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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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152
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Huntley KS, Raber J, Fine L, Bernstein JA. Influence of the Microbiome on Chronic Rhinosinusitis With and Without Polyps: An Evolving Discussion. FRONTIERS IN ALLERGY 2021; 2:737086. [PMID: 35386978 PMCID: PMC8974788 DOI: 10.3389/falgy.2021.737086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is widely prevalent within the population and often leads to decreased quality of life, among other related health complications. CRS has classically been stratified by the presence of nasal polyps (CRSwNP) or the absence nasal polyps (CRSsNP). Management of these conditions remains a challenge as investigators continue to uncover potential etiologies and therapeutic targets. Recently, attention has been given to the sinunasal microbiota as both an inciting and protective influence of CRS development. The healthy sinunasal microbiologic environment is largely composed of bacteria, with the most frequent strains including Staphylococcus aureus, Streptococcus epidermidis, and Corynebacterium genera. Disruptions in this milieu, particularly increases in S. aureus concentration, have been hypothesized to perpetuate both Th1 and Th2 inflammatory changes within the nasal mucosa, leading to CRS exacerbation and potential polyp formation. Other contributors to the sinunasal microbiota include fungi, viruses, and bacteriophages which may directly contribute to underlying inflammation or impact bacterial prevalence. Modifiable risk factors, such as smoking, have also been linked to microbiota alterations. Research interest in CRS continues to expand, and thus the goal of this review is to provide clinicians and investigators alike with a current discussion on the microbiologic influence on CRS development, particularly with respect to the expression of various phenotypes. Although this subject is rapidly evolving, a greater understanding of these potential factors may lead to novel research and targeted therapies for this often difficult to treat condition.
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Affiliation(s)
- Kyle S. Huntley
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Joshua Raber
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Lauren Fine
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jonathan A. Bernstein
- Department of Internal Medicine, Division of Immunology/Allergy Section, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Jonathan A. Bernstein
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153
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Shi Z, Li X, Wang X, Zhang L, Li L, Fu X, Sun Z, Li Z, Zhang X, Zhang M. Characteristics and Clinical Implications of the Nasal Microbiota in Extranodal NK/T-Cell Lymphoma, Nasal Type. Front Cell Infect Microbiol 2021; 11:686595. [PMID: 34568086 PMCID: PMC8461088 DOI: 10.3389/fcimb.2021.686595] [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: 04/01/2021] [Accepted: 08/25/2021] [Indexed: 01/22/2023] Open
Abstract
Natural killer/T cell lymphoma (NKTCL) most frequently affects the nasal cavity and upper aerodigestive tract (UAT) and is often mistaken for reactive disease processes, such as chronic rhinosinusitis (CRS). Recently, alterations of the nasal resident microbiota have been found in CRS. However, nasal microbial features in NKTCL have never been reported. This case-control study collected 46 NKTCL patients, 25 CRS patients and 24 matched healthy controls (HCs) to analyze nasal microbial profiles via 16S rRNA sequencing technology to improve our understanding of changes in the nasal microbiota in NKTCL. We found that alpha diversity was significantly decreased, while beta diversity was significantly increased in NKTCL compared with those in CRS and HCs. The genus Corynebacterium was significantly depleted in CRS and NKTCL versus that in HCs, while genus Staphylococcus was the most abundant in the NKTCL compared to that in the other two groups. The nasal microbial community was significantly different between UAT-NKTCL and non-UAT NKTCL patients. Importantly, based on a panel of taxa, excellent classification power with an AUC of 0.875 between UAT-NKTCL and CRS was achieved. Furthermore, the alpha diversity of the nasal microbiota was associated with several clinical covariates of NKTCL. Finally, PICRUSt analysis implicated an array of distinct functions in NKTCL that might be involved in the pathogenesis of the disease. In conclusion, the nasal microbial profile was unique in NKTCL. The nose-microbiota-UAT NKTCL axis represents a panel of promising biomarkers for clinical practice and contributes to revealing the potential pathogenesis of this malignancy.
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Affiliation(s)
- Zhuangzhuang Shi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Xin Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Xinhua Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Lei Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Ling Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Xiaorui Fu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Zhenchang Sun
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Xudong Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, China
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154
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Park SC, Park IH, Lee JS, Park SM, Kang SH, Hong SM, Byun SH, Jung YG, Hong SJ. Microbiome of Unilateral Chronic Rhinosinusitis: A Controlled Paired Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18189878. [PMID: 34574801 PMCID: PMC8469123 DOI: 10.3390/ijerph18189878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023]
Abstract
The sinonasal microbiota in human upper airway may play an important role in chronic rhinosinusitis (CRS). Thus, this study aimed to investigate the human upper airway microbiome in patients with unilateral CRS, and compare the sinonasal microbiome of the unilateral diseased site with that of a contralateral healthy site. Thirty samples, 15 each from the diseased and healthy sites, were collected from the middle meatus and/or anterior ethmoid region of 15 patients with unilateral CRS during endoscopic sinus surgery. DNA extraction and bacterial microbiome analysis via 16S rRNA gene sequencing were then performed. Corynebacterium showed the highest relative abundance, followed by Staphylococcus in samples from both the diseased and healthy sites. Further, the relative abundances of Staphylococcus and Pseudomonas were significantly lower in samples from diseased sites than in those from healthy sites. Conversely, anaerobes, including Fusobacterium, Bacteroides, and Propionibacterium, were abundantly present in samples from both sites, more so in samples from diseased sites. However, the sites showed no significant difference with respect to richness or diversity (p > 0.05). Our results indicate that CRS might be a polymicrobial infection, and also suggest that Corynebacterium and Staphylococcus may exist as commensals on the sinus mucosal surface in the upper respiratory tract.
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Affiliation(s)
- Sang Chul Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul 07441, Korea;
| | - Il-Ho Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Guro Hospital, Korea University College of Medicine, Seoul 08308, Korea;
- Medical Device Usability Test Center, Guro Hospital, Korea University College of Medicine, Seoul 08308, Korea
| | - Joong Seob Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Hallym Sacred Heart Hospital, Anyang 14068, Korea;
| | - Sung Min Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Dongtan Sacred Heart Hospital, Hwaseong 18450, Korea; (S.M.P.); (S.-M.H.)
| | - Sung Hun Kang
- Department of Biomedical Sciences, College of Medicine, Hallym University, Chuncheon 24252, Korea;
| | - Seok-Min Hong
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Dongtan Sacred Heart Hospital, Hwaseong 18450, Korea; (S.M.P.); (S.-M.H.)
| | - Soo-Hwan Byun
- Department of Oral & Maxillofacial Surgery, Dentistry, Hallym University College of Medicine, Hallym Sacred Heart Hospital, Anyang 14068, Korea;
| | - Yong Gi Jung
- Department of Otorhinolaryngology-Head and Neck Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
- Correspondence: (Y.G.J.); (S.J.H.); Tel.: +82-2-3410-3579 (Y.G.J.); +82-31-8086-2670 (S.J.H.); Fax: +82-2-3410-3879 (Y.G.J.); +82-31-8086-3449 (S.J.H.)
| | - Seok Jin Hong
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Dongtan Sacred Heart Hospital, Hwaseong 18450, Korea; (S.M.P.); (S.-M.H.)
- Correspondence: (Y.G.J.); (S.J.H.); Tel.: +82-2-3410-3579 (Y.G.J.); +82-31-8086-2670 (S.J.H.); Fax: +82-2-3410-3879 (Y.G.J.); +82-31-8086-3449 (S.J.H.)
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155
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Kattner AA. We refuse to die - T cells causing havoc. Biomed J 2021; 44:377-382. [PMID: 34508914 PMCID: PMC8514847 DOI: 10.1016/j.bj.2021.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 10/28/2022] Open
Abstract
This issue of the Biomedical Journal offers insights into the origin and consequences of different lymphoproliferative disorders and autoimmunity. Furthermore we learn about RASopathies, a group of congenital disorders that occur rather frequently. Then the current ELISA assays for measuring antibody avidity are critically examined, the relationship between female sex steroid hormones and cardiovascular disease is explored, and an assessment of persistent diarrhea as a leading cause of child death in India is performed. Additionally, there are several articles about COVID-19, presenting its connection to neutrophil recruitment and acute respiratory distress syndrome, as well as its relation to changes in the vascular glycocalyx. A COVID-19 case study from the emergency room is presented. We are also introduced to novel treatment approaches against COVID-19 like the construction of peptide-based vaccines, or targeting the respiratory tract microbiome. Finally, there is an assessment about how prepared medical students at a Taiwan University feel for independent practice, and another article about the treatment of intravascular large B cell lymphoma in a Taiwanese institution. Lastly, we discover possible surgery techniques in the case of external auditory canal osteoma.
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156
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Velmurugan G, Vasudevan D. Metagenomic analysis of RNA sequencing data reveals SARS-CoV-2-mediated progressive dysbiosis of upper respiratory tract microbiota. Biomed J 2021; 44:504-507. [PMID: 34507920 PMCID: PMC7912354 DOI: 10.1016/j.bj.2021.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 01/06/2023] Open
Abstract
COVID-19, an infectious disease caused by a novel coronavirus (SARS-CoV-2) has emerged as global pandemic. Here, we described the changes in microbiota of upper respiratory tract by analyzing the publically available RNA sequencing data of SARS-CoV-2-infected ferrets. The bacterial dysbiosis due to SARS-CoV-2 was largely inversely proportional to the dysbiosis caused by influenza-A virus. The bacterial taxa which are defined as healthy ecostate were significantly reduced during SARS-CoV-2 infection. Altogether, this preliminary study provides a new insight on the possible role of bacterial communities of upper respiratory tract in determining the immunity, susceptibility, and mortality for COVID-19.
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Affiliation(s)
- Ganesan Velmurugan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center & Hospital, Coimbatore, Tamil Nadu, India.
| | - Dinakaran Vasudevan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center & Hospital, Coimbatore, Tamil Nadu, India
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157
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The Role of Respiratory Flora in the Pathogenesis of Chronic Respiratory Diseases. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6431862. [PMID: 34435047 PMCID: PMC8382525 DOI: 10.1155/2021/6431862] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/20/2021] [Accepted: 07/31/2021] [Indexed: 12/13/2022]
Abstract
Large quantities of bacteria, including Firmicutes, Actinobacteria, and Bacteroidetes, colonize the surface of the respiratory mucosa of healthy people. They interact and coexist with the local mucosal immune system of the human airway, maintaining the immune stability and balance of the respiratory system. While suffering from chronic respiratory diseases, the microbial population in the airway changes and the proportion of Proteobacteria is increased in patients with asthma. The abundance of the microbial population in patients with chronic obstructive pulmonary disease (COPD) is decreased, and conversely, the proportion of Firmicutes and Proteobacteria increased. The diversity of airway microorganisms in cystic fibrosis (CF) patients is decreased, while pathogenic bacteria and conditional pathogenic bacteria are proliferated in large numbers. The proportion of Firmicutes and Proteobacteria is increased in patients with upper airway cough syndrome (UACS), which replaces the dominance of Streptococcus and Neisseria in the pharynx of a normal population. Therefore, a clear understanding of the immune process of the airway flora and the immune dysfunction of the flora on the pathogenesis of chronic respiratory diseases can provide new ideas for the prevention and treatment of human respiratory diseases.
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158
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Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek. Appl Environ Microbiol 2021; 87:e0122521. [PMID: 34191530 PMCID: PMC8388827 DOI: 10.1128/aem.01225-21] [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: 01/04/2023] Open
Abstract
Drivers of pig trucks constitute a potential route of human transmission of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398). In this study, we determined MRSA prevalence in pig truck drivers (n = 47) and monitored the nasal microbiota of 9 drivers 3 times daily throughout 1 workweek (n = 113 samples) and compared it to that of their spouses (n = 25 samples from 6 spouses) and 89 nonexposed subjects. S. aureus isolates (n = 232) derived from a subset of nasal and truck samples were whole-genome sequenced. The nasal alpha diversity of drivers in the beginning of the workday was lower than that of nonexposed subjects. During the workday, it increased significantly. Similarly, the drivers’ nasal composition shifted during the workday, becoming increasingly different from that of their spouses and nonexposed individuals. Clustering into community state types (CSTs) revealed frequent switches from either S. aureus- or Corynebacterium-dominated CSTs in the mornings to a Psychrobacter-dominated CST during the workday. Six intermittent MRSA carriers were mostly MRSA negative in the mornings, and their nasal microbiota resembled that of nonexposed subjects. When acquiring MRSA during the workday, they switched to the Psychrobacter-dominated CST. In contrast, the nasal microbiota of two persistent MRSA carriers was dominated by staphylococci. In conclusion, we show that the nasal microbiota of pig truck drivers is very dynamic, undergoes drastic changes during workdays, and differs from that of nonexposed subjects even before pig contact. MRSA-carrying drivers may eventually introduce MRSA into the community and health care facilities. Carriage dynamics, however, showed that for most drivers, CC398 MRSA is rapidly lost and only rarely causes transmission to spouses. IMPORTANCE In Denmark, the number of human methicillin-resistant Staphylococcus aureus (MRSA) cases has increased dramatically since the early 2000s, starting from imported cases and spreading in the community. However, today, approximately one-third of all new cases are attributed to livestock-associated MRSA clonal complex 398 (LA-MRSA CC398). This mirrors the increase in pig farms, of which 95% are now positive for LA-MRSA, and this has been caused mainly by three dominant lineages enriched for a number of key antimicrobial resistance genes. Although most human LA-MRSA CC398 infections in Denmark are linked to livestock contact, still up to one-third are not. Pig truck drivers constitute a previously understudied occupation group which may transmit LA-MRSA CC398 to household members, the community, and hospitals. In this study, we demonstrate dramatic work-related changes in the nasal microbiota of pig truck drivers, as well as in their carriage of LA-MRSA CC398. However, they likely do not constitute an important reservoir for LA-MRSA CC398 dissemination.
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159
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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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160
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Abdullahi IN, Lozano C, Ruiz-Ripa L, Fernández-Fernández R, Zarazaga M, Torres C. Ecology and Genetic Lineages of Nasal Staphylococcus aureus and MRSA Carriage in Healthy Persons with or without Animal-Related Occupational Risks of Colonization: A Review of Global Reports. Pathogens 2021; 10:1000. [PMID: 34451464 PMCID: PMC8400700 DOI: 10.3390/pathogens10081000] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/16/2023] Open
Abstract
In this conceptual review, we thoroughly searched for appropriate English articles on nasal staphylococci carriage among healthy people with no reported risk of colonization (Group A), food handlers (Group B), veterinarians (Group C), and livestock farmers (Group D) published between 2000 and 2021. Random-effects analyses of proportions were performed to determine the pooled prevalence of S. aureus, MRSA, MRSA-CC398, and MSSA-CC398, as well as the prevalence of PVL-positive S. aureus from all eligible studies. A total of 166 eligible papers were evaluated for Groups A/B/C/D (n = 58/31/26/51). The pooled prevalence of S. aureus and MRSA in healthy humans of Groups A to D were 15.9, 7.8, 34.9, and 27.1%, and 0.8, 0.9, 8.6, and 13.5%, respectively. The pooled prevalence of MRSA-CC398 nasal carriage among healthy humans was as follows: Group A/B (<0.05%), Group C (1.4%), Group D (5.4%); and the following among Group D: pig farmers (8.4%) and dairy farmers (4.7%). The pooled prevalence of CC398 lineage among the MSSA and MRSA isolates from studies of the four groups were Group A (2.9 and 6.9%), B (1.5 and 0.0%), C (47.6% in MRSA), and D (11.5 and 58.8%). Moreover, MSSA-CC398 isolates of Groups A and B were mostly of spa-t571 (animal-independent clade), while those of Groups C and D were spa-t011 and t034. The MRSA-CC398 was predominately of t011 and t034 in all the groups (with few other spa-types, livestock-associated clades). The pooled prevalence of MSSA and MRSA isolates carrying the PVL encoding genes were 11.5 and 9.6% (ranges: 0.0-76.9 and 0.0-28.6%), respectively. Moreover, one PVL-positive MSSA-t011-CC398 isolate was detected in Group A. Contact with livestock and veterinary practice seems to increase the risk of carrying MRSA-CC398, but not in food handlers. Thus, this emphasizes the need for integrated molecular epidemiology of zoonotic staphylococci.
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Affiliation(s)
| | | | | | | | | | - Carmen Torres
- Area of Biochemistry and Molecular Biology, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain; (I.N.A.); (C.L.); (L.R.-R.); (R.F.-F.); (M.Z.)
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161
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Rouchka EC, Chariker JH, Alejandro B, Adcock RS, Singhal R, Ramirez J, Palmer KE, Lasnik AB, Carrico R, Arnold FW, Furmanek S, Zhang M, Wolf LA, Waigel S, Zacharias W, Bordon J, Chung D. Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients. Sci Rep 2021; 11:15715. [PMID: 34344959 PMCID: PMC8333042 DOI: 10.1038/s41598-021-95197-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
Key elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.
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Affiliation(s)
- Eric C Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY, USA
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
| | - Julia H Chariker
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
- Department of Neuroscience Training, University of Louisville, Louisville, KY, USA
| | - Brian Alejandro
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Robert S Adcock
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Richa Singhal
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Julio Ramirez
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Kenneth E Palmer
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Amanda B Lasnik
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Ruth Carrico
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Forest W Arnold
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Stephen Furmanek
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Mei Zhang
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Leslie A Wolf
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Sabine Waigel
- Department of Medicine, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Wolfgang Zacharias
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Jose Bordon
- Washington Health Institute, George Washington University School of Medicine, Washington, D.C, USA
- Department of Medicine, George Washington University School of Medicine, Washington, D.C, USA
| | - Donghoon Chung
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA.
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA.
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162
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Characteristics of the bacterial microbiota in the upper respiratory tract of children. Eur Arch Otorhinolaryngol 2021; 279:1081-1089. [PMID: 34304297 DOI: 10.1007/s00405-021-07013-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: 04/15/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE The respiratory tract microbiota are deemed as the gatekeeper to health. Consequently, microbiota dysbiosis can lead to the development of diseases. To identify the exact origins of the localized pathogenic bacteria, we investigated bacterial composition in the upper airway tract. METHODS Separate mucosal swabs were collected from nostril or oropharynx of each participant. Meanwhile, the lymphoid tissues including adenoids and tonsils were collected during operation. DNAs were exacted from all the samples for the following 16S rRNA analysis. RESULTS At the phylum level, the basic bacterial structures in the adenoids, tonsils, oropharynx, and nostrils were generally similar: five main phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria form the majority of the microbiota. However, across these four sites, the microbiota composition differed. More specifically, the bacterial composition in the nostrils was unique. There, Firmicutes and Actinobacteria were the most abundant phyla, while Bacteroides and Fusobacteria were the least abundant. At the genus level, Staphylococcus, Dolosigranulum, Corynebacterium, and Moraxella were the most plentiful, while Fusobacteria was the least ample. Across all sites, Streptococcus displayed similar abundances. Fusobacteria exhibited higher abundances in the lymphoid tissues and oropharynx. Haemophilus and Neisseria were more plentiful in the tonsils and oropharynx. Notably, Klebsiella, which is normally localized to the gut, was abundant in the adenoids and tonsils. CONCLUSION Our data indicate that promising pathogenic bacteria originate from all sites in the upper airway. The upper tract lymphoid tissues, normally considered as immune organs, may also serve as reservoirs for pathogenic bacteria.
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163
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Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza? J Fungi (Basel) 2021; 7:jof7070550. [PMID: 34356929 PMCID: PMC8305266 DOI: 10.3390/jof7070550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Fungal ball (FB) rhinosinusitis (RS) is the main type of non-invasive fungal RS. Despite positive direct examination (DE) of biopsies, culture remains negative in more than 60% of cases. The aim of the study was to evaluate the performance/efficacy of targeted metagenomics (TM) to analyze microbiota and mycobiota in FB and find microbial associations. Forty-five sinus biopsies from patients who underwent surgery for chronic RS were included. After DE and culture, DNA was extracted, then fungal ITS1–ITS2 and bacterial V3–V4 16S rDNA loci were sequenced (MiSeqTM Illumina). Operational taxonomic units (OTUs) were defined via QIIME and assigned to SILVA (16S) and UNITE (ITS) databases. Statistical analyses were performed using SHAMAN. Thirty-eight patients had FB and seven had non-fungal rhinosinusitis (NFRS). DE and culture of FB were positive for fungi in 97.3 and 31.6% of patients, respectively. TM analysis of the 38 FB yielded more than one fungal genus in 100% of cases, with Aspergillus in 89.5% (34/38). Haemophilus was over-represented in FB with >1000 reads/sample in 47.3% (18/38) compared to NFRS (p < 0.001). TM allowed fungal identification in biopsies with negative culture. Haemophilus was associated with FB. Pathogenesis could result from fungi–bacteria interactions in a mixed biofilm-like structure.
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164
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Custodio R, Ford RM, Ellison CJ, Liu G, Mickute G, Tang CM, Exley RM. Type VI secretion system killing by commensal Neisseria is influenced by expression of type four pili. eLife 2021; 10:63755. [PMID: 34232858 PMCID: PMC8263058 DOI: 10.7554/elife.63755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/27/2021] [Indexed: 12/14/2022] Open
Abstract
Type VI Secretion Systems (T6SSs) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here, we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can limit growth of related pathogens. We explored the impact of Tfp on N. cinerea T6SS-dependent killing within a colony and show that pilus expression by a prey strain enhances susceptibility to T6SS compared to a non-piliated prey, by preventing segregation from a T6SS-wielding attacker. Our findings have important implications for understanding how spatial constraints during contact-dependent antagonism can shape the evolution of microbial communities.
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Affiliation(s)
- Rafael Custodio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rhian M Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Cara J Ellison
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gerda Mickute
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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165
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Raya Tonetti F, Tomokiyo M, Ortiz Moyano R, Quilodrán-Vega S, Yamamuro H, Kanmani P, Melnikov V, Kurata S, Kitazawa H, Villena J. The Respiratory Commensal Bacterium Dolosigranulum pigrum 040417 Improves the Innate Immune Response to Streptococcus pneumoniae. Microorganisms 2021; 9:microorganisms9061324. [PMID: 34207076 PMCID: PMC8234606 DOI: 10.3390/microorganisms9061324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Previously, we demonstrated that the nasal administration of Dolosigranulum pigrum 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of D. pigrum 040417 in the context of Streptococcus pneumoniae infection and characterize the role of alveolar macrophages (AMs) in the immunomodulatory properties of this respiratory commensal bacterium. The nasal administration of D. pigrum 040417 to infant mice significantly increased their resistance to pneumococcal infection, differentially modulated respiratory cytokines production, and reduced lung injuries. These effects were associated to the ability of the 040417 strain to modulate AMs function. Depletion of AMs significantly reduced the capacity of the 040417 strain to improve both the reduction of pathogen loads and the protection against lung tissue damage. We also demonstrated that the immunomodulatory properties of D. pigrum are strain-specific, as D. pigrum 030918 was not able to modulate respiratory immunity or to increase the resistance of mice to an S. pneumoniae infection. These findings enhanced our knowledge regarding the immunological mechanisms involved in modulation of respiratory immunity induced by beneficial respiratory commensal bacteria and suggested that particular strains could be used as next-generation probiotics.
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Affiliation(s)
- Fernanda Raya Tonetti
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Ramiro Ortiz Moyano
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
| | - Sandra Quilodrán-Vega
- Laboratory of Food Microbiology, Faculty of Veterinary Sciences, University of Concepción, Chillán 3780000, Chile;
| | - Hikari Yamamuro
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Paulraj Kanmani
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
| | - Vyacheslav Melnikov
- Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia;
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (H.K.); (J.V.)
| | - Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina; (F.R.T.); (R.O.M.)
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan; (M.T.); (H.Y.); (P.K.)
- Correspondence: (H.K.); (J.V.)
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166
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Abdellatif AM. Evaluating the distribution of T-lymphocytes and S-phase proliferating cells across the nasal mucosa of dromedary camel (Camelus dromedarius). Tissue Cell 2021; 72:101580. [PMID: 34130855 DOI: 10.1016/j.tice.2021.101580] [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: 01/04/2021] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022]
Abstract
The lining mucosa of the nasal cavity performs important roles for the host adaptation to the external environment. Camels are unique in their adaptation to the lifestyle of nomadic deserts. The present study aimed to evaluate the distribution pattern of T lymphocytes and S-phase proliferating cells within the nasal mucosa of camel using antibodies against CD3 and PCNA, respectively. The mucosa of the rostral, middle, and caudal parts of the nasal cavity was collected and processed for immunohistochemical staining. CD3-immunoreactive (-IR) cells were observed within the epithelium and lamina propria of all examined parts. However, the numbers of these cells were significantly higher in the rostral part of the nasal mucosa compared to its middle and caudal parts (P < 0.05). Such expression of CD3-IR cells within the rostral nasal mucosa was most pronounced within its lamina propria which also revealed aggregations of lymphoid cells. The increased frequency of CD3 expressing cells at the rostral part of the nasal mucosa suggests a potential role of the nasal vestibule in limiting the infection via constant clearance of encountered pathogens. PCNA-IR cells were mainly found within the basal layers of the nasal epithelium at the rostral part of the nasal cavity, though they showed a significant decrease in their frequencies on moving caudad. The results of the present work will form a basis for assessment of various nasal pathologies affecting camels particularly those associated with increased rates of T lymphocytes infiltration and/or cell proliferation.
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Affiliation(s)
- Ahmed M Abdellatif
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.
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167
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. MICROBIOME 2021; 9:132. [PMID: 34103074 PMCID: PMC8186369 DOI: 10.1186/s40168-021-01083-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. METHODS We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. RESULTS Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. CONCLUSIONS These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Mac Kenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA
| | | | - Laxmi Parida
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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Iorio A, Biazzo M, Gardini S, Muda AO, Perno CF, Dallapiccola B, Putignani L. Cross-correlation of virome-bacteriome-host-metabolome to study respiratory health. Trends Microbiol 2021; 30:34-46. [PMID: 34052095 DOI: 10.1016/j.tim.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
A comprehensive understanding of the microbiome-host relationship in respiratory diseases can be elucidated by exploring the landscape of virome-bacteriome-host metabolome data through unsupervised 'multi-omics' approaches. Here, we describe how the composition and function of airway and gut virome and bacteriome may contribute to pathogen establishment and propagation in airway districts and how the virome-bacteriome communities may react to respiratory diseases. A new systems medicine approach, including the characterization of respiratory and gut microbiome, may be crucial to demonstrate the likelihood and odds of respiratory disease pathophysiology, opening new avenues to the discovery of a chain of causation for key bacteria and viruses in disease severity.
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Affiliation(s)
- Andrea Iorio
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuele Biazzo
- The BioArte Ltd, The Victoria Centre, Mosta, Malta; SienaBioActive, University of Siena, Siena, Italy
| | | | - Andrea Onetti Muda
- Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Unit of Microbiology and Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Children's Hospital and Research Institute 'Bambino Gesù', IRCCS, Rome
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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169
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Nur Husna SM, Tan HTT, Md Shukri N, Mohd Ashari NS, Wong KK. Nasal Epithelial Barrier Integrity and Tight Junctions Disruption in Allergic Rhinitis: Overview and Pathogenic Insights. Front Immunol 2021; 12:663626. [PMID: 34093555 PMCID: PMC8176953 DOI: 10.3389/fimmu.2021.663626] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022] Open
Abstract
Allergic rhinitis (AR) is a common disorder affecting up to 40% of the population worldwide and it usually persists throughout life. Nasal epithelial barrier constitutes the first line of defense against invasion of harmful pathogens or aeroallergens. Cell junctions comprising of tight junctions (TJs), adherens junctions, desmosomes and hemidesmosomes form the nasal epithelial barrier. Impairment of TJ molecules plays causative roles in the pathogenesis of AR. In this review, we describe and discuss the components of TJs and their disruption leading to development of AR, as well as regulation of TJs expression by epigenetic changes, neuro-immune interaction, epithelial-derived cytokines (thymic stromal lymphopoietin, IL-25 and IL-33), T helper 2 (Th2) cytokines (IL-4, IL-5, IL-6 and IL-13) and innate lymphoid cells. These growing evidence support the development of novel therapeutic approaches to restore nasal epithelial TJs expression in AR patients.
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Affiliation(s)
- Siti Muhamad Nur Husna
- Department of Immunology, School of Medical Sciences Malaysia, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Hern-Tze Tina Tan
- Department of Immunology, School of Medical Sciences Malaysia, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Norasnieda Md Shukri
- Hospital Universiti Sains Malaysia, Kubang Kerian, Malaysia.,Department of Otorhinolaryngology, Head and Neck Surgery, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Noor Suryani Mohd Ashari
- Department of Immunology, School of Medical Sciences Malaysia, Universiti Sains Malaysia, Kubang Kerian, Malaysia.,Hospital Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Kah Keng Wong
- Department of Immunology, School of Medical Sciences Malaysia, Universiti Sains Malaysia, Kubang Kerian, Malaysia.,Hospital Universiti Sains Malaysia, Kubang Kerian, Malaysia
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170
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Stewart HL, Engiles JB, Richardson DW, Levine DG. The clinical and histopathologic effects of potentiated chlorhexidine in the upper respiratory tract of horses. Vet Surg 2021; 50:1209-1217. [PMID: 33974283 DOI: 10.1111/vsu.13649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/30/2021] [Accepted: 04/17/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To describe the bactericidal and fungicidal properties of a 0.0005% chlorhexidine (CHD) solution potentiated with EDTA-Tris buffers (CHD-EDTA-Tris) and evaluate the safety of 0.0005% CHD-EDTA-Tris in the upper respiratory tract (URT) of normal horses. STUDY DESIGN Clinical, prospective study. ANIMALS Eight healthy, skeletally mature horses. METHODS In vitro-serial dilutions of CHD-EDTA-Tris and EDTA-Tris alone were evaluated for bactericidal and fungicidal activity against Aspergillus fumigatus, Escherichia coli, Staphylococcus aureus, Streptococcus equi subspecies ssp. equi, Streptococcus equi ssp. zooepidemicus, and Pseudomonas aeruginosa. In vivo-eight healthy horses were topically treated twice with 30 ml of 0.0005% CHD-EDTA-Tris. Mucosal samples from each location were evaluated for the presence of inflammation or pathologic lesions. RESULTS Solutions containing CHD were superior in fungal and bacterial killing to those without. In vitro-a 0.005% CHD-EDTA-Tris was 100% effective against all bacterial and fungal species evaluated, while a 0.0005% CHD-EDTA-Tris was less efficacious against A. fumigatus and S. equi ssp. equi. In vivo-a 0.0005% CHD-EDTA-Tris did not cause any clinical, gross, or histologic abnormalities when topically applied to the equine URT. CONCLUSIONS A 0.0005% CHD-EDTA-Tris was highly effective for killing of common bacterial and fungal isolates in the equine upper respiratory tract. Short-term topical treatment of the equine URT with dilute CHD did not cause gross or histological inflammation in the tissue. CLINICAL SIGNIFICANCE A 0.0005% CHD solution with EDTA-Tris should be considered for treatment of clinically relevant inflammatory or infectious conditions or in the URT of the horse.
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Affiliation(s)
- Holly L Stewart
- Translational Medicine Institute, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Dean W Richardson
- Department of Clinical Sciences, New Bolton Center, University of Pennsylvania, Kennett Square, Pennsylvania, USA
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171
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Jiang M, Chen J, Ding Y, Gan C, Hou Y, Lei J, Wan M, Li X, Xiao Z. Efficacy and Safety of Sea Salt-Derived Physiological Saline Nasal Spray as Add-On Therapy in Patients with Acute Upper Respiratory Infection: A Multicenter Retrospective Cohort Study. Med Sci Monit 2021; 27:e929714. [PMID: 33974619 PMCID: PMC8122848 DOI: 10.12659/msm.929714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background The purpose of this study was to assess the effects of seawater on nasal congestion and runny nose symptoms in adults with an acute upper respiratory infection (URI). Material/Methods This was a multicenter retrospective cohort trial of patients with acute URI and symptoms of nasal congestion and runny nose. The patients were assigned to 2 groups and were administered regular non-drug supportive treatment or supportive treatment with nasal irrigation with sea salt-derived physiological saline. The primary efficacy endpoint was the effective rate (percentage of patients with ≥30% symptom score reduction from baseline for nasal congestion and runny nose). Results In total, 144 patients were enrolled, including 72 in each group, and 143 patients completed the study. Both groups had similar demographics and vital signs. The effective rates for nasal congestion and runny nose were significantly increased in the seawater group compared with patients in the control group (87.3% vs 59.7% for nasal congestion; 85.9% vs 61.1% for runny nose; both P<0.001). In addition, the 2 groups showed markedly different degrees of patient symptom score improvement in sleep quality and appetite (both P<0.01), but not in cough and fatigue (both P>0.05). There were no adverse events in either group. Conclusions The sea salt-derived physiological saline nasal spray device satisfactorily improved nasal congestion, runny nose, sleep quality, and appetite in adults with URI, with no adverse effects.
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Affiliation(s)
- Min Jiang
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Junwen Chen
- Department of Respiratory and Critical Care Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei, China (mainland)
| | - Yuanhua Ding
- Department of Respiratory Medicine, Taizhou Hospital of Traditional Chinese Medicine, Taizhou, Jiangsu, China (mainland)
| | - Chenxi Gan
- Office of Drug Clinical Trial Management, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Ya Hou
- Department of Biological Statistics, Jiangsu Famai Sheng Medical Science and Technology Co., Ltd., Zhenjiang, Jiangsu, China (mainland)
| | - Junge Lei
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Mengzhi Wan
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Xing Li
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Zuke Xiao
- Department of Respiratory and Critical Care Medicine, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, Jiangxi, China (mainland)
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172
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Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA, Siddiki AZ. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. GENE REPORTS 2021; 23:101200. [PMID: 33977168 PMCID: PMC8102076 DOI: 10.1016/j.genrep.2021.101200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesize that microbiome diversity and composition, and their genomic features are associated with different pathological conditions of these human respiratory tract diseases. To test this hypothesis, we analyzed 21 RNASeq metagenomic data including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the microbiome diversity and related genomic metabolic functions. The metagenomic data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19 > COPD > URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively. However, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, virulence, disease and defense, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, we detected comparatively higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful in developing microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.
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Affiliation(s)
- M Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Rasel Ahmed
- Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | | | | | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), BSMRAU, Gazipur 1706, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh.,Vice-Chancellor, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Amam Zonaed Siddiki
- Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram 4202, Bangladesh
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173
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De Boeck I, Spacova I, Vanderveken OM, Lebeer S. Lactic acid bacteria as probiotics for the nose? Microb Biotechnol 2021; 14:859-869. [PMID: 33507624 PMCID: PMC8085937 DOI: 10.1111/1751-7915.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.
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Affiliation(s)
- Ilke De Boeck
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Irina Spacova
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Olivier M. Vanderveken
- ENT, Head and Neck Surgery and Communication DisordersAntwerp University HospitalEdegemBelgium
- Faculty of Medicine and Health SciencesTranslational NeurosciencesUniversity of AntwerpAntwerpBelgium
| | - Sarah Lebeer
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
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174
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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: 14] [Impact Index Per Article: 4.7] [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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175
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Mac Aogáin M, Narayana JK, Tiew PY, Ali NABM, Yong VFL, Jaggi TK, Lim AYH, Keir HR, Dicker AJ, Thng KX, Tsang A, Ivan FX, Poh ME, Oriano M, Aliberti S, Blasi F, Low TB, Ong TH, Oliver B, Giam YH, Tee A, Koh MS, Abisheganaden JA, Tsaneva-Atanasova K, Chalmers JD, Chotirmall SH. Integrative microbiomics in bronchiectasis exacerbations. Nat Med 2021; 27:688-699. [PMID: 33820995 DOI: 10.1038/s41591-021-01289-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/16/2021] [Indexed: 02/01/2023]
Abstract
Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion ( https://integrative-microbiomics.ntu.edu.sg ). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.
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Affiliation(s)
- Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jayanth Kumar Narayana
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | | | - Valerie Fei Lee Yong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Albert Yick Hou Lim
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Holly R Keir
- School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Alison J Dicker
- School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Akina Tsang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | - Mau Ern Poh
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Martina Oriano
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Stefano Aliberti
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Francesco Blasi
- Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Teck Boon Low
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | - Thun How Ong
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Brian Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Yan Hui Giam
- School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Augustine Tee
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | | | - Krasimira Tsaneva-Atanasova
- Department of Mathematics and Living Systems Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - James D Chalmers
- School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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176
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Crawford MS, Nordgren TM, McCole DF. Every breath you take: Impacts of environmental dust exposure on intestinal barrier function-from the gut-lung axis to COVID-19. Am J Physiol Gastrointest Liver Physiol 2021; 320:G586-G600. [PMID: 33501887 PMCID: PMC8054554 DOI: 10.1152/ajpgi.00423.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
As countries continue to industrialize, major cities experience diminished air quality, whereas rural populations also experience poor air quality from sources such as agricultural operations. These exposures to environmental pollution from both rural and populated/industrialized sources have adverse effects on human health. Although respiratory diseases (e.g., asthma and chronic obstructive pulmonary disease) are the most commonly reported following long-term exposure to particulate matter and hazardous chemicals, gastrointestinal complications have also been associated with the increased risk of lung disease from inhalation of polluted air. The interconnectedness of these organ systems has offered valuable insights into the roles of the immune system and the micro/mycobiota as mediators of communication between the lung and the gut during disease states. A topical example of this relationship is provided by reports of multiple gastrointestinal symptoms in patients with coronavirus disease 2019 (COVID-19), whereas the rapid transmission and increased risk of COVID-19 has been linked to poor air quality and high levels of particulate matter. In this review, we focus on the mechanistic effects of environmental pollution on disease progression with special emphasis on the gut-lung axis.
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Affiliation(s)
- Meli'sa S Crawford
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Tara M Nordgren
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Declan F McCole
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
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177
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Majak P, Molińska K, Latek M, Rychlik B, Wachulec M, Błauż A, Budniok A, Gruchała M, Lach J, Sobalska-Kwapis M, Baranowska M, Królikowska K, Strapagiel D, Majak J, Czech D, Pałczyński C, Kuna P. Upper-airway dysbiosis related to frequent sweets consumption increases the risk of asthma in children with chronic rhinosinusitis. Pediatr Allergy Immunol 2021; 32:489-500. [PMID: 33222307 DOI: 10.1111/pai.13417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND Innate immunity response to local dysbiosis seems to be one of the most important immunologic backgrounds of chronic rhinosinusitis (CRS) and concomitant asthma. We aimed to assess clinical determinants of upper-airway dysbiosis and its effect on nasal inflammatory profile and asthma risk in young children with CRS. METHODS We recruited one hundred and thirty-three children, aged 4-8 years with doctor-diagnosed CRS with or without asthma. The following procedures were performed in all participants: face-to-face standardized Sinus and Nasal Quality of Life questionnaire, skin prick test, taste perception testing, nasopharynx swab, and sampling of the nasal mucosa. Upper-airway dysbiosis was defined separately by asthma-specific microbiome composition and reduced biodiversity. Multivariate methods were used to define the risk factors for asthma and upper-airway dysbiosis and their specific inflammatory profile of nasal mucosa. RESULTS The asthma-specific upper-airway microbiome composition reflected by the decreased ratio of Patescibacteria/Actinobacteria independently of atopy increased the risk of asthma (OR:8.32; 95%CI: 2.93-23.6). This asthma-specific microbiome composition was associated with ≥ 7/week sweet consumption (OR:2.64; 95%C:1.11-6.28), reduced biodiversity (OR:3.83; 95%CI:1.65-8.87), the presence of Staphylococcus strains in the nasopharynx (OR:4.25; 95%CI:1.12-16.1), and lower expression of beta-defensin 2, IL-5, and IL-13 in the nasal mucosa. The reduced biodiversity was associated with frequent antibiotic use and with a higher nasal expression of IL-17 and T1R3 (sweet taste receptor). In asthmatic children, reduced sweet taste perception was observed. CONCLUSIONS Specific upper-airway dysbiosis related to frequent sweet consumption, frequent antibiotic courses, and altered nasal immune function increases the risk of asthma in young children with CRS.
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Affiliation(s)
- Paweł Majak
- Department of Pediatric Pulmonology, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Molińska
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Marta Latek
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
| | - Błażej Rychlik
- Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Marcin Wachulec
- Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Andrzej Błauż
- Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | | | - Martyna Gruchała
- Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Jakub Lach
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | | | - Monika Baranowska
- Biobank Lab, Department of Molecular Biophysics, University of Lodz, Lodz, Poland
| | - Klaudyna Królikowska
- Biobank 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
| | - Dorota Czech
- Department of Paediatric Otolaryngology, Audiology and Phoniatrics, Medical University of Lodz, Lodz, Poland
| | | | - Piotr Kuna
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, Lodz, Poland
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178
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Hu C, Duijts L, van Meel ER, Looman KIM, Kiefte-de Jong JC, Pardo LM, Hijnen D, Pasmans SGMA, de Jongste JC, Moll HA, Nijsten T. Association between nasal and nasopharyngeal bacterial colonization in early life and eczema phenotypes. Clin Exp Allergy 2021; 51:716-725. [PMID: 33759242 PMCID: PMC8252109 DOI: 10.1111/cea.13869] [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: 10/26/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Background An association has been reported between early life Staphylococcus aureus nasal carriage and higher risk of childhood eczema, but it is unclear whether this relationship is causal and associations with other bacterial species are unclear. Objective To examine the associations of early life nasal and nasopharyngeal bacterial carriage with eczema phenotypes, and the direction of any associations identified. Methods Among 996 subjects of a population‐based prospective cohort study, nasal swabs for Staphylococcus aureus, and nasopharyngeal swabs for Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae were collected and cultured from age 6 weeks to 6 years. Never, early, mid‐, late transient and persistent eczema phenotypes were identified from parental‐reported physician‐diagnosed eczema from age 6 months until 10 years. Multinomial regression models and cross‐lagged models were applied. Results Staphylococcus aureus nasal carriage at 6 months was associated with an increased risk of early transient and persistent eczema (OR (95% CI): 2.69 (1.34, 5.39) and 4.17 (1.12, 15.51)). The associations between Staphylococcus aureus nasal carriage and eczema were mostly cross‐sectional, and not longitudinal. No associations of Staphylococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenza nasopharyngeal bacterial carriage with eczema and eczema phenotypes were observed (OR range (95% CI): 0.71 (0.35, 1.44) to 1.77 (0.84, 3.73)). Conclusions Early life Staphylococcus aureus nasal carriage, but not Staphylococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenza nasopharyngeal carriage, was associated with early transient and persistent eczema. Staphylococcus aureus nasal carriage and eczema were mostly cross‐sectionally associated, and not longitudinally, making a causal relationship in either direction unlikely.
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Affiliation(s)
- Chen Hu
- The Generation R Study Group, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands.,Department of Dermatology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands.,Division of Neonatology, Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Evelien R van Meel
- The Generation R Study Group, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands.,Division of Respiratory Medicine and Allergology, Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Kirsten I M Looman
- The Generation R Study Group, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands.,Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands.,Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Luba M Pardo
- Department of Dermatology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - DirkJan Hijnen
- Department of Dermatology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Suzanne G M A Pasmans
- Department of Dermatology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Henriette A Moll
- Department of Pediatrics, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, University Medical Center Rotterdam, Erasmus MC, Rotterdam, The Netherlands
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Saksena N, Bonam SR, Miranda-Saksena M. Epigenetic Lens to Visualize the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Infection in COVID-19 Pandemic. Front Genet 2021; 12:581726. [PMID: 33828579 PMCID: PMC8019793 DOI: 10.3389/fgene.2021.581726] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
In <20 years, we have witnessed three different epidemics with coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2 in human populations, causing widespread mortality. SARS-CoV-2, through its rapid global spread, has led to the pandemic that we call COVID-19. As of February 1, 2021, the global infections linked to SARS-CoV-2 stand at 103,503,340, with 2,236,960 deaths, and 75,108,099 recoveries. This review attempts to highlight host-pathogen interaction with particular emphasis on the role of epigenetic machinery in regulating the disease. Although researchers, since the start of the pandemic, have been intensely engaged in diverse areas to understand the mechanisms involved in SARS-CoV-2 infection to find answers that can bring about innovative ways to swiftly treat and prevent disease progression, this review provides an overview on how the host epigenetics is modulated and subverted by SARS-CoV-2 to enter the host cells and drive immunopathogenesis. Epigenetics is the study that combines genetic and non-genetic factors controlling phenotypic variation, which are primarily a consequence of external and environmental stimuli. These stimuli alter the activity of a gene without impinging on the DNA code. In viral-host interactions, DNA/RNA methylation, non-coding RNAs, chromatin remodeling, and histone modifications are known to regulate and modulate host gene expression patterns. Viruses such as Coronaviruses (an RNA virus) show intrinsic association with these processes. They have evolved the ability to tamper with host epigenetic machinery to interfere with immune sensing pathways to evade host immune response, thereby enhancing its replication and pathogenesis post-entry. These epigenetic alterations allow the virus to weaken the host's immune response to successfully spread infection. How this occurs, and what epigenetic mechanisms are altered is poorly understood both for coronaviruses and other respiratory RNA viruses. The review highlights several cutting-edge aspects of epigenetic work primarily pertinent to SARS-CoV-2, which has been published between 2019 and 2020 to showcase the current knowledge both in terms of success and failures and take lessons that will assist us in understanding the disease to develop better treatments suited to kill SARS-CoV-2.
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Affiliation(s)
- Nitin Saksena
- EPIGENES Australia Pty Ltd, Melbourne, VIC, Australia
- Institute of Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Srinivasa Reddy Bonam
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Equipe- Immuno-pathologie et Immuno-intervention Thérapeutique, Sorbonne Université, Université de Paris, Paris, France
| | - Monica Miranda-Saksena
- Herpes Neuropathogenesis Research Group, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
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180
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Presence of microorganisms in children with pharyngotonsillitis and healthy controls: a prospective study in primary healthcare. Infection 2021; 49:715-724. [PMID: 33686635 PMCID: PMC7938884 DOI: 10.1007/s15010-021-01595-9] [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: 12/09/2020] [Accepted: 02/23/2021] [Indexed: 11/29/2022]
Abstract
Purpose Most studies on paediatric pharyngotonsillitis focus on group A streptococci. This study, however, analyses a broad spectrum of bacteria and viruses related to paediatric pharyngotonsillitis and evaluates their associated clinical symptoms and courses. Methods This observational prospective study in primary healthcare includes 77 children aged < 15 with a sore throat and 34 asymptomatic children, all of whom were sampled from the tonsils with an E-swab® for analysis with culture and PCR for 14 bacteria and 15 viruses. Patients were evaluated clinically, and their symptoms recorded in diaries for 10 days. Participants were followed up for 3 months by reviewing medical records. Results A pathogen was detected in 86% of patients and in 71% of controls (P = 0.06). Bacteria were found in 69% of patients and 59% of controls (P = 0.3), and viruses in 36% and 26%, respectively (P = 0.3). Group A streptococci was the most common finding, with a prevalence of 49% and 32%, respectively (P = 0.1). Clinical signs were not useful for distinguishing pathogens. None of the controls and 16% of the patients reconsulted for a sore throat within 3 months. Conclusion Bacteria were more common than viruses in both study groups. The high rate of pathogens in asymptomatic children interferes with diagnoses based on aetiology. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-021-01595-9.
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Cyprian F, Sohail MU, Abdelhafez I, Salman S, Attique Z, Kamareddine L, Al-Asmakh M. SARS-CoV-2 and immune-microbiome interactions: Lessons from respiratory viral infections. Int J Infect Dis 2021; 105:540-550. [PMID: 33610778 PMCID: PMC7891052 DOI: 10.1016/j.ijid.2021.02.071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
By the beginning of 2020, infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had rapidly evolved into an emergent worldwide pandemic, an outbreak whose unprecedented consequences highlighted many existing flaws within public healthcare systems across the world. While coronavirus disease 2019 (COVID-19) is bestowed with a broad spectrum of clinical manifestations, involving the vital organs, the respiratory system transpires as the main route of entry for SARS-CoV-2, with the lungs being its primary target. Of those infected, up to 20% require hospitalization on account of severity, while the majority of patients are either asymptomatic or exhibit mild symptoms. Exacerbation in the disease severity and complications of COVID-19 infection have been associated with multiple comorbidities, including hypertension, diabetes mellitus, cardiovascular disorders, cancer, and chronic lung disease. Interestingly, a recent body of evidence indicated the pulmonary and gut microbiomes as potential modulators for altering the course of COVID-19, potentially via the microbiome-immune system axis. While the relative concordance between microbes and immunity has yet to be fully elucidated with regards to COVID-19, we present an overview of our current understanding of COVID-19-microbiome-immune cross talk and discuss the potential contributions of microbiome-related immunity to SARS-CoV-2 pathogenesis and COVID-19 disease progression.
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Affiliation(s)
- Farhan Cyprian
- College of Medicine, QU Health, Qatar University, Doha, Qatar; Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Muhammad Umar Sohail
- Proteomics Core, Weill Cornell Medicine, Qatar Foundation-Education City, PO Box 24144, Doha, Qatar
| | | | - Salma Salman
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Zakria Attique
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Layla Kamareddine
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Maha Al-Asmakh
- Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar; Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar; Biomedical Research Centre, Qatar University, Doha, Qatar.
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Abstract
Like other microbes that live on or in the human body, the bacteria that inhabit the upper respiratory tract, in particular the nasal cavity, have evolved to survive in an environment that presents a number of physical and chemical challenges; these microbes are constantly bombarded with nutritional fluctuations, changes in humidity, the presence of inhaled particulate matter (odorants and allergens), and competition with other microbes. Indeed, only a specialized set of species is able to colonize this niche and successfully contend with the host's immune system and the constant threat from competitors. To this end, bacteria that live in the nasal cavity have evolved a variety of approaches to outcompete contenders for the limited nutrients and space; broadly speaking, these strategies may be considered a type of "bacterial warfare." A greater molecular understanding of bacterial warfare has the potential to reveal new approaches or molecules that can be developed as novel therapeutics. As such, there are many studies within the last decade that have sought to understand the complex polymicrobial interactions that occur in various environments. Here, we review what is currently known about the age-dependent structure and interbacterial relationships within the nasal microbiota and summarize the molecular mechanisms that are predicted to dictate bacterial warfare in this niche. Although the currently described interactions are complex, in reality, we have likely only scratched the surface in terms of a true understanding of the types of interbacterial competition and cooperation that are thought to take place in and on the human body.
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183
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Shah V. Letter to the Editor: Microbiota in the Respiratory System-A Possible Explanation to Age and Sex Variability in Susceptibility to SARS-CoV-2. Microbiol Insights 2021; 14:1178636120988604. [PMID: 33519207 PMCID: PMC7818001 DOI: 10.1177/1178636120988604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
The Human respiratory tract is colonized by a variety of microbes and the microbiota change as we age. In this perspective, literature support is presented for the hypothesis that the respiratory system microbiota could explain the differential age and sex breakdown amongst COVID-19 patients. The number of patients in the older and elderly adult group is higher than the other age groups. The perspective presents the possibility that certain genera of bacteria present in the respiratory system microbiota in children and young adults could be directly or through eliciting an immune response from the host, prevent full-fledged infection of SARS-CoV-2. The possibility also exists that the microbiota in older adults and the elderly population have bacteria that make it easier for the virus to cause infection. I call upon the scientific community to investigate the link between human microbiota and SARS-CoV-2 susceptibility to further understand the viral pathogenesis.
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Affiliation(s)
- Vishal Shah
- College of the Sciences and Mathematics, West Chester University, PA, USA
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184
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Dobson GP, Biros E, Letson HL, Morris JL. Living in a Hostile World: Inflammation, New Drug Development, and Coronavirus. Front Immunol 2021; 11:610131. [PMID: 33552070 PMCID: PMC7862725 DOI: 10.3389/fimmu.2020.610131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022] Open
Abstract
We present a brief history of the immune response and show that Metchnikoff's theory of inflammation and phagocytotic defense was largely ignored in the 20th century. For decades, the immune response was believed to be triggered centrally, until Lafferty and Cunningham proposed the initiating signal came from the tissues. This shift opened the way for Janeway's pattern recognition receptor theory, and Matzinger's danger model. All models failed to appreciate that without inflammation, there can be no immune response. The situation changed in the 1990s when cytokine biology was rapidly advancing, and the immune system's role expanded from host defense, to the maintenance of host health. An inflammatory environment, produced by immune cells themselves, was now recognized as mandatory for their attack, removal and repair functions after an infection or injury. We explore the cellular programs of the immune response, and the role played by cytokines and other mediators to tailor the right response, at the right time. Normally, the immune response is robust, self-limiting and restorative. However, when the antigen load or trauma exceeds the body's internal tolerances, as witnessed in some COVID-19 patients, excessive inflammation can lead to increased sympathetic outflows, cardiac dysfunction, coagulopathy, endothelial and metabolic dysfunction, multiple organ failure and death. Currently, there are few drug therapies to reduce excessive inflammation and immune dysfunction. We have been developing an intravenous (IV) fluid therapy comprising adenosine, lidocaine and Mg2+ (ALM) that confers a survival advantage by preventing excessive inflammation initiated by sepsis, endotoxemia and sterile trauma. The multi-pronged protection appears to be unique and may provide a tool to examine the intersection points in the immune response to infection or injury, and possible ways to prevent secondary tissue damage, such as that reported in patients with COVID-19.
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Affiliation(s)
- Geoffrey P. Dobson
- Heart, Trauma and Sepsis Research Laboratory, College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
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185
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Daniel S, Phillippi D, Schneider LJ, Nguyen KN, Mirpuri J, Lund AK. Exposure to diesel exhaust particles results in altered lung microbial profiles, associated with increased reactive oxygen species/reactive nitrogen species and inflammation, in C57Bl/6 wildtype mice on a high-fat diet. Part Fibre Toxicol 2021; 18:3. [PMID: 33419468 PMCID: PMC7796587 DOI: 10.1186/s12989-020-00393-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Exposure to traffic-generated emissions is associated with the development and exacerbation of inflammatory lung disorders such as chronic obstructive pulmonary disorder (COPD) and idiopathic pulmonary fibrosis (IPF). Although many lung diseases show an expansion of Proteobacteria, the role of traffic-generated particulate matter pollutants on the lung microbiota has not been well-characterized. Thus, we investigated the hypothesis that exposure to diesel exhaust particles (DEP) can alter commensal lung microbiota, thereby promoting alterations in the lung's immune and inflammatory responses. We aimed to understand whether diet might also contribute to the alteration of the commensal lung microbiome, either alone or related to exposure. To do this, we used male C57Bl/6 mice (4-6-week-old) on either regular chow (LF) or high-fat (HF) diet (45% kcal fat), randomly assigned to be exposed via oropharyngeal aspiration to 35 μg DEP, suspended in 35 μl 0.9% sterile saline or sterile saline only (control) twice a week for 30 days. A separate group of study animals on the HF diet was concurrently treated with 0.3 g/day of Winclove Ecologic® Barrier probiotics in their drinking water throughout the study. RESULTS Our results show that DEP-exposure increases lung tumor necrosis factor (TNF)-α, interleukin (IL)-10, Toll-like receptor (TLR)-2, TLR-4, and the nuclear factor kappa B (NF-κB) histologically and by RT-qPCR, as well as Immunoglobulin A (IgA) and Immunoglobulin G (IgG) in the bronchoalveolar lavage fluid (BALF), as quantified by ELISA. We also observed an increase in macrophage infiltration and peroxynitrite, a marker of reactive oxygen species (ROS) + reactive nitrogen species (RNS), immunofluorescence staining in the lungs of DEP-exposed and HF-diet animals, which was further exacerbated by concurrent DEP-exposure and HF-diet consumption. Histological examinations revealed enhanced inflammation and collagen deposition in the lungs DEP-exposed mice, regardless of diet. We observed an expansion of Proteobacteria, by qPCR of bacterial 16S rRNA, in the BALF of DEP-exposed mice on the HF diet, which was diminished with probiotic-treatment. CONCLUSIONS Our findings suggest that exposure to DEP causes persistent and sustained inflammation and bacterial alterations in a ROS-RNS mediated fashion, which is exacerbated by concurrent consumption of an HF diet.
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Affiliation(s)
- Sarah Daniel
- Advanced Environmental Research Institute, Department of Biological Sciences, University of North Texas, EESAT - 215, 1704 W. Mulberry, Denton, TX, 76201, USA
| | - Danielle Phillippi
- Advanced Environmental Research Institute, Department of Biological Sciences, University of North Texas, EESAT - 215, 1704 W. Mulberry, Denton, TX, 76201, USA
| | - Leah J Schneider
- Advanced Environmental Research Institute, Department of Biological Sciences, University of North Texas, EESAT - 215, 1704 W. Mulberry, Denton, TX, 76201, USA
| | - Kayla N Nguyen
- Advanced Environmental Research Institute, Department of Biological Sciences, University of North Texas, EESAT - 215, 1704 W. Mulberry, Denton, TX, 76201, USA
| | - Julie Mirpuri
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Amie K Lund
- Advanced Environmental Research Institute, Department of Biological Sciences, University of North Texas, EESAT - 215, 1704 W. Mulberry, Denton, TX, 76201, USA.
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Viegas C, Dias M, Monteiro A, Faria T, Lage J, Carolino E, Caetano LA, Gomes AQ, Almeida SM, Verde SC, Belo J, Canha N. Bioburden in sleeping environments from Portuguese dwellings. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116417. [PMID: 33465652 DOI: 10.1016/j.envpol.2020.116417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/20/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
A wider characterization of indoor air quality during sleep is still lacking in the literature. This study intends to assess bioburden before and after sleeping periods in Portuguese dwellings through active methods (air sampling) coupled with passive methods, such as electrostatic dust cloths (EDC); and investigate associations between before and after sleeping and bioburden. In addition, and driven by the lack of information regarding fungi azole-resistance in Portuguese dwellings, a screening with supplemented media was also performed. The most prevalent genera of airborne bacteria identified in the indoor air of the bedrooms were Micrococcus (41%), Staphylococcus (15%) and Neisseria (9%). The major indoor bacterial species isolated in all ten studied bedrooms were Micrococcus luteus (30%), Staphylococcus aureus (13%) and Micrococcus varians (11%). Our results highlight that our bodies are the source of the majority of the bacteria found in the indoor air of our homes. Regarding air fungal contamination, Chrysosporium spp. presented the highest prevalence both in after the sleeping period (40.8%) and before the sleeping period (28.8%) followed by Penicillium spp. (23.47% morning; 23.6% night) and Chrysonilia spp. (12.4% morning; 20.3% night). Several Aspergillus sections were identified in air and EDC samples. However, none of the fungal species/strains (Aspergillus sections Fumigati, Flavi, Nidulantes and Circumdati) were amplified by qPCR in the analyzed EDC. The correlations observed suggest reduced susceptibility to antifungal drugs of some fungal species found in sleeping environments. Toxigenic fungal species and indicators of harmful fungal contamination were observed in sleeping environments.
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Affiliation(s)
- Carla Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de, Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal.
| | - Marta Dias
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Ana Monteiro
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Tiago Faria
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Joana Lage
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Elisabete Carolino
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Liliana Aranha Caetano
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Anita Quintal Gomes
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; University of Lisbon Institute of Molecular Medicine, Faculty of Medicine, Lisbon, Portugal
| | - Susana Marta Almeida
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Sandra Cabo Verde
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Joana Belo
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; Integrated Pathophysiological Mechanisms Research Group (CEDOC) - NMS-UNL, Lisboa, Portugal
| | - Nuno Canha
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal; Centre for Environmental and Marine Studies, Department of Environment and Planning, University of Aveiro, 3810-193, Aveiro, Portugal
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187
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Macrophage metabolic reprogramming during chronic lung disease. Mucosal Immunol 2021; 14:282-295. [PMID: 33184475 PMCID: PMC7658438 DOI: 10.1038/s41385-020-00356-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/13/2020] [Accepted: 10/24/2020] [Indexed: 02/04/2023]
Abstract
Airway macrophages (AMs) play key roles in the maintenance of lung immune tolerance. Tissue tailored, highly specialised and strategically positioned, AMs are critical sentinels of lung homoeostasis. In the last decade, there has been a revolution in our understanding of how metabolism underlies key macrophage functions. While these initial observations were made during steady state or using in vitro polarised macrophages, recent studies have indicated that during many chronic lung diseases (CLDs), AMs adapt their metabolic profile to fit their local niche. By generating reactive oxygen species (ROS) for pathogen defence, utilising aerobic glycolysis to rapidly generate cytokines, and employing mitochondrial respiration to fuel inflammatory responses, AMs utilise metabolic reprogramming for host defence, although these changes may also support chronic pathology. This review focuses on how metabolic alterations underlie AM phenotype and function during CLDs. Particular emphasis is given to how our new understanding of AM metabolic plasticity may be exploited to develop AM-focused therapies.
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188
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Mirzaei R, Attar A, Papizadeh S, Jeda AS, Hosseini-Fard SR, Jamasbi E, Kazemi S, Amerkani S, Talei GR, Moradi P, Jalalifar S, Yousefimashouf R, Hossain MA, Keyvani H, Karampoor S. The emerging role of probiotics as a mitigation strategy against coronavirus disease 2019 (COVID-19). Arch Virol 2021; 166:1819-1840. [PMID: 33745067 PMCID: PMC7980799 DOI: 10.1007/s00705-021-05036-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023]
Abstract
COVID-19 is an acute respiratory infection accompanied by pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has affected millions of people globally. To date, there are no highly efficient therapies for this infection. Probiotic bacteria can interact with the gut microbiome to strengthen the immune system, enhance immune responses, and induce appropriate immune signaling pathways. Several probiotics have been confirmed to reduce the duration of bacterial or viral infections. Immune fitness may be one of the approaches by which protection against viral infections can be reinforced. In general, prevention is more efficient than therapy in fighting viral infections. Thus, probiotics have emerged as suitable candidates for controlling these infections. During the COVID-19 pandemic, any approach with the capacity to induce mucosal and systemic reactions could potentially be useful. Here, we summarize findings regarding the effectiveness of various probiotics for preventing virus-induced respiratory infectious diseases, especially those that could be employed for COVID-19 patients. However, the benefits of probiotics are strain-specific, and it is necessary to identify the bacterial strains that are scientifically established to be beneficial.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Adeleh Attar
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Saher Papizadeh
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Salimi Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Elaheh Jamasbi
- Department of Anatomical Sciences, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Sima Kazemi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saman Amerkani
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholam Reza Talei
- Department of Virology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Lorestan, Iran
| | - Pouya Moradi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saba Jalalifar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Akhter Hossain
- The Florey University of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Sajad Karampoor
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
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189
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Bio-synthesis of silver nanoparticles with the brackish water blue-green alga Oscillatoria princeps and antibacterial assessment. APPLIED NANOSCIENCE 2020. [DOI: 10.1007/s13204-020-01593-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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190
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Di Stadio A, Costantini C, Renga G, Pariano M, Ricci G, Romani L. The Microbiota/Host Immune System Interaction in the Nose to Protect from COVID-19. Life (Basel) 2020; 10:life10120345. [PMID: 33322584 PMCID: PMC7763594 DOI: 10.3390/life10120345] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is characterized by variable clinical presentation that ranges from asymptomatic to fatal multi-organ damage. The site of entry and the response of the host to the infection affect the outcomes. The role of the upper airways and the nasal barrier in the prevention of infection is increasingly being recognized. Besides the epithelial lining and the local immune system, the upper airways harbor a community of microorganisms, or microbiota, that takes an active part in mucosal homeostasis and in resistance to infection. However, the role of the upper airway microbiota in COVID-19 is not yet completely understood and likely goes beyond protection from viral entry to include the regulation of the immune response to the infection. Herein, we discuss the hypothesis that restoring endogenous barriers and anti-inflammatory pathways that are defective in COVID-19 patients might represent a valid strategy to reduce infectivity and ameliorate clinical symptomatology.
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Affiliation(s)
- Arianna Di Stadio
- Department of Otolaryngology, University of Perugia, 06132 Perugia, Italy;
- Correspondence: (A.D.S.); (L.R.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Giorgia Renga
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Marilena Pariano
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Giampietro Ricci
- Department of Otolaryngology, University of Perugia, 06132 Perugia, Italy;
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
- Correspondence: (A.D.S.); (L.R.)
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Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol 2020; 21:301. [PMID: 33308267 PMCID: PMC7731505 DOI: 10.1186/s13059-020-02209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life. RESULTS We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains. CONCLUSIONS This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.
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Affiliation(s)
- Emma K. Accorsi
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Eric A. Franzosa
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Tiffany Hsu
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Regina Joice Cordy
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Wake Forest University, 1834 Wake Forest Rd., Winston-Salem, NC 27109 USA
| | - Ayala Maayan-Metzger
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Hanaa Jaber
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | | | - Madeleine Kline
- Harvard Medical School, 25 Shattuck St., Boston, MA 02115 USA
| | - Casey DuLong
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Marc Lipsitch
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Gili Regev-Yochay
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Curtis Huttenhower
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
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192
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Lagomarsino VN, Kostic AD, Chiu IM. Mechanisms of microbial-neuronal interactions in pain and nociception. NEUROBIOLOGY OF PAIN 2020; 9:100056. [PMID: 33392418 PMCID: PMC7772816 DOI: 10.1016/j.ynpai.2020.100056] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Molecular mechanisms of how microorganisms communicate with sensory afferent neurons. How pathogenic microorganisms directly communicate with nociceptor neurons to inflict pain on the host. Symbiotic bacterial communication with gut-extrinsic sensory afferent neurons. Plausible roles on how gut symbionts directly mediate pain and nociception.
Nociceptor sensory neurons innervate barrier tissues that are constantly exposed to microbial stimuli. During infection, pathogenic microorganisms can breach barrier surfaces and produce pain by directly activating nociceptors. Microorganisms that live in symbiotic relationships with their hosts, commensals and mutualists, have also been associated with pain, but the molecular mechanisms of how symbionts act on nociceptor neurons to modulate pain remain largely unknown. In this review, we will discuss the known molecular mechanisms of how microbes directly interact with sensory afferent neurons affecting nociception in the gut, skin and lungs. We will touch on how bacterial, viral and fungal pathogens signal to the host to inflict or suppress pain. We will also discuss recent studies examining how gut symbionts affect pain. Specifically, we will discuss how gut symbionts may interact with sensory afferent neurons either directly, through secretion of metabolites or neurotransmitters, or indirectly,through first signaling to epithelial cells or immune cells, to regulate visceral, neuropathic and inflammatory pain. While this area of research is still in its infancy, more mechanistic studies to examine microbial-sensory neuron crosstalk in nociception may allow us to develop new therapies for the treatment of acute and chronic pain.
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Affiliation(s)
- Valentina N Lagomarsino
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.,Joslin Diabetes Center, Boston, MA 02115, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksandar D Kostic
- Joslin Diabetes Center, Boston, MA 02115, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac M Chiu
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
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193
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.19.20234229. [PMID: 33236030 PMCID: PMC7685343 DOI: 10.1101/2020.11.19.20234229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, California, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | | | - Laxmi Parida
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, California, USA
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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194
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Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients. mBio 2020; 11:e01969-20. [PMID: 33219095 PMCID: PMC7686804 DOI: 10.1128/mbio.01969-20] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.
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Affiliation(s)
- Heba H Mostafa
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Fissel
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Yehudit Bergman
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rita R Colwell
- CosmosID, Inc., Rockville, Maryland, USA
- University of Maryland College Park, Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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195
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Preliminary insights into the impact of primary radiochemotherapy on the salivary microbiome in head and neck squamous cell carcinoma. Sci Rep 2020; 10:16582. [PMID: 33024215 PMCID: PMC7538973 DOI: 10.1038/s41598-020-73515-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Squamous cell carcinoma is the most common type of throat cancer. Treatment options comprise surgery, radiotherapy, and/or chemo(immuno)therapy. The salivary microbiome is shaped by the disease, and likely by the treatment, resulting in side effects caused by chemoradiation that severely impair patients’ well-being. High-throughput amplicon sequencing of the 16S rRNA gene provides an opportunity to investigate changes in the salivary microbiome in health and disease. In this preliminary study, we investigated alterations in the bacterial, fungal, and archaeal components of the salivary microbiome between healthy subjects and patients with head and neck squamous cell carcinoma before and close to the end point of chemoradiation (“after”). We enrolled 31 patients and 11 healthy controls, with 11 patients providing samples both before and after chemoradiation. Analysis revealed an effect on the bacterial and fungal microbiome, with a partial antagonistic reaction but no effects on the archaeal microbial community. Specifically, we observed an individual increase in Candida signatures following chemoradiation, whereas the overall diversity of the microbial and fungal signatures decreased significantly after therapy. Thus, our study indicates that the patient microbiome reacts individually to chemoradiation but has potential for future optimization of disease diagnostics and personalized treatments.
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196
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Santoro A, Zhao J, Wu L, Carru C, Biagi E, Franceschi C. Microbiomes other than the gut: inflammaging and age-related diseases. Semin Immunopathol 2020; 42:589-605. [PMID: 32997224 PMCID: PMC7666274 DOI: 10.1007/s00281-020-00814-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022]
Abstract
During the course of evolution, bacteria have developed an intimate relationship with humans colonizing specific body sites at the interface with the body exterior and invaginations such as nose, mouth, lung, gut, vagina, genito-urinary tract, and skin and thus constituting an integrated meta-organism. The final result has been a mutual adaptation and functional integration which confers significant advantages to humans and bacteria. The immune system of the host co-evolved with the microbiota to develop complex mechanisms to recognize and destroy invading microbes, while preserving its own bacteria. Composition and diversity of the microbiota change according to development and aging and contribute to humans' health and fitness by modulating the immune system response and inflammaging and vice versa. In the last decades, we experienced an explosion of studies on the role of gut microbiota in aging, age-related diseases, and longevity; however, less reports are present on the role of the microbiota at different body sites. In this review, we describe the key steps of the co-evolution between Homo sapiens and microbiome and how this adaptation can impact on immunosenescence and inflammaging. We briefly summarized the role of gut microbiota in aging and longevity while bringing out the involvement of the other microbiota.
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Affiliation(s)
- Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72703, USA
| | - Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ciriaco Carru
- Department of Biomedical Sciences, University Hospital (AOU) - University of Sassari, Sassari, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology (FABIT), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
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197
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Santacroce L, Charitos IA, Ballini A, Inchingolo F, Luperto P, De Nitto E, Topi S. The Human Respiratory System and its Microbiome at a Glimpse. BIOLOGY 2020; 9:E318. [PMID: 33019595 PMCID: PMC7599718 DOI: 10.3390/biology9100318] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
The recent COVID-19 pandemic promoted efforts to better understand the organization of the respiratory microbiome and its evolution from birth to adulthood and how it interacts with external pathogens and the host immune system. This review aims to deepen understanding of the essential physiological functions of the resident microbiome of the respiratory system on human health and diseases. First, the general characteristics of the normal microbiota in the different anatomical sites of the airways have been reported in relation to some factors such as the effect of age, diet and others on its composition and stability. Second, we analyze in detail the functions and composition and the correct functionality of the microbiome in the light of current knowledge. Several studies suggest the importance of preserving the micro-ecosystem of commensal, symbiotic and pathogenic microbes of the respiratory system, and, more recently, its relationship with the intestinal microbiome, and how it also leads to the maintenance of human health, has become better understood.
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Affiliation(s)
- Luigi Santacroce
- Ionian Department, Microbiology and Virology Laboratory, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Clinical Disciplines, University of Elbasan, Rruga Ismail Zyma, 3001 Elbasan, Albania;
| | | | - Andrea Ballini
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Paolo Luperto
- ENT Service, Brindisi Local Health Agency, Via Dalmazia 3, 72100 Brindisi, Italy;
| | - Emanuele De Nitto
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Skender Topi
- Department of Clinical Disciplines, University of Elbasan, Rruga Ismail Zyma, 3001 Elbasan, Albania;
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198
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Lee AJ, Einarsson GG, Gilpin DF, Tunney MM. Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis? Front Pharmacol 2020; 11:569821. [PMID: 33013411 PMCID: PMC7509435 DOI: 10.3389/fphar.2020.569821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
The advent of high-throughput multi-omics technologies has underpinned the expansion in lung microbiome research, increasing our understanding of the nature, complexity and significance of the polymicrobial communities harbored by people with CF (PWCF). Having established that structurally complex microbial communities exist within the airways, the focus of recent research has now widened to investigating the function and dynamics of the resident microbiota during disease as well as in health. With further refinement, multi-omics approaches present the opportunity to untangle the complex interplay between microbe-microbe and microbe-host interactions in the lung and the relationship with respiratory disease progression, offering invaluable opportunities to discover new therapeutic approaches for our management of airway infection in CF.
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Affiliation(s)
- Andrew J. Lee
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Gisli G. Einarsson
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Deirdre F. Gilpin
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| | - Michael M. Tunney
- Halo Research Group, Queen’s University Belfast, Belfast, United Kingdom
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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199
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Laabei M, Colineau L, Bettoni S, Maziarz K, Ermert D, Riesbeck K, Ram S, Blom AM. Antibacterial Fusion Proteins Enhance Moraxella catarrhalis Killing. Front Immunol 2020; 11:2122. [PMID: 32983170 PMCID: PMC7492680 DOI: 10.3389/fimmu.2020.02122] [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: 04/04/2020] [Accepted: 08/05/2020] [Indexed: 01/10/2023] Open
Abstract
Moraxella catarrhalis is a human-specific commensal of the respiratory tract and an opportunistic pathogen. It is one of the leading cause of otitis media in children and of acute exacerbations in patients with chronic obstructive pulmonary disease, resulting in significant morbidity and economic burden. Vaccines and new immunotherapeutic strategies to treat this emerging pathogen are needed. Complement is a key component of innate immunity that mediates the detection, response, and subsequent elimination of invading pathogens. Many pathogens including M. catarrhalis have evolved complement evasion mechanisms, which include the binding of human complement inhibitors such as C4b-binding protein (C4BP) and Factor H (FH). Inhibiting C4BP and FH acquisition by M. catarrhalis may provide a novel therapeutic avenue to treat infections. To achieve this, we created two chimeric proteins that combined the Moraxella-binding domains of C4BP and FH fused to human immunoglobulin Fcs: C4BP domains 1 and 2 and FH domains 6 and 7 fused to IgM and IgG Fc, respectively. As expected, FH6-7/IgG displaced FH from the bacterial surface while simultaneously activating complement via Fc-C1q interactions, together increasing pathogen elimination. C4BP1-2/IgM also increased serum killing of the bacteria through enhanced complement deposition, but did not displace C4BP from the surface of M. catarrhalis. These Fc fusion proteins could act as anti-infective immunotherapies. Many microbes bind the complement inhibitors C4BP and FH through the same domains as M. catarrhalis, therefore these Fc fusion proteins may be promising candidates as adjunctive therapy against many different drug-resistant pathogens.
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Affiliation(s)
- Maisem Laabei
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden.,Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Lucie Colineau
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Serena Bettoni
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Karolina Maziarz
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - David Ermert
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Sanjay Ram
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
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Challenges in Human Skin Microbial Profiling for Forensic Science: A Review. Genes (Basel) 2020; 11:genes11091015. [PMID: 32872386 PMCID: PMC7564248 DOI: 10.3390/genes11091015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach.
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