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Li CX, Lv M, Liu HY, Lin YX, Pan JB, You CX, Su J. Comparison of the upper and lower airway microbiome in early postoperative lung transplant recipients. Microbiol Spectr 2024; 12:e0379123. [PMID: 38747583 DOI: 10.1128/spectrum.03791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 06/06/2024] Open
Abstract
The upper and lower respiratory tract may share microbiome because they are directly continuous, and the nasal microbiome contributes partially to the composition of the lung microbiome. But little is known about the upper and lower airway microbiome of early postoperative lung transplant recipients (LTRs). Using 16S rRNA gene sequencing, we compared paired nasal swab (NS) and bronchoalveolar lavage fluid (BALF) microbiome from 17 early postoperative LTRs. The microbiome between the two compartments were significantly different in Shannon diversity and beta diversity. Four and eight core NS-associated and BALF-associated microbiome were identified, respectively. NS samples harbored more Corynebacterium, Acinetobacter, and Pseudomonas, while BALF contained more Ralstonia, Stenotrophomonas, Enterococcus, and Pedobacter. The within-subject dissimilarity was higher than the between-subject dissimilarity, indicating a greater impact of sampling sites than sampling individuals on microbial difference. There were both difference and homogeneity between NS and BALF microbiome in early postoperative LTRs. High levels of pathogens were detected in both samples, suggesting that both of them can reflect the diseases characteristics of transplanted lung. The differences between upper and lower airway microbiome mainly come from sampling sites instead of sampling individuals. IMPORTANCE Lung transplantation is the only therapeutic option for patients with end-stage lung disease, but its outcome is much worse than other solid organ transplants. Little is known about the NS and BALF microbiome of early postoperative LTRs. Here, we compared paired samples of the nasal and lung microbiome from 17 early postoperative LTRs and showed both difference and homogeneity between the two samples. Most of the "core" microbiome in both NS and BALF samples were recognized respiratory pathogens, suggesting that both samples can reflect the diseases characteristics of transplanted lung. We also found that the differences between upper and lower airway microbiome in early postoperative LTRs mainly come from sampling sites instead of sampling individuals.
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Affiliation(s)
- Chun-Xi Li
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Meng Lv
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hai-Yue Liu
- Department of laboratory medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yan-Xia Lin
- Hospital Infection-Control Department, Shenzhen University General Hospital, Shenzhen, China
| | - Jian-Bing Pan
- Department of Respiratory Medicine, Meizhou People's Hospital, Meizhou, China
| | - Chang-Xuan You
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Su
- Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Thorsen J, Li XJ, Peng S, Sunde RB, Shah SA, Bhattacharyya M, Poulsen CS, Poulsen CE, Leal Rodriguez C, Widdowson M, Neumann AU, Trivedi U, Chawes B, Bønnelykke K, Bisgaard H, Sørensen SJ, Stokholm J. The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria. Nat Commun 2023; 14:6668. [PMID: 37863895 PMCID: PMC10589220 DOI: 10.1038/s41467-023-42309-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC2000 prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC2010 cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria's abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC2010 cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC2000 nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.
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Affiliation(s)
- Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Xuan Ji Li
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Shuang Peng
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Bjersand Sunde
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Madhumita Bhattacharyya
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Casper Sahl Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Christina Egeø Poulsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Leal Rodriguez
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael Widdowson
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Avidan Uriel Neumann
- Chair of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
- Institute of Environmental Medicine, Helmholtz Munich, Munich, Germany
| | - Urvish Trivedi
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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Kloepfer KM, Kennedy JL. Childhood respiratory viral infections and the microbiome. J Allergy Clin Immunol 2023; 152:827-834. [PMID: 37607643 PMCID: PMC10592030 DOI: 10.1016/j.jaci.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023]
Abstract
The human microbiome associated with the respiratory tract is diverse, heterogeneous, and dynamic. The diversity and complexity of the microbiome and the interactions between microorganisms, host cells, and the host immune system are complex and multifactorial. Furthermore, the lymphatics provide a direct highway, the gut-lung axis, for the gut microbiome to affect outcomes related to respiratory disease and the host immune response. Viral infections in the airways can also alter the presence or absence of bacterial species, which might increase the risks for allergies and asthma. Viruses infect the airway epithelium and interact with the host to promote inflammatory responses that can trigger a wheezing illness. This immune response may alter the host's immune response to microbes and allergens, leading to T2 inflammation. However, exposure to specific bacteria may also tailor the host's response long before the virus has infected the airway. The frequency of viral infections, age at infection, sampling season, geographic location, population differences, and preexisting composition of the microbiota have all been linked to changes in microbiota diversity and stability. This review aims to evaluate the current reported evidence for microbiome interactions and the influences that viral infection may have on respiratory and gut microbiota, affecting respiratory outcomes in children.
