosis, and antimicrobial resistance. Monoclonal antibodies (mAb) against two biofilm-associated structural proteins, NTHi-specific type IV pilus PilA (anti-rsPilA) and protective tip-region epitopes of NTHi integration host factor (anti-tip-chimer), were previously shown to disrupt biofilms and restore antibiotic sensitivity in vitro. However, the additional criterion for clinical relevance includes the absence of consequential microbiome alterations. Here, nine chinchilla cohorts (n = 3/cohort) without disease were established to evaluate whether TT delivery of mAbs disrupted nasopharyngeal or fecal microbiomes relative to SOC-OM antibiotics. Cohort treatments included a 7d regimen of oral amoxicillin-clavulanate (AC) or 2d regimen of TT-delivered mAb, AC, Trimethoprim-sulfamethoxazole (TS), ofloxacin, or saline. Fecal and nasopharyngeal lavage (NPL) samples were collected before and several days post treatment (DPT) for 16S sequencing. While antibiotic-treated cohorts displayed beta-diversity shifts (PERMANOVA, P < 0.05) and reductions in alpha diversity (q < 0.20) relative to baseline, mAb antibodies failed to affect diversity, indicating maintenance of a eubiotic state. Taxonomic and longitudinal analyses showed blooms in opportunistic pathogens (ANCOM) and greater magnitudes of compositional change (P < 0.05) following broad-spectrum antibiotic but not mAb treatments. Collectively, results showed broad-spectrum antibiotics induced significant fecal and nasopharyngeal microbiome disruption regardless of delivery route. Excitingly, biofilm-targeting antibodies had little effect on fecal and nasopharyngeal microbiomes.
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Affiliation(s)
- Audrey F Duff
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Tendy Chiang
- Department of Otolaryngology at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
- Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Michael T Bailey
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.
- Oral and Gastrointestinal Microbiology Research Affinity Group, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.
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Huffines JT, Boone RL, Kiedrowski MR. Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model. mSphere 2024; 9:e0058923. [PMID: 38179905 PMCID: PMC10826359 DOI: 10.1128/msphere.00589-23] [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: 10/07/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024] Open
Abstract
Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.
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Affiliation(s)
- Joshua T. Huffines
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - RaNashia L. Boone
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Megan R. Kiedrowski
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
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Loperfido A, Cavaliere C, Begvarfaj E, Ciofalo A, D’Erme G, De Vincentiis M, Greco A, Millarelli S, Bellocchi G, Masieri S. The Impact of Antibiotics and Steroids on the Nasal Microbiome in Patients with Chronic Rhinosinusitis: A Systematic Review According to PICO Criteria. J Pers Med 2023; 13:1583. [PMID: 38003898 PMCID: PMC10671981 DOI: 10.3390/jpm13111583] [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: 10/16/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND The nasal microbiome represents the main environmental factor of the inflammatory process in chronic rhinosinusitis (CRS). Antibiotics and steroids constitute the mainstay of CRS therapies. However, their impact on microbial communities needs to be better understood. This systematic review summarizes the evidence about antibiotics' and steroids' impact on the nasal microbiota in patients with CRS. METHODS The search strategy was conducted in accordance with the PRISMA guidelines for systematic reviews. The authors searched all papers in the three major medical databases (PubMed, Scopus, and Cochrane Library) using the PICO tool (population, intervention, comparison, and outcomes). The search was carried out using a combination of the key terms "Microbiota" or "Microbiome" and "Chronic Rhinosinusitis". RESULTS Overall, 402 papers were identified, and after duplicate removal (127 papers), excluding papers off-topic (154) and for other structural reasons (110), papers were assessed for eligibility; finally, only 11 papers were included and summarized in the present systematic review. Some authors used only steroids, other researchers used only antibiotics, and others used both antibiotics and steroids. With regard to the use of steroids as exclusive medical treatment, topical mometasone and budesonide were investigated. With regard to the use of antibiotics as exclusive medical treatments, clarithromycin, doxycycline, roxithromycin, and amoxicillin clavulanate were investigated. Regarding the use of both antibiotics and steroids, two associations were investigated: systemic prednisone combined with amoxicillin clavulanate and topical budesonide combined with azithromycin. CONCLUSIONS The impact that therapies can have on the nasal microbiome of CRS patients is very varied. Further studies are needed to understand the role of the nasal microbiome, prevent CRS, and improve therapeutic tools for personalized medicine tailored to the individual patient.
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Affiliation(s)
| | - Carlo Cavaliere
- Department of Sense Organs, Sapienza University, 00185 Rome, Italy
| | - Elona Begvarfaj
- Department of Sense Organs, Sapienza University, 00185 Rome, Italy
| | - Andrea Ciofalo
- Department of Sense Organs, Sapienza University, 00185 Rome, Italy
| | - Giovanni D’Erme
- UOC Otorinolaringoiatria, Policlinico Umberto I, 00161 Rome, Italy
| | | | - Antonio Greco
- Department of Sense Organs, Sapienza University, 00185 Rome, Italy
| | | | | | - Simonetta Masieri
- Department of Oral and Maxillofacial Sciences, Sapienza University, 00185 Rome, Italy
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Ai D, Chen L, Xie J, Cheng L, Zhang F, Luan Y, Li Y, Hou S, Sun F, Xia LC. Identifying local associations in biological time series: algorithms, statistical significance, and applications. Brief Bioinform 2023; 24:bbad390. [PMID: 37930023 DOI: 10.1093/bib/bbad390] [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: 05/25/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023] Open
Abstract
Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.
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Affiliation(s)
- Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Lulu Chen
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiemin Xie
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Longwei Cheng
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Fang Zhang
- Shenwan Hongyuan Securities Co. Ltd., Shanghai 200031, China
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Yang Li
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, California, 90007, USA
| | - Li Charlie Xia
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
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Lowman ME, Tipton CD, Labordère AL, Brown JA. Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing. Equine Vet J 2023; 55:798-807. [PMID: 36199163 DOI: 10.1111/evj.13884] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Information regarding the microbiome in sinusitis using genetic sequencing is lacking and more-in-depth understanding of the microbiome could improve antimicrobial selection and treatment outcomes for cases of primary sinusitis. OBJECTIVES To describe sinus microbiota in samples from horses with sinusitis and compare microbiota and the presence of antimicrobial resistance genes between primary, dental-related and other secondary causes of sinusitis. STUDY DESIGN Retrospective case series. METHODS Records of equine sinusitis from 2017 to 2021 were reviewed and historical microbial amplicon sequence data were obtained from clinical diagnostic testing of sinus secretions. Following bioinformatic processing of bacterial and fungal sequence data, the sinus microbiota and importance of sinusitis aetiology among other factors were investigated from the perspectives of alpha diversity (e.g., number of operational taxonomic units [OTUs], Hill1 Diversity), beta diversity, and differentially abundant taxa. Quantitative PCR allowed for comparisons of estimated bacterial abundance and detection rate of common antibiotic resistance-associated genes. In a smaller subset, longitudinal analysis was performed to evaluate similarity in samples over time. RESULTS Of 81 samples analysed from 70 horses, the bacterial microbiome was characterised in 66, and fungal in five. Only sinusitis aetiology was shown to significantly influence microbiome diversity and composition (p < 0.05). Dental-related sinusitis (n = 44) was associated with a significantly higher proportion of obligate anaerobic bacteria, whereas primary sinusitis (n = 12) and other (n = 10) groups were associated with fewer bacteria and higher proportions of facultative anaerobic and aerobic genera. Antimicrobial resistance genes and fungal components were exclusively identified in dental-related sinusitis. MAIN LIMITATIONS Retrospective nature, incomplete prior antimicrobial administration data. CONCLUSIONS Molecular characterisation in sinusitis identifies microbial species which may be difficult to isolate via culture, and microbiome profiling can differentiate sinusitis aetiology, which may inform further treatment, including antimicrobial therapy.
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Affiliation(s)
- Megan E Lowman
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
| | | | - Alexandra L Labordère
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
| | - James A Brown
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
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Wu J, Zheng M, Zhao Y, Yin W, Sima Y, Zhao J, Wang X, Lin J, Zhang L. Bacterial diversity and community characteristics of the sinus and dental regions in adults with odontogenic sinusitis. BMC Microbiol 2023; 23:201. [PMID: 37516855 PMCID: PMC10386777 DOI: 10.1186/s12866-023-02917-7] [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: 02/08/2023] [Accepted: 06/28/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND The microbiome plays a crucial role in odontogenic sinusitis (OS); however, the bacterial characteristics of the sinuses and connected dental regions in OS are poorly understood. In this study, nasal secretion samples were collected from 41 OS patients and 20 simple nasal septum deviation patients, and oral mucosa samples from dental regions were collected from 28 OS patients and 22 impacted tooth extraction patients. DNA was extracted, and 16S rRNA sequencing was performed to explore the characteristics and structure of the microbiome in the sinuses and dental regions of OS patients. RESULTS The alpha diversity of the oral and nasal microbiomes in OS patients was higher than that in controls. Principal coordinate analysis (PCoA) showed that oral samples clustered separately from nasal samples, and the beta diversity of oral and nasal samples in OS patients was higher than that in controls. The dominant phylum was Bacteroidetes in OS patients and Firmicutes in controls in both the oral and nasal cavity. The dominant genera in the oral microbiome and nasal microbiome of OS patients were similar, including Fusobacterium, Porphyromonas and Prevotella. Co-occurrence network analysis showed decreased microbial connectivity in the oral mucosa and nasal secretion samples of OS patients. CONCLUSIONS Odontogenic infection promotes structural and functional disorders of the nasal microbiome in OS. The interaction of dominant pathogens in the nasal and oral regions may promote the development of OS. Our study provides the microbiological aetiology of the nasal and connected dental regions in OS and is expected to provide novel insights into the diagnosis and therapeutic strategies for OS.
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Affiliation(s)
- Jianyou Wu
- Department of Stomatology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Ming Zheng
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Weihong Yin
- Department of Stomatology, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Yutong Sima
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Jinming Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Xiangdong Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China.
| | - Jiang Lin
- Department of Stomatology, Beijing TongRen Hospital, Capital Medical University, Beijing, China.
| | - Luo Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.
- Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China.
- Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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11
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Morawska-Kochman M, Malecha ZM, Zub K, Kielar J, Dudek K, Nelke K, Zatonski T. Physical Conditions Prevailing in the Nasal and Maxillary Sinus Cavities Based on Numerical Simulation. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1094. [PMID: 37374298 DOI: 10.3390/medicina59061094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023]
Abstract
Background and Objectives: This paper presents a unique study that links the physical conditions in the nasal passage with conditions that favour the development of bacterial strains and the colonization of the mucous membranes of the nose and paranasal sinuses. The physical parameters considered were air flow, pressure, humidity, and temperature. Materials and Methods: Numerical models of the human nose and maxillary sinus were retrospectively reconstructed from CT images of generally healthy young subjects. The state-of-the-art numerical methods and tools were then used to determine the temperature, humidity, airflow velocity, and pressure at specific anatomical locations. Results: The results were compared with optimal conditions for bacterial growth in the nose and sinuses. Conclusions: Temperature, humidity, air velocity, and pressure were shown to play critical roles in the selection and distribution of microorganisms. Furthermore, certain combinations of physical parameters can favour mucosal colonisation by various strains of bacteria.
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Affiliation(s)
- Monika Morawska-Kochman
- Department of Otolaryngology, Head and Neck Surgery, Medical University, Borowska 213, 50-556 Wroclaw, Poland
| | - Ziemowit Miłosz Malecha
- Department of Cryogenics and Aerospace Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Krzysztof Zub
- Department of Otolaryngology, Head and Neck Surgery, Medical University, Borowska 213, 50-556 Wroclaw, Poland
| | - Jakub Kielar
- Department of Cryogenics and Aerospace Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Krzysztof Dudek
- Statistical Analysis Centre, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Kamil Nelke
- Maxillofacial Surgery Ward, EMC Hospital, Pilczycka 144, 54-144 Wroclaw, Poland
- Health Department, Academy of Applied Sciences, Academy of Silesius, Zamkowa 4, 58-300 Walbrzych, Poland
| | - Tomasz Zatonski
- Department of Otolaryngology, Head and Neck Surgery, Medical University, Borowska 213, 50-556 Wroclaw, Poland
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12
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Liang Y, Xie R, Xiong X, Hu Z, Mao X, Wang X, Zhang J, Sun P, Yue Z, Wang W, Zhang G. Alterations of nasal microbiome in eosinophilic chronic rhinosinusitis. J Allergy Clin Immunol 2023; 151:1286-1295.e2. [PMID: 36736796 DOI: 10.1016/j.jaci.2022.11.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/16/2022] [Accepted: 11/04/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Exposure to microbes may be important in the development of chronic rhinosinusitis (CRS). Dysbiosis of the nasal microbiome is considered to be related to CRS with nasal polyps (CRSwNP). The link between the nasal microbiota and eosinophilic CRSwNP (eCRSwNP) has rarely been studied. OBJECTIVE The aim of this study was to rigorously characterize nasal dysbiosis in a cohort of patients with eCRSwNP and compare the nasal microbiomes of these patients with those of healthy controls (HCs). METHODS We performed a cross-sectional study of 34 patients with eCRSwNP, 10 patients without CRSwNP, and 44 HCs by using 16S rRNA gene sequencing. An independent cohort of 14 patients with eCRSwNP, 9 patients without CRSwNP, and 11 HCs was used to validate the results. RESULTS Compared with the nasal microbiome of healthy controls, the nasal microbiome of patients with eCRSwNP was characterized by higher α-diversity (Shannon and Chao1 index) and a distinct composition of microbes. Notably, the distinct differences in microbial composition between patients with eCRSwNP and HCs were significantly correlated with eCRSwNP disease status. Furthermore, in a diagnostic model generated by using these differences, a combination of 15 genera could be used to distinguish patients with eCRSwNP from HCs, with an area under the curve of approximately 0.8 in both the exploration and validation cohorts. CONCLUSION Our study establishes the compositional alterations in the nasal microbiome in eCRSwNP and suggests the potential for using the nasal microbiota as a noninvasive predictive classifier for the diagnosis of eCRSwNP.
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Affiliation(s)
- Yibo Liang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Runxiang Xie
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Xiong
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Zhanjun Hu
- Department of Pathology, Tianjin First Central Hospital, Tianjin, China
| | - Xiang Mao
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Xiaoyu Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Jinmei Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Peiyong Sun
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Zhenzhong Yue
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Wei Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Guimin Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China.
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13
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Vangrinsven E, Fastrès A, Taminiau B, Billen F, Daube G, Clercx C. Assessment of the nasal microbiota in dogs with fungal rhinitis before and after cure and in dogs with chronic idiopathic rhinitis. BMC Microbiol 2023; 23:104. [PMID: 37061685 PMCID: PMC10105444 DOI: 10.1186/s12866-023-02828-7] [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: 05/28/2022] [Accepted: 03/17/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Pathogenesis of canine fungal rhinitis is still not fully understood. Treatment remains challenging, after cure turbinate destruction may be associated with persistent clinical signs and recurrence of fungal rhinitis can occur. Alterations of the nasal microbiota have been demonstrated in dogs with chronic idiopathic rhinitis and nasal neoplasia, although whether they play a role in the pathogenesis or are a consequence of the disease is still unknown. The objectives of the present study were (1) to describe nasal microbiota alterations associated with fungal rhinitis in dogs, compared with chronic idiopathic rhinitis and controls, (2) to characterize the nasal microbiota modifications associated with successful treatment of fungal rhinitis. Forty dogs diagnosed with fungal rhinitis, 14 dogs with chronic idiopathic rhinitis and 29 healthy control dogs were included. Nine of the fungal rhinitis dogs were resampled after successful treatment with enilconazole infusion. RESULTS Only disease status contributed significantly to the variability of the microbiota. The relative abundance of the genus Moraxella was decreased in the fungal rhinitis (5.4 ± 18%) and chronic idiopathic rhinitis (4.6 ± 8.7%) groups compared to controls (51.8 ± 39.7%). Fungal rhinitis and chronic idiopathic rhinitis groups also showed an increased richness and α-diversity at species level compared with controls. Increase in unique families were associated with fungal rhinitis (Staphyloccaceae, Porphyromonadaceae, Enterobacteriaceae and Neisseriaceae) and chronic idiopathic rhinitis (Pasteurellaceae and Lactobacillaceae). In dogs with fungal rhinitis at cure, only 1 dog recovered a high relative abundance of Moraxellaceae. CONCLUSIONS Results confirm major alterations of the nasal microbiota in dogs affected with fungal rhinitis and chronic idiopathic rhinitis, consisting mainly in a decrease of Moraxella. Besides, a specific dysbiotic profile further differentiated fungal rhinitis from chronic idiopathic rhinitis. In dogs with fungal rhinitis, whether the NM returns to its pre-infection state or progresses toward chronic idiopathic rhinitis or fungal rhinitis recurrence warrants further investigation.
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Affiliation(s)
- Emilie Vangrinsven
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Aline Fastrès
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Bernard Taminiau
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Frédéric Billen
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Georges Daube
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Cécile Clercx
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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14
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Latek M, Łacwik P, Molińska K, Błauż A, Lach J, Rychlik B, Strapagiel D, Majak J, Molińska J, Czech D, Seweryn M, Kuna P, Pałczyński C, Majak P. Effect of an Intranasal Corticosteroid on Quality of Life and Local Microbiome in Young Children With Chronic Rhinosinusitis: A Randomized Clinical Trial. JAMA Pediatr 2023; 177:345-352. [PMID: 36848113 PMCID: PMC9972242 DOI: 10.1001/jamapediatrics.2022.6172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/14/2022] [Indexed: 03/01/2023]
Abstract
Importance Intranasal corticosteroids (INCs) remain the first-line treatment of chronic rhinosinusitis (CRS) in both adults and children, despite the lack of evidence regarding their efficacy in the pediatric population. Similarly, their effect on the sinonasal microbiome has not been well documented. Objective To assess the clinical, immunological, and microbiological effects of 12 weeks of an INC in young children with CRS. Design, Setting, and Participants This open-label randomized clinical trial was performed in a pediatric allergy outpatient clinic in 2017 and 2018. Children aged 4 to 8 years with CRS diagnosed by a specialist were included. Data were analyzed from January 2022 to June 2022. Interventions Patients were randomized to receive intranasal mometasone in an atomizer for 12 weeks (1 application per nostril, once per day) and supplemental 3-mL sodium chloride (NaCl), 0.9%, solution in a nasal nebulizer once a day for 12 weeks (INC group) or 3-mL NaCl, 0.9%, solution in a nasal nebulizer once a day for 12 weeks (control group). Main Outcomes and Measures Measures taken both before and after treatment included the Sinus and Nasal Quality of Life Survey (SN-5), a nasopharynx swab for microbiome analysis by next-generation sequencing methods, and nasal mucosa sampling for occurrence of innate lymphoid cells (ILCs). Results Of the 66 children enrolled, 63 completed the study. The mean (SD) age of the cohort was 6.1 (1.3) years; 38 participants (60.3%) were male and 25 (39.7%) were female. The clinical improvement reflected by reduction in SN-5 score was significantly higher in the INC group compared with the control group (INC group score before and after treatment, 3.6 and 3.1, respectively; control group score before and after treatment, 3.4 and 3.8, respectively; mean between-group difference, -0.58; 95% CI, -1.31 to -0.19; P = .009). The INC group had a greater increase in nasopharyngeal microbiome richness and larger decrease in nasal ILC3 abundance compared with the control group. A significant interaction was observed between change in microbiome richness and the INC intervention on the prediction of significant clinical improvement (odds ratio, 1.09; 95% CI, 1.01-1.19; P = .03). Conclusions and Relevance This randomized clinical trial demonstrated that treatment with an INC improved the quality of life of children with CRS and had a significant effect on increasing sinonasal biodiversity. Although further investigation is needed of the long-term efficacy and safety of INCs, these data may reinforce the recommendation of using INCs as a first-line treatment of CRS in children. Trial Registration ClinicalTrials.gov Identifier: NCT03011632.
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Affiliation(s)
- Marta Latek
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Piotr Łacwik
- Collegium Medicum, Jan Kochanowski University, Kielce, Poland
| | - Katarzyna Molińska
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Andrzej Błauż
- Cytometry Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Błażej Rychlik
- Cytometry Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Joanna Majak
- Audiology and Phoniatrics Clinic, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Joanna Molińska
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Dorota Czech
- Department of Paediatric Otolaryngology, Audiology and Phoniatrics, Medical University of Lodz, Lodz, Poland
| | - Michał Seweryn
- Biobank Lab, Faculty of Biology and Environmental Protection and Centre for Data Analysis, Modeling and Computational Sciences (CAMiNO), University of Lodz, Lodz, Poland
| | - Piotr Kuna
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | | | - Paweł Majak
- Department of Pediatric Pulmonology, Medical University of Lodz, Lodz, Poland
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15
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Sarkar S, Routhray S, Ramadass B, Parida PK. A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments. Indian J Otolaryngol Head Neck Surg 2023; 75:755-763. [PMID: 37206729 PMCID: PMC10188862 DOI: 10.1007/s12070-022-03205-y] [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: 06/10/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.
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Affiliation(s)
- Saurav Sarkar
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Samapika Routhray
- Department of Dentistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Balamurugan Ramadass
- Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Pradipta Kumar Parida
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
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16
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Mahmud ASM, Seers CA, Shaikh AA, Taznin T, Uzzaman MS, Osman E, Habib MA, Akter S, Banu TA, Sarkar MMH, Goswami B, Jahan I, Okeoma CM, Khan MS, Reynolds EC. A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients. Sci Rep 2023; 13:4122. [PMID: 36914691 PMCID: PMC10009844 DOI: 10.1038/s41598-023-30504-3] [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: 08/30/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.
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Affiliation(s)
- A Sayeed M Mahmud
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Christine A Seers
- The Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Tarannum Taznin
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | | | - Eshrar Osman
- SciTech Consulting and Solutions, Dhaka, 1213, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Md Murshed Hasan Sarkar
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh
| | - Chioma M Okeoma
- Department of Pathology, Microbiology, and Immunology, New York Medical College, 40 Sunshine Cottage Rd, Valhalla, NY, 10595, USA
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research, Dr. Qudrat-E-Khuda Road, Dhaka, 1205, Bangladesh.
| | - Eric C Reynolds
- The Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
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17
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Zhu Z, Lan J, Wei R, Xu Y, Hong Y, Bao W, He G. Microbiome and
Th
cytokines association in chronic rhinosinusitis with or without nasal polyp. Laryngoscope Investig Otolaryngol 2023; 8:335-345. [PMID: 37090867 PMCID: PMC10116975 DOI: 10.1002/lio2.1026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/20/2022] [Accepted: 02/12/2023] [Indexed: 03/11/2023] Open
Abstract
Objective Chronic rhinosinusitis (CRS), a common disease in otorhinolaryngology, seriously affects the life quality of patients. The existing therapy has certain limitations, and it is very urgent to deeply explore the pathogenesis and classification of CRS. Microbiome and inflammation are considered the causes of CRS, but the precise roles and the associations between these two factors in the pathogenesis of CRS remain controversial. Methods Secretions were collected from the middle nasal canal, maxillary sinus and ethmoid sinus in CRS patients, then subjected to 16 S rRNA gene sequencing to profile microbiota community. Operational Taxonomic Units clustering and species annotation were adopted to obtain species diversity, prevalence rate and average relative abundance. Comparisons were performed at the level of microbial species and genus between CRS and control using NMDS, Anosim and MetaStat analysis. Th1 cytokines and Th2 cytokines were detected by ELISA. Spearman analysis were adopted to probe into the correlation between Th cytokines and microbial species in CRS. Results Thirty-seven patients were enrolled, among them 22 with CRS and 15 were controls. The most abundant genera were Corynebacterium and Staphylococcus no matter in CRS patients or control. Corynebacterium propinquum was significant decreased in CRS patients no matter with nasal polyp or not. The abundances of Prevotella birria and Carnobacterium maltaromaticum were significantly different between CRSsNP and CRSwNP group. The levels of cytokines IL-2, TNF-α, IFN-ɣ, IL-4, IL-6, IL-10 were all increased in CRS patients. The cytokines levels were associated with specific microbial species in nasal tissue. Conclusion The changes of species richness and complexity in nasal microbiome were obvious in CRS patients with nasal polyps or not. The different cytokines levels and microbiome between CRS patients without nasal polyps and patients with nasal polyps suggest heterogeneity in pathogenesis of chronic rhinosinusitis. Distinct microbiota and different cytokines were strongly linked in CRS. Level of Evidence NA.
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Affiliation(s)
- ZhongShou Zhu
- The Third Clinical Medical College Fujian Medical University Fuzhou China
| | - Jiao Lan
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
| | - Rifu Wei
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
| | - Yangbin Xu
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
| | - Yiyun Hong
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
| | - Weijing Bao
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
| | - Guanwen He
- Department of Otolaryngology Ningde Municipal Hospital Affliated of Ningde Normal University (Ningde Institute of Otolaryngology) Ningde Fujian China
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18
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Bartosik TJ, Campion NJ, Freisl K, Liu DT, Gangl K, Stanek V, Tu A, Pjevac P, Hausmann B, Eckl-Dorna J, Schneider S. The nasal microbiome in patients suffering from non-steroidal anti-inflammatory drugs-exacerbated respiratory disease in absence of corticosteroids. Front Immunol 2023; 14:1112345. [PMID: 37122714 PMCID: PMC10140405 DOI: 10.3389/fimmu.2023.1112345] [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: 11/30/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a chronic inflammatory disease phenotypically classified by the absence (CRSsNP) or presence of nasal polyps (CRSwNP). The latter may also be associated with asthma and hypersensitivity towards non-steroidal anti-inflammatory drugs (NSAID) as a triad termed NSAID-exacerbated respiratory disease (N-ERD). The role of the microbiome in these different disease entities with regard to the underlying inflammatory process and disease burden is yet not fully understood. To address this question, we measured clinical parameters and collected nasal samples (nasal mucosal fluids, microbiome swabs from middle meatus and anterior naris) of patients suffering from CRSsNP (n=20), CRSwNP (n=20) or N-ERD (n=20) as well as from patients without CRS (=disease controls, n=20). Importantly, all subjects refrained from taking local or systemic corticosteroids or immunosuppressants for at least two weeks prior to sampling. The nasal microbiome was analyzed using 16S rRNA gene amplicon sequencing, and levels of 33 inflammatory cytokines were determined in nasal mucosal fluids using the MSD platform. Patients suffering from N-ERD and CRSwNP showed significantly worse smell perception and significantly higher levels of type 2 associated cytokines IL-5, IL-9, Eotaxin and CCL17. Across all 4 patient groups, Corynebacteria and Staphylococci showed the highest relative abundances. Although no significant difference in alpha and beta diversity was observed between the control and the CRS groups, pairwise testing revealed a higher relative abundance of Staphylococci in the middle meatus in N-ERD patients as compared to CRSwNP (p<0.001), CRSsNP (p<0.01) and disease controls (p<0.05) and of Lawsonella in patients suffering from CRSwNP in middle meatus and anterior naris in comparison to CRSsNP (p<0.0001 for both locations) and disease controls (p<0.01 and p<0.0001). Furthermore, we observed a positive correlation of Staphylococci with IL-5 (Pearson r=0.548) and a negative correlation for Corynebacteria and Eotaxin-3 (r=-0.540). Thus, in patients refraining from oral and nasal corticosteroid therapy for at least two weeks known to alter microbiome composition, we did not observe differences in microbiome alpha or beta diversity between various CRS entities and disease controls. However, our data suggest a close association between increased bacterial colonization with Staphylococci and decreased colonization by Corynebacteria as well as increased type 2 inflammation.
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Affiliation(s)
- Tina J. Bartosik
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Nicholas J. Campion
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Kilian Freisl
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - David T. Liu
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Katharina Gangl
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Victoria Stanek
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Aldine Tu
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Julia Eckl-Dorna
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
- *Correspondence: Julia Eckl-Dorna,
| | - Sven Schneider
- Department of Otorhinolaryngology, General Hospital and Medical University of Vienna, Vienna, Austria
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19
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Shrestha J, Razavi Bazaz S, Ding L, Vasilescu S, Idrees S, Söderström B, Hansbro PM, Ghadiri M, Ebrahimi Warkiani M. Rapid separation of bacteria from primary nasal samples using inertial microfluidics. LAB ON A CHIP 2022; 23:146-156. [PMID: 36484411 DOI: 10.1039/d2lc00794k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.
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Affiliation(s)
- Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Lin Ding
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Steven Vasilescu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Maliheh Ghadiri
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
- Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
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20
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The Changes in Bacterial Microbiome Associated with Immune Disorder in Allergic Respiratory Disease. Microorganisms 2022; 10:microorganisms10102066. [PMID: 36296340 PMCID: PMC9610723 DOI: 10.3390/microorganisms10102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/05/2022] [Accepted: 10/16/2022] [Indexed: 12/02/2022] Open
Abstract
Allergic respiratory disease is a worldwide and increasingly prevalent health problem. Many researchers have identified complex changes in the microbiota of the respiratory and intestinal tracts in patients with allergic respiratory diseases. These affect immune response and influence the progression of disease. However, the diversity of bacterial changes in such cases make it difficult to identify a specific microorganism to target for adjustment. Recent research evidence suggests that common bacterial variations present in allergic respiratory disease are associated with immune disorders. This finding could lead to the discovery of potential therapeutic targets in cases of allergic respiratory disease. In this review, we summarize current knowledge of bacteria changes in cases of allergic respiratory disease, to identify changes commonly associated with immune disorders, and thus provide a theoretical basis for targeting therapies of allergic respiratory disease through effective modulation of key bacteria.
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21
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Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R. Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiol Spectr 2022; 10:e0231121. [PMID: 35579429 PMCID: PMC9241827 DOI: 10.1128/spectrum.02311-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/17/2022] [Indexed: 12/13/2022] Open
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.
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Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kriti Khare
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sujeet Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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22
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Role and Function of Regulatory T Cell in Chronic Rhinosinusitis with Nasal Polyposis. J Immunol Res 2022; 2022:1144563. [PMID: 35378904 PMCID: PMC8976649 DOI: 10.1155/2022/1144563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/28/2022] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) is a subtype of chronic rhinosinusitis characterized by high edema in the stroma, albumin deposition, and formation of pseudocysts. The pathogenesis of CRSwNP is not yet fully understood. Regulatory T (Treg) cells are a subset of CD4+ T cells that play a suppressive immunoregulatory role in the process of CRSwNP. Recent studies have found that there was a significant reduction in Treg cells in polyp tissues, which leads to the onset of CRSwNP. An imbalance between Th17 and Treg cells can also aggravate inflammation toward the Th2 type. This review focuses on our understanding of the function and role of Treg cells and their regulatory factors and clinical significance in CRSwNP. We also summarize the current drug treatments for CRSwNP with Tregs as the potential therapeutic target, which will provide new ideas for the treatment of CRSwNP in the future.
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23
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16SrDNA-Based Detection Technology in Patients with Chronic Pharyngitis to Analyze the Distribution Characteristics of Pharyngeal Bacteria. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:5186991. [PMID: 35310189 PMCID: PMC8933068 DOI: 10.1155/2022/5186991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022]
Abstract
In order to analyze the distribution characteristics of pharyngeal bacteria in patients with chronic pharyngitis (CP) by 16SrDNA-based detection technology, a prospective study is conducted to collect pharyngeal secretion samples from patients diagnosed with CP who are admitted to the Otorhinolaryngology Department of The Third People's Hospital of Shenzhen from May 2021 to September 2021. Among them, 11 cases are chronic simple pharyngitis (CSP), 11 cases are chronic hypertrophic pharyngitis (CHP), and 8 cases are healthy subjects. All samples are detected by the 16SrDNA technique and analyzed by bioinformatics. 55724.64 ± 1772.80, 53697.73 ± 2252.19, and 55177.5 ± 1661.80 optimized sequences are obtained by 16SrDNA sequencing. The α diversity analysis of pharyngeal microflora showed that the abundance index SOBS of pharyngeal microflora is upregulated in patients with CHP compared with normal controls (NC), but the diversity index of pharyngeal bacteria in the three groups is not significantly changed, indicating that the abundance of pharyngeal bacteria in the CHP group is increased. The β diversity analysis of pharyngeal microflora showed that the three groups are similar in structure and composition, and there is no significant statistical difference. The structural difference analysis of pharyngeal flora combined with LEfSe difference analysis showed that at the phylum level, the relative abundance of Spirochaetes and Synergistetes in the CHP group is significantly higher than that in the CSP group. At the genus level, the relative abundance of opportunistic pathogens such as Selenomonas and Campylobacter increased significantly in the CSP group. The relative abundance of Escherichia, Mycoplasma, and Porphyromonas are significantly increased in the CHP group. The abundance of beneficial symbiotic bacteria decreased significantly in patients with CP. The pharyngitis of patients with CP is characterized by an increase in the abundance of pharyngitis, changes in the structure of pharyngitis, a decline in the symbiotic beneficial bacteria, and an increase in the content of opportunistic pathogens, which may be closely related to the onset and development of CP.
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24
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Horn KJ, Jaberi Vivar AC, Arenas V, Andani S, Janoff EN, Clark SE. Corynebacterium Species Inhibit Streptococcus pneumoniae Colonization and Infection of the Mouse Airway. Front Microbiol 2022; 12:804935. [PMID: 35082772 PMCID: PMC8784410 DOI: 10.3389/fmicb.2021.804935] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022] Open
Abstract
The stability and composition of the airway microbiome is an important determinant of respiratory health. Some airway bacteria are considered to be beneficial due to their potential to impede the acquisition and persistence of opportunistic bacterial pathogens such as Streptococcus pneumoniae. Among such organisms, the presence of Corynebacterium species correlates with reduced S. pneumoniae in both adults and children, in whom Corynebacterium abundance is predictive of S. pneumoniae infection risk. Previously, Corynebacterium accolens was shown to express a lipase which cleaves host lipids, resulting in the production of fatty acids that inhibit growth of S. pneumoniae in vitro. However, it was unclear whether this mechanism contributes to Corynebacterium-S. pneumoniae interactions in vivo. To address this question, we developed a mouse model for Corynebacterium colonization in which colonization with either C. accolens or another species, Corynebacterium amycolatum, significantly reduced S. pneumoniae acquisition in the upper airway and infection in the lung. Moreover, the lungs of co-infected mice had reduced pro-inflammatory cytokines and inflammatory myeloid cells, indicating resolution of infection-associated inflammation. The inhibitory effect of C. accolens on S. pneumoniae in vivo was mediated by lipase-dependent and independent effects, indicating that both this and other bacterial factors contribute to Corynebacterium-mediated protection in the airway. We also identified a previously uncharacterized bacterial lipase in C. amycolatum that is required for inhibition of S. pneumoniae growth in vitro. Together, these findings demonstrate the protective potential of airway Corynebacterium species and establish a new model for investigating the impact of commensal microbiota, such as Corynebacterium, on maintaining respiratory health.
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Affiliation(s)
- Kadi J. Horn
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexander C. Jaberi Vivar
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Vera Arenas
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sameer Andani
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Edward N. Janoff
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, United States
- Denver Veterans Affairs Medical Center, Aurora, CO, United States
| | - Sarah E. Clark
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
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25
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Korkmaz H, Çetinkol Y, Korkmaz M, Çalgın MK, Kaşko Arıcı Y. Effect of Antibiotic Exposure on Upper Respiratory Tract Bacterial Flora. Med Sci Monit 2022; 28:e934931. [PMID: 34987147 PMCID: PMC8750656 DOI: 10.12659/msm.934931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background The human microbiota modulates the immune system and forms the surface flora. Antibiotic administration causes dysbiosis in the intestinal flora. It is not clear if antibiotic administration in the community effects the upper airway flora in the mid-term or long-term. This study aims to define long-term influence of antibiotics on upper airway flora. Material/Methods In this prospective study, aerobic microbiological analysis of nasal and nasopharyngeal surfaces was performed. Antibiotic administration history of the last 6 months was retrieved using the social insurance database. Culture results of antibiotic-treated and antibiotic-naïve subjects were compared by Pearson’s chi-square test or Fisher’s exact test. Results A total of 210 subjects were included in the study. Normal flora were documented in 86 nasal swabs and 99 nasopharyngeal swabs. Most of the remaining cases demonstrated gram-positive bacterial overgrowth. There were 113 subjects who did not receive any antibiotic, and 93% of the remaining 97 patients received broad-spectrum antibiotics. Statistical analysis showed that nasal and nasopharyngeal flora did not change upon antibiotic administration, but antibiotic administration during the last month caused increased methicillin resistance development of coagulase-negative Staphylococcus and Staphylococcus aureus microorganisms. Conclusions Antibiotic exposure did not lead to perturbations in general composition of upper airway flora within 6 months, although the incidence of methicillin resistance in coagulase-positive and -negative Staphylococci demonstrated significant increases when patients received antibiotic during the last month. This should be considered in case of broad-spectrum antibiotic administration, since methicillin resistance increases the morbidity and mortality of nosocomial Staphylococcus infections.
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Affiliation(s)
- Hakan Korkmaz
- Department of Otorhinolaryngology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Yeliz Çetinkol
- Department of Medical Microbiology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Mukadder Korkmaz
- Department of Otorhinolaryngology, Private Practice, Ordu, Turkey
| | - Mustafa Kerem Çalgın
- Department of Medical Microbiology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Yeliz Kaşko Arıcı
- Department of Biostatistics and Medical Informatics, Ordu University Faculty of Medicine, Ordu, Turkey
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26
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27
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Nepal R, Houtak G, Shaghayegh G, Bouras G, Shearwin K, Psaltis AJ, Wormald PJ, Vreugde S. Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps. Microb Genom 2021; 7. [PMID: 34907894 PMCID: PMC8767322 DOI: 10.1099/mgen.0.000726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in Staphylococcus aureus from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various in silico tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund–Mackay scores. Fifty-eight S. aureus clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %) S. aureus strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as sak, scn, chp, lukE/D, sea. Intact prophages were more frequently identified in CRSwNP than in CRSsNP (P=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (P=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (P=0.007). Our results expand the knowledge of prophages in S. aureus isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system, S. aureus evolution and CRS disease pathophysiology.
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Affiliation(s)
- Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Keith Shearwin
- School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia.,The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
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Bianco MR, Ralli M, Modica DM, Amata M, Poma S, Mattina G, Allegra E. The Role of Probiotics in Chronic Rhinosinusitis Treatment: An Update of the Current Literature. Healthcare (Basel) 2021; 9:healthcare9121715. [PMID: 34946441 PMCID: PMC8701913 DOI: 10.3390/healthcare9121715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is a significant health problem. It affects 5–12% of the general population. The causes that underlie the onset of CRS are not yet well known. However, many factors may contribute to its onset, such as environmental factors and the host’s general condition. Medical treatment mainly uses local corticosteroids, nasal irrigation, and antibiotics. In recent years, a new therapeutic approach that employs the use of probiotics emerged. Probiotics have been extensively studied as a therapy for dysbiosis and inflammatory pathologies of various parts of the body. We aimed to examine the studies in vivo and in vitro and clinicals reports in the existing literature to update probiotics’ role in rhinosinusitis chronic medical treatment.
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Affiliation(s)
- Maria Rita Bianco
- Otolaryngology-Department of Health Science, University of Catanzaro, 88100 Catanzaro, Italy;
- Correspondence: ; Tel.: +39-0961-3647130; Fax: +39-0961-3647131
| | - Massimo Ralli
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy;
| | - Domenico Michele Modica
- Otolaryngology Unit-“Villa Sofia”-Cervello Hospital, 90146 Palermo, Italy; (D.M.M.); (S.P.); (G.M.)
| | - Marta Amata
- Department of Biomedicine and Internal and Specialistic Medicine (DIBIMIS), University of Palermo, 90133 Palermo, Italy;
| | - Salvatore Poma
- Otolaryngology Unit-“Villa Sofia”-Cervello Hospital, 90146 Palermo, Italy; (D.M.M.); (S.P.); (G.M.)
| | - Gianfranco Mattina
- Otolaryngology Unit-“Villa Sofia”-Cervello Hospital, 90146 Palermo, Italy; (D.M.M.); (S.P.); (G.M.)
| | - Eugenia Allegra
- Otolaryngology-Department of Health Science, University of Catanzaro, 88100 Catanzaro, Italy;
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Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
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Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Particulate Matter Exposure and Allergic Rhinitis: The Role of Plasmatic Extracellular Vesicles and Bacterial Nasal Microbiome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182010689. [PMID: 34682436 PMCID: PMC8535327 DOI: 10.3390/ijerph182010689] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/11/2022]
Abstract
Particulate matter (PM) exposure is linked to the worsening of respiratory conditions, including allergic rhinitis (AR), as it can trigger nasal and systemic inflammation. To unveil the underlying molecular mechanisms, we investigated the effects of PM exposure on the release of plasmatic extracellular vesicles (EV) and on the complex cross-talk between the host and the nasal microbiome. To this aim, we evaluated the effects of PM10 and PM2.5 exposures on both the bacteria-derived-EV portion (bEV) and the host-derived EVs (hEV), as well as on bacterial nasal microbiome (bNM) features in 26 AR patients and 24 matched healthy subjects (HS). In addition, we assessed the role exerted by the bNM as a modifier of PM effects on the complex EV signaling network in the paradigmatic context of AR. We observed that PM exposure differently affected EV release and bNM composition in HS compared to AR, thus potentially contributing to the molecular mechanisms underlying AR. The obtained results represent the first step towards the understanding of the complex signaling network linking external stimuli, bNM composition, and the immune risponse.
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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: 4] [Impact Index Per Article: 1.3] [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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Elgamal Z, Singh P, Geraghty P. The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease. ACTA ACUST UNITED AC 2021; 57:medicina57080823. [PMID: 34441029 PMCID: PMC8402057 DOI: 10.3390/medicina57080823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.
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Affiliation(s)
- Ziyad Elgamal
- Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
| | - Pratyush Singh
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada;
| | - Patrick Geraghty
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
- Correspondence: ; Tel.: +1-718-270-3141
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刘 肖, 刘 红, 李 春. [Advances in the study of chronic sinusitis microbiology using 16SrRNA gene sequencing technology]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2021; 35:658-661. [PMID: 34304501 PMCID: PMC10127899 DOI: 10.13201/j.issn.2096-7993.2021.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 11/12/2022]
Abstract
Traditional conventional bacterial culture techniques can cultivate fewer types of bacteria, aiming to isolate and identify specific pathogens, guide antibiotic treatment and eradicate pathogens.Macrogenomics techniques can simultaneously identify both cultured and uncultured bacteria in the flora, providing the possibility for the study of symbiotic flora. With the vigorous development of SrRNA and application of 16 gene sequencing technology, the microbial ecology research of chronic sinusitis (chronic rhinosinusitis,CRS) has once again become a hot topic.And the CRS view of microbial community composition and microbial diversity were presented. This review describes the use of 16 SrRNA gene sequencing in recent years advances in technical studies CRS microbial ecology.
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Affiliation(s)
- 肖 刘
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
| | - 红兵 刘
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
| | - 春花 李
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
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Kim YS, Han D, Mo JH, Kim YM, Kim DW, Choi HG, Park JW, Shin HW. Antibiotic-Dependent Relationships Between the Nasal Microbiome and Secreted Proteome in Nasal Polyps. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2021; 13:589-608. [PMID: 34212546 PMCID: PMC8255347 DOI: 10.4168/aair.2021.13.4.589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/27/2020] [Accepted: 12/27/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Chronic rhinosinusitis (CRS) is a heterogeneous chronic inflammatory condition of the paranasal sinuses and nasal passages. Although antibiotics are used to reduce inflammation or to treat an episode of acute rhinosinusitis, their effects on the nasal environment and host response in CRS is unclear. METHODS We analyzed the effects of antibiotics on the nasal microbiome and secreted proteome in CRS using multi-omic analysis. Nasal secretions were collected from 29 controls, 30 CRS patients without nasal polyps (NP), and 40 CRS patients with NP. A total of 99 subjects were divided into 2 groups that included subjects who had taken antibiotics 3 months prior to sampling and those who had not. We performed 16S ribosomal DNA sequence analyses and Orbitrap mass spectrometry-based proteomic analyses. Spearman correlation was used to assess the correlations between the nasal microbiome and secreted proteome. RESULTS The associations between the nasal microbiome and secreted proteome were noted in subjects who had used antibiotics. Antibiotics could have stronger effects on their associations in patients with CRS with NP than in those without. It remains unknown whether these holistic changes caused by antibiotics are beneficial or harmful to CRS, however, the associations could be differentially affected by disease severity. CONCLUSION These findings provide new insight into the nasal environment and the host response in CRS.
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Affiliation(s)
- Yi Sook Kim
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Hun Mo
- Department of Otorhinolaryngology-Head and Neck Surgery, Dankook University Hospital, Cheonan, Korea
- Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Yong Min Kim
- Clinical Mucosal Immunology Study Group, Seoul, Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Chungnam National University Hospital, Daejeon, Korea
| | - Dae Woo Kim
- Clinical Mucosal Immunology Study Group, Seoul, Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Boramae Medical Center; Seoul, Korea
| | - Hyo Guen Choi
- Department of Otorhinolaryngology-Head & Neck Surgery, Hallym University College of Medicine, Anyang, Korea
| | - Jong Wan Park
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Woo Shin
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Clinical Mucosal Immunology Study Group, Seoul, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Korea.
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Tai J, Han MS, Kwak J, Kim TH. Association Between Microbiota and Nasal Mucosal Diseases in terms of Immunity. Int J Mol Sci 2021; 22:4744. [PMID: 33947066 PMCID: PMC8124637 DOI: 10.3390/ijms22094744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/23/2022] Open
Abstract
The pathogenesis of nasal inflammatory diseases is related to various factors such as anatomical structure, heredity, and environment. The nasal microbiota play a key role in coordinating immune system functions. Dysfunction of the microbiota has a significant impact on the occurrence and development of nasal inflammation. This review will introduce the positive and negative roles of microbiota involved in immunity surrounding nasal mucosal diseases such as chronic sinusitis and allergic rhinitis. In addition, we will also introduce recent developments in DNA sequencing, metabolomics, and proteomics combined with computation-based bioinformatics.
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Affiliation(s)
- Junhu Tai
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea
| | - Mun Soo Han
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea
| | - Jiwon Kwak
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea
| | - Tae Hoon Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, College of Medicine, Korea University, Seoul 02841, Korea
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Siu J, Mackenzie BW, Klingler L, Biswas K, Wang Y, Hung CT, Jeong SH, Barnett D, Tingle MD, Douglas RG. Sinonasal and gastrointestinal bacterial composition and abundance are stable after 1 week of once-daily oral antibiotic treatment for chronic rhinosinusitis. Int Forum Allergy Rhinol 2021; 11:1355-1366. [PMID: 33877743 DOI: 10.1002/alr.22799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Despite the widespread prescription of antibiotics for the treatment of chronic rhinosinusitis (CRS), their efficacy remains uncertain. Limited penetration of systemic antibiotics into the sinonasal mucosa has been reported previously by this group. This study aimed to investigate the short-term effects of antibiotics on the sinus and gut microbiota as well as any relationships these had with drug distribution. METHODS Thirty subjects undergoing functional endoscopic sinus surgery for CRS were randomized to one of three groups: (1) doxycycline (100 mg daily for 7 days); (2) roxithromycin (300 mg daily for 7 days); and (3) control (no antibiotics given). Sinonasal and stool samples collected before and after treatment were analyzed using 16S ribosomal RNA (rRNA) gene-targeted amplicon sequencing and Droplet Digital polymerase chain reaction (PCR) for bacterial community composition and the quantification of bacterial DNA, respectively. RESULTS There were no significant major bacterial community shifts or changes to bacterial diversity and load following the treatment period in all patient groups. Non-significant trend reductions were observed in gut microbial diversity with antibiotics. For the roxithromycin group, sinonasal bacterial diversity was negatively correlated with serum drug levels and reduced overall compared to controls (p < 0.05). The relative abundance of Staphylococcus ASV129 in sinonasal samples reduced with increasing mucus doxycycline levels (p = 0.01). CONCLUSION Antibiotic prescription for CRS should be further investigated because of preliminary evidence of poor sinonasal drug penetration, unproven efficacy, and the potential impact of dysbiosis in the sinuses and off-target sites. Further studies should consider distinguishing the presence of DNA from viable and nonviable bacteria.
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Affiliation(s)
- Joey Siu
- Department of Surgery, University of Auckland, Auckland, New Zealand
| | | | - Lilian Klingler
- Research and Development, Zenith Technology Corporation Limited, Dunedin, New Zealand
| | - Kristi Biswas
- Department of Surgery, University of Auckland, Auckland, New Zealand
| | - Yi Wang
- Research and Development, Zenith Technology Corporation Limited, Dunedin, New Zealand
| | - Cheung-Tak Hung
- Research and Development, Zenith Technology Corporation Limited, Dunedin, New Zealand
| | - Soo Hee Jeong
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Daniel Barnett
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Malcolm Drummond Tingle
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
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Cho SW, Kim DY, Choi S, Won S, Kang HR, Yi H. Microbiome profiling of uncinate tissue and nasal polyps in patients with chronic rhinosinusitis using swab and tissue biopsy. PLoS One 2021; 16:e0249688. [PMID: 33831071 PMCID: PMC8031401 DOI: 10.1371/journal.pone.0249688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/19/2021] [Indexed: 12/26/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is characterized according to the presence or absence of nasal polyps (NPs) and displays nasal microbiota dysbiosis. However, optimal sampling methods of the nasal microbiome in CRS have not been identified. We aimed to assess the microbial composition in patients with CRS, comparing different sampling methods (swab and tissue biopsy), tissue types (uncinate tissue and NP), and disease subtypes. Samples were obtained by swabbing the middle meatus and taking a biopsy of uncinate tissue (UT) in patients with CRS with (CRSwNP, N = 8) or without NP (CRSsNP, N = 6) and controls (N = 8). NPs were also harvested in CRSwNP. DNAs were extracted from fifty-two samples and analyzed by 16S rRNA gene amplicon sequencing. As a result, a great interpersonal variance was observed in nasal swabs, while UT samples presented distinct microbiome with low inter-personal differences. Moreover, the UT microbiomes were further differentiated into three clusters which are associated with disease status (control, CRSsNP, and CRSwNP). Compared to UT, NP revealed a unique microbiome profile with significantly less bacterial diversity. Prevotella was the genus whose abundance was negatively correlated with disease severity in NP. In conclusion, tissue samples are better specimens than nasal swabs for assessing the microbiomes of CRS patients. Several bacteria in UT and NP tissues revealed an association with clinical severity of CRSwNP.
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Affiliation(s)
- Sung-Woo Cho
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Young Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungmi Choi
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Hye-Ryun Kang
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- * E-mail: (HRK); (HY)
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Republic of Korea
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
- * E-mail: (HRK); (HY)
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Szaleniec J, Gibała A, Hartwich P, Hydzik-Sobocińska K, Konior M, Gosiewski T, Szaleniec M. Challenging the gold standard: methods of sampling for microbial culture in patients with chronic rhinosinusitis. Eur Arch Otorhinolaryngol 2021; 278:4795-4803. [PMID: 33772608 PMCID: PMC8553703 DOI: 10.1007/s00405-021-06747-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
Purpose Chronic rhinosinusitis (CRS) is a highly prevalent multifactorial disorder. Culture-directed antibiotics are frequently prescribed to patients with CRS and the middle nasal meatus (MM) is traditionally believed to be a representative sampling site of the sinuses as a whole. The purpose of our study was to reevaluate the reliability of the MM as a sampling site in patients with CRS who suffer from impaired drainage from the sinuses to the MM. Methods Swabs and tissue biopsies were collected from the MM, maxillary sinus and frontal sinus from 50 patients with CRS. The results of bacterial culture were compared between sampling methods and sites in relation to the patency of the sinus ostia. Results 782 bacterial isolates were cultured from the samples. Concordant results between the MM and the sinus cavity were noted in 80% of patients for the maxillary sinus, but only 66% for the frontal sinus and 76% for the sinuses a whole. The differences were similarly prevalent in patients with open and occluded sinus ostia. Notably, swabs from all three sites provided representative information in 92% of patients and tissue biopsies did not provide additional information compared to multiple swabs. Conclusion The traditional method of sampling from the middle meatus provides inadequate information in 24% of patients with CRS, which may result in inadequate antibiotic therapy and contribute to increasing antibiotic resistance. Additional sampling from the sinuses should be recommended whenever possible, while invasive sampling is not necessary. Supplementary Information The online version contains supplementary material available at 10.1007/s00405-021-06747-z.
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Affiliation(s)
- Joanna Szaleniec
- Department of Otolaryngology, Faculty of Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688, Kraków, Poland.
| | - Agnieszka Gibała
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
- Department of Molecular Medical Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Patryk Hartwich
- Department of Otolaryngology, Faculty of Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Karolina Hydzik-Sobocińska
- Department of Otolaryngology, Faculty of Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Marcin Konior
- Department of Otolaryngology, Faculty of Medicine, Jagiellonian University Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Tomasz Gosiewski
- Department of Molecular Medical Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Czysta 18, 31-121, Krakow, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
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The influence of nasal microbiome diversity and inflammatory patterns on the prognosis of nasal polyps. Sci Rep 2021; 11:6364. [PMID: 33737534 PMCID: PMC7973562 DOI: 10.1038/s41598-021-85292-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 02/05/2023] Open
Abstract
To understand the inflammatory microenvironment and microbiome factors for prognosis of chronic rhinosinusitis with polyps (CRSwNP), we explored the difference in characteristics of the microbiome of the nasal sinuses and inflammatory cytokines between recurrent and non-recurrent groups. We collected nasal secretions and polyp tissue from 77 CRSwNP patients. Then, we extracted microbial DNA from cotton swabs, performed high-throughput sequencing based on 16S rRNA to detect bacterial community composition, and analyzed cytokines such as IL-5, IL-8, IL-17a, IL-17e, IL-18, IL-27 and INF-gamma from polyp tissue using Luminex. The eosinophil and neutrophil cells in the peripheral blood and polyp tissue were counted. Postoperative follow-up of patients with CRSwNP for 1 year was conducted to record the recurrence of nasal polyps and analyze the correlation between the recurrence of nasal polyps and the characteristics of inflammatory cytokines, inflammatory cell count and nasal microbial diversity. After 1 year of follow-up, there were 12 recurrent patients, including 5 males and 7 females. Postoperative recurrence of nasal polyps was not significantly correlated with age, sex, asthma, allergic rhinitis or other allergic diseases in CRSwNP patients. In terms of the total nasal symptom score, the recurrent group was significantly higher than the non-recurrent group. In nasal polyp tissues, eosinophils (40.83/HP) and neutrophils (30.83/HP) in patients with CRSwNP in the recurrent group were significantly higher than those in the non-recurrent group (13.72/HP), and neutrophils (18.5/HP) were also significantly higher in the recurrent group than the non-recurrent group. The expression levels of IFN-, IL-17A, IL-17E and IL-18 were significantly higher in the recurrent group than in the non-recurrent group, and the positive rates were not different. In Southwest China, Enterobacteria and anaerobic bacteria may be correlated with the inflammatory pattern expression of nasal polyps. The neutrophil-mediated inflammatory response plays an important role in patients with CRSwNP in Southwest China and is correlated with nasal polyp recurrence. Recurrence of nasal polyps after endoscopic sinus surgery may be potentially associated with a reduced abundance of protective microorganisms and an increased number of pathogenic microorganisms.
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Orlandi RR, Kingdom TT, Smith TL, Bleier B, DeConde A, Luong AU, Poetker DM, Soler Z, Welch KC, Wise SK, Adappa N, Alt JA, Anselmo-Lima WT, Bachert C, Baroody FM, Batra PS, Bernal-Sprekelsen M, Beswick D, Bhattacharyya N, Chandra RK, Chang EH, Chiu A, Chowdhury N, Citardi MJ, Cohen NA, Conley DB, DelGaudio J, Desrosiers M, Douglas R, Eloy JA, Fokkens WJ, Gray ST, Gudis DA, Hamilos DL, Han JK, Harvey R, Hellings P, Holbrook EH, Hopkins C, Hwang P, Javer AR, Jiang RS, Kennedy D, Kern R, Laidlaw T, Lal D, Lane A, Lee HM, Lee JT, Levy JM, Lin SY, Lund V, McMains KC, Metson R, Mullol J, Naclerio R, Oakley G, Otori N, Palmer JN, Parikh SR, Passali D, Patel Z, Peters A, Philpott C, Psaltis AJ, Ramakrishnan VR, Ramanathan M, Roh HJ, Rudmik L, Sacks R, Schlosser RJ, Sedaghat AR, Senior BA, Sindwani R, Smith K, Snidvongs K, Stewart M, Suh JD, Tan BK, Turner JH, van Drunen CM, Voegels R, Wang DY, Woodworth BA, Wormald PJ, Wright ED, Yan C, Zhang L, Zhou B. International consensus statement on allergy and rhinology: rhinosinusitis 2021. Int Forum Allergy Rhinol 2021; 11:213-739. [PMID: 33236525 DOI: 10.1002/alr.22741] [Citation(s) in RCA: 357] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
I. EXECUTIVE SUMMARY BACKGROUND: The 5 years since the publication of the first International Consensus Statement on Allergy and Rhinology: Rhinosinusitis (ICAR-RS) has witnessed foundational progress in our understanding and treatment of rhinologic disease. These advances are reflected within the more than 40 new topics covered within the ICAR-RS-2021 as well as updates to the original 140 topics. This executive summary consolidates the evidence-based findings of the document. METHODS ICAR-RS presents over 180 topics in the forms of evidence-based reviews with recommendations (EBRRs), evidence-based reviews, and literature reviews. The highest grade structured recommendations of the EBRR sections are summarized in this executive summary. RESULTS ICAR-RS-2021 covers 22 topics regarding the medical management of RS, which are grade A/B and are presented in the executive summary. Additionally, 4 topics regarding the surgical management of RS are grade A/B and are presented in the executive summary. Finally, a comprehensive evidence-based management algorithm is provided. CONCLUSION This ICAR-RS-2021 executive summary provides a compilation of the evidence-based recommendations for medical and surgical treatment of the most common forms of RS.
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Affiliation(s)
| | | | | | | | | | - Amber U Luong
- University of Texas Medical School at Houston, Houston, TX
| | | | - Zachary Soler
- Medical University of South Carolina, Charleston, SC
| | - Kevin C Welch
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | | | | | | | - Claus Bachert
- Ghent University, Ghent, Belgium.,Karolinska Institute, Stockholm, Sweden.,Sun Yatsen University, Gangzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David A Gudis
- Columbia University Irving Medical Center, New York, NY
| | - Daniel L Hamilos
- Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Richard Harvey
- University of New South Wales and Macquarie University, Sydney, New South Wales, Australia
| | | | | | | | | | - Amin R Javer
- University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | | | | | | | | | | | | | | | | - Valerie Lund
- Royal National Throat Nose and Ear Hospital, UCLH, London, UK
| | - Kevin C McMains
- Uniformed Services University of Health Sciences, San Antonio, TX
| | | | - Joaquim Mullol
- IDIBAPS Hospital Clinic, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | - Alkis J Psaltis
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | | | - Luke Rudmik
- University of Calgary, Calgary, Alberta, Canada
| | - Raymond Sacks
- University of New South Wales, Sydney, New South Wales, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | - De Yun Wang
- National University of Singapore, Singapore, Singapore
| | | | | | | | - Carol Yan
- University of California San Diego, La Jolla, CA
| | - Luo Zhang
- Capital Medical University, Beijing, China
| | - Bing Zhou
- Capital Medical University, Beijing, China
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Menberu MA, Liu S, Cooksley C, Hayes AJ, Psaltis AJ, Wormald PJ, Vreugde S. Corynebacterium accolens Has Antimicrobial Activity against Staphylococcus aureus and Methicillin-Resistant S. aureus Pathogens Isolated from the Sinonasal Niche of Chronic Rhinosinusitis Patients. Pathogens 2021; 10:pathogens10020207. [PMID: 33672855 PMCID: PMC7918835 DOI: 10.3390/pathogens10020207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
Corynebacterium accolens is the predominant species of the healthy human nasal microbiota, and its relative abundance is decreased in the context of chronic rhinosinusitis (CRS). This study aimed to evaluate the antimicrobial potential of C. accolens isolated from a healthy human nasal cavity against planktonic and biofilm growth of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) clinical isolates (CIs) from CRS patients. Nasal swabs from twenty non-CRS control subjects were screened for the presence of C. accolens using microbiological and molecular techniques. C. accolens CIs and their culture supernatants were tested for their antimicrobial activity against eight S. aureus and eight MRSA 4CIs and S. aureus ATCC25923. The anti-biofilm potential of C. accolens cell-free culture supernatants (CFCSs) on S. aureus biofilms was also assessed. Of the 20 nasal swabs, 10 C. accolens CIs were identified and confirmed with rpoB gene sequencing. All isolates showed variable antimicrobial activity against eight out of 8 S. aureus and seven out of eight MRSA CIs. Culture supernatants from all C. accolens CIs exhibited a significant dose-dependent antibacterial activity (p < 0.05) against five out of five representative S. aureus and MRSA CIs. This inhibition was abolished after proteinase K treatment. C. accolens supernatants induced a significant reduction in metabolic activity and biofilm biomass of S. aureus and MRSA CIs compared to untreated growth control (p < 0.05). C. accolens exhibited antimicrobial activity against S. aureus and MRSA CIs in both planktonic and biofilm forms and holds promise for the development of innovative probiotic therapies to promote sinus health.
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Affiliation(s)
- Martha Alemayehu Menberu
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar 196, Ethiopia
| | - Sha Liu
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
| | - Clare Cooksley
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
| | - Andrew James Hayes
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne and The Royal Melbourne Hospital, Melbourne 3000, Australia;
| | - Alkis James Psaltis
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
| | - Sarah Vreugde
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville 5011, Australia; (M.A.M.); (S.L.); (C.C.); (A.J.P.); (P.-J.W.)
- Correspondence: ; Tel.: +61-(0)8-8222-6928
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刘 肖, 刘 红, 李 春. [The role of bacterial infection in the pathogenesis of chronic sinusitis]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2021; 35:189-192. [PMID: 33541008 PMCID: PMC10127868 DOI: 10.13201/j.issn.2096-7993.2021.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Indexed: 11/12/2022]
Abstract
Chronic rhinosinusitis(CRS) is a highly heterogeneous chronic inflammatory disease of the sinus mucosa. Despite extensive research, the etiology of CRS remains unclear. Studies of upper respiratory tract microbiology have found that microorganisms may be the influencing factors of CRS, and bacteria may be the potential pathogenic factors of CRS. The study of the role of bacterial infection in the initiation, development and maintenance of CRS has become a hot spot in the pathogenesis of CRS. In this review, we describes the research progress of the relationship between bacteria infection and CRS.
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Affiliation(s)
- 肖 刘
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
| | - 红兵 刘
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
| | - 春花 李
- 南昌大学第二附属医院耳鼻咽喉头颈外科(南昌,330006)
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Hoggard M, Jacob B, Wheeler D, Zoing M, Chang K, Biswas K, Middleditch M, Douglas RG, Taylor MW. Multiomic analysis identifies natural intrapatient temporal variability and changes in response to systemic corticosteroid therapy in chronic rhinosinusitis. IMMUNITY INFLAMMATION AND DISEASE 2020; 9:90-107. [PMID: 33220024 PMCID: PMC7860613 DOI: 10.1002/iid3.349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 08/29/2020] [Indexed: 01/07/2023]
Abstract
INTRODUCTION The pathophysiology and temporal dynamics of affected tissues in chronic rhinosinusitis (CRS) remain poorly understood. Here, we present a multiomics-based time-series assessment of nasal polyp biopsies from three patients with CRS, assessing natural variability over time and local response to systemic corticosteroid therapy. METHODS Polyp tissue biopsies were collected at three time points over two consecutive weeks. Patients were prescribed prednisone (30 mg daily) for 1 week between Collections 2 and 3. Polyp transcriptome, proteome, and microbiota were assessed via RNAseq, SWATH mass spectrometry, and 16S ribosomal RNA and ITS2 amplicon sequencing. Baseline interpatient variability, natural intrapatient variability over time, and local response to systemic corticosteroids, were investigated. RESULTS Overall, the highly abundant transcripts and proteins were associated with pathways involved in inflammation, FAS, cadherin, integrin, Wnt, apoptosis, and cytoskeletal signaling, as well as coagulation and B- and T-cell activation. Transcripts and proteins that naturally varied over time included those involved with inflammation- and epithelial-mesenchymal transition-related pathways, and a number of common candidate target biomarkers of CRS. Ten transcripts responded significantly to corticosteroid therapy, including downregulation of TNF, CCL20, and GSDMA, and upregulation of OVGP1, and PCDHGB1. Members of the bacterial genus Streptococcus positively correlated with immunoglobulin proteins IGKC and IGHG1. CONCLUSIONS Understanding natural dynamics of CRS-associated tissues is essential to provide baseline context for all studies on putative biomarkers, mechanisms, and subtypes of CRS. These data further our understanding of the natural dynamics within nasal polypoid tissue, as well as local changes in response to systemic corticosteroid therapy.
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Affiliation(s)
- Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Bincy Jacob
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Auckland Science Analytical Services, The University of Auckland, Auckland, New Zealand
| | - David Wheeler
- Nextgen Bioinformatic Services, Palmerston North, New Zealand
| | - Melissa Zoing
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Kevin Chang
- Department of Statistics, Statistical Consulting Centre, The University of Auckland, Auckland, New Zealand
| | - Kristi Biswas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Martin Middleditch
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Auckland Science Analytical Services, The University of Auckland, Auckland, New Zealand
| | - Richard G Douglas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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Gan W, Zhang H, Yang F, Liu S, Liu F, Meng J. The influence of nasal bacterial microbiome diversity on the pathogenesis and prognosis of chronic rhinosinusitis patients with polyps. Eur Arch Otorhinolaryngol 2020; 278:1075-1088. [PMID: 32960349 DOI: 10.1007/s00405-020-06370-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/10/2020] [Indexed: 02/05/2023]
Abstract
PURPOSE The role of the microbiome in the paranasal sinuses and its contribution to sinus mucosal health and disease remains poorly understood. Consequently, we examined the nasal microbiome of chronic rhinosinusitis patients with polyps (CRSwNP), chronic sinusitis without nasal polyps (CRSsNP) and a control population, associated with IL-5 of nasal polyp tissues and postoperative follow-up of CRSwNP patients, in search of nasal microbial community characteristics related to pathogenesis and prognosis of CRSwNP, providing a new perspective for further understanding of the disease. METHODS The middle meatus secretions of 77 CRSwNP, 36 CRSsNP and 34 non-CRS subjects were collected. The bacterial microbiome composition was detected using high-throughput sequencing technology based on 16S rRNA, and the differences in the nasal microbial diversity among the three groups were compared. At the same time, nasal polyp tissues were collected to detect the expression of IL-5 and analyse its relationship with the structural characteristics of nasal microbial colonies. Postoperative follow-up of patients with CRSwNP was conducted for 1 year to record the recurrence of nasal polyps and analyse the correlation between the recurrence of nasal polyps and IL-5 as well as the characteristics of nasal microbial diversity. RESULTS The results showed that the average Sobs index (579.31) of the non-CRS group was significantly higher than that of the CRSwNP group (387.31, P = 0.03). PCoA analysis showed that the microbial distribution in the three groups was mostly similar, with only a few unique to each group. At the phylum level, Actinobacteria and Chlamydia in the non-CRS group were significantly higher than those in the CRSwNP and CRSsNP groups. At the genus level, Corynebacterium and Dolosigranulum in the non-CRS group were significantly higher than those in the CRSwNP and CRSsNP groups. Twenty-five CRSwNP patients had nasal polyps that were IL-5 positive, accounting for 32.47%, and the relative abundance of Enterobacter was 6.37% ± 5.92%, which was significantly higher than 0.58% ± 0.11% in the IL-5 negative group. No significant difference was found after correction (p = 0.026, FDR p > 0.05). One year after surgery, 77 patients with CRSwNP who underwent surgery were successfully followed up, and 12 patients with CRSwNP relapsed, with a recurrence rate of 15.6%. Total nasal symptom scores (TNSS) were significantly higher in the recurrent group than in the nonrecurrent group (P = 0.000). No differences in microbial diversity were found between the CRSwNP populations in the recurrent group and the nonrecurrent group at both the phylum and genus levels. For the nonrecurrent CRSwNP group, the relative abundance of Actinobacteria (PDR P = 0.012) and Corynebacterium (PDR P = 0.003) was higher than that before surgery, and the relative abundance of Bacteroidetes (PDR P = 0.040) was lower than that before surgery. However, for the recurrence CRSwNP group, there was no significant difference in the nasal microbiome between postoperation and preoperation. CONCLUSION In conclusion, microbial dysbiosis in the nasal cavity is associated with the pathogenesis of CRSwNP. In Southwest China, the inflammatory pattern of nasal polyps is not dominated by eosinophilic infiltration of Th2-type inflammation. The recurrence of nasal polyps after ESS may be potentially related to the decrease in protective bacteria and the increase in pathogenic bacteria, and the improvement of postoperative bacterial disorder is correlated with the nonrecurrence of CRSwNP.
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Affiliation(s)
- Weigang Gan
- Department of Otorhinolaryngology-Head and Neck Surgery, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Hongting Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Fengjuan Yang
- Department of Otorhinolaryngology-Head and Neck Surgery, Nanchong Fifth People's Hospital, Nanchong, Sichuan, People's Republic of China
| | - Shixi Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Feng Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Juan Meng
- Department of Otorhinolaryngology-Head and Neck Surgery, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
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Abstract
Staphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae. Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae. Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae. Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae. Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigruml-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D. pigrum’s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments. IMPORTANCEStaphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae. Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae. Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.
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Wagner Mackenzie B, West AG, Waite DW, Lux CA, Douglas RG, Taylor MW, Biswas K. A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis. Front Cell Infect Microbiol 2020; 10:398. [PMID: 32850496 PMCID: PMC7423975 DOI: 10.3389/fcimb.2020.00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/29/2020] [Indexed: 01/07/2023] Open
Abstract
Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.
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Affiliation(s)
| | - Annie G. West
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - David W. Waite
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Christian A. Lux
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Richard G. Douglas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kristi Biswas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
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Welp AL, Bomberger JM. Bacterial Community Interactions During Chronic Respiratory Disease. Front Cell Infect Microbiol 2020; 10:213. [PMID: 32477966 PMCID: PMC7240048 DOI: 10.3389/fcimb.2020.00213] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.
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Affiliation(s)
- Allison L Welp
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States.,Graduate Program in Microbiology and Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
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48
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Laulajainen-Hongisto A, Toppila-Salmi SK, Luukkainen A, Kern R. Airway Epithelial Dynamics in Allergy and Related Chronic Inflammatory Airway Diseases. Front Cell Dev Biol 2020; 8:204. [PMID: 32292784 PMCID: PMC7118214 DOI: 10.3389/fcell.2020.00204] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
Allergic rhinitis, chronic rhinosinusitis, and asthma are highly prevalent, multifactorial chronic airway diseases. Several environmental and genetic factors affect airway epithelial dynamics leading to activation of inflammatory mechanisms in the airways. This review links environmental factors to host epithelial immunity in airway diseases. Understanding altered homeostasis of the airway epithelium might provide important targets for diagnostics and therapy of chronic airway diseases.
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Affiliation(s)
- Anu Laulajainen-Hongisto
- Department of Otorhinolaryngology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Sanna Katriina Toppila-Salmi
- Haartman Institute, Medicum, University of Helsinki, Helsinki, Finland.,Skin and Allergy Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Annika Luukkainen
- Haartman Institute, Medicum, University of Helsinki, Helsinki, Finland
| | - Robert Kern
- Department of Otolaryngology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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49
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Wang JC, Moore CA, Epperson MV, Sedaghat AR. Association of the sinonasal bacterial microbiome with clinical outcomes in chronic rhinosinusitis: a systematic review. Int Forum Allergy Rhinol 2020; 10:433-443. [PMID: 32052920 PMCID: PMC9290466 DOI: 10.1002/alr.22524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022]
Abstract
Background The association between sinonasal microbiome and clinical outcomes of patients with chronic rhinosinusitis (CRS) is unclear. We performed a systematic review of prior studies evaluating the CRS microbiome in relation to clinical outcomes. Methods Computerized searches of PubMed/Medline, Cochrane, and EMBASE were updated through October 2019 revealing a total of 9 studies including 244 CRS patients. A systematic review of the literature was performed, including data extraction focusing on sample region, sequencing platforms, predominant organisms, and outcomes measures. Results Nine criterion‐meeting studies included 244 CRS patients, with varied results. Eight studies used 16s–ribosomal RNA (16s‐rRNA) gene sequencing to assess the sinonasal microbiome and 1 used 16s‐rRNA PhyloChip analysis. Seven studies used Sino‐Nasal Outcome Test scores, 1 applied another CRS symptom metric, and 1 used need for additional procedures/antibiotics as the primary clinical outcome. Three studies suggest that baseline abundance of phylum Actinobacteria (specifically genus Corynebacterium) was predictive of better surgical outcome. One study found C. tuberculostearicum was positively correlated with symptom severity. Another study revealed genus Escherichia was overrepresented in CRS and had positive correlation with increased symptom scores. In addition, 1 study identified Acinetobacter johnsonii to be associated with improvement in symptom scores while supporting Pseudomonas aeruginosa as having a negative impact on quality of life. Conclusion Microbiome data are varied in their association with clinical outcomes of CRS patients. Further research is required to identify if predominance of certain microbes within the microbiome is predictive of CRS patients’ outcomes.
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Affiliation(s)
- James C Wang
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Charles A Moore
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Madison V Epperson
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Ahmad R Sedaghat
- Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
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50
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Cho DY, Hunter RC, Ramakrishnan VR. The Microbiome and Chronic Rhinosinusitis. Immunol Allergy Clin North Am 2020; 40:251-263. [PMID: 32278449 DOI: 10.1016/j.iac.2019.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic rhinosinusitis (CRS) is persistent inflammation and/or infection of the nasal cavity and paranasal sinuses. Recent advancements in culture-independent molecular techniques have enhanced understanding of interactions between sinus microbiota and upper airway microenvironment. The dysbiosis hypothesis-alteration of microbiota associated with perturbation of the local ecological landscape-is suggested as a mechanism involved in CRS pathogenesis. This review discusses the complex role of the microbiota in health and in CRS and considerations in sinus microbiome investigation, dysbiosis of sinus microbiota in CRS, microbial interactions in CRS, and development of preclinical models. The authors conclude with future directions for CRS-associated microbiome research.
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Affiliation(s)
- Do-Yeon Cho
- Department of Otolaryngology-Head & Neck Surgery, University of Alabama at Birmingham, 1155 Faculty Office Tower, 510 20th Street South, Birmingham, AL 35233, USA; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, 3-115 Microbiology Research Facility, 689 23rd Avenue SE, Minneapolis, MN 55455, USA
| | - Vijay R Ramakrishnan
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado, 12631 East 17th Avenue, B205, Aurora, CO 80045, USA.
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