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Affiliation(s)
- Kirsten M Kloepfer
- Pulmonology, Allergy/Immunology, and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Ind.
| | - Joshua L Kennedy
- Pulmonology, Allergy, and Critical Care Medicine, University of Arkansas for Medical Sciences, Little Rock, Ark; Allergy and Immunology, Department of Pediatrics, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Ark; Arkansas Children's Research Institute, Little Rock, Ark
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Wang L, Lu S, Guo Y, Liu J, Wu P, Yang S. Comparative study of diagnostic efficacy of sputum and bronchoalveolar lavage fluid specimens in community-acquired pneumonia children treated with fiberoptic bronchoscopy. BMC Infect Dis 2023; 23:565. [PMID: 37644391 PMCID: PMC10466683 DOI: 10.1186/s12879-023-08522-3] [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: 02/23/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is usually diagnosed in children, and the type of respiratory specimen is critical. Differences in pathogens detection between induced sputum (IS) and bronchoalveolar lavage fluid (BALF) have not been evaluated. METHODS In 2018, paired sputum and BALF samples from CAP hospitalised children with indications for bronchoalveolar lavage (BAL) were subjected to multiplex PCR for the detection of 11 common respiratory pathogens. RESULTS A total of 142 children with paired sputum and BALF were tested. The overall positivity rate was 85.9% (122/142) for sputum and 80.3% (114/142) for BALF. The two specimens presented almost perfect agreement between the detection on M. pneumoniae, influenza A, influenza B, bocavirus and RSV. In contrast, adenovirus had the lowest kappa value of 0.156, and a false negative rate (FNR) of 66.7%. Rhinovirus had the highest false positive rate (FPR) as 18.5%. The consistent rate was significantly higher in school-age children than those under 1 year old (p = .005). Bacterial co-infection in BALF specimens were observed in 14.8% (21/142). Of the 11 discordant pairs of specimens, 9 cases were sputum(+)/BALF(-) with adenovirus predominating. CONCLUSION Our findings suggest that the consistency of results between sputum and BALF is pathogen specific. Careful consideration needs to be given to whether sputum can be used as a substitute for BALF when children are young or co-infections with bacteria are suspected.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China
| | - Sukun Lu
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China
| | - Yinghui Guo
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China
| | - Jianhua Liu
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China
| | - Peng Wu
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, 133 Zhonghua South Street, Shijiazhuang, 050031, Hebei Province, China.
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Bar K, Litera-Bar M, Sozańska B. Bacterial Microbiota of Asthmatic Children and Preschool Wheezers' Airways-What Do We Know? Microorganisms 2023; 11:1154. [PMID: 37317128 DOI: 10.3390/microorganisms11051154] [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: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Asthma is the most chronic pulmonary disease in pediatric population, and its etiopathology still remains unclear. Both viruses and bacteria are suspected factors of disease development and are responsible for its exacerbation. Since the launch of The Human Microbiome Project, there has been an explosion of research on microbiota and its connection with various diseases. In our review, we have collected recent data about both upper- and lower-airway bacterial microbiota of asthmatic children. We have also included studies regarding preschool wheezers, since asthma diagnosis in children under 5 years of age remains challenging due to the lack of an objective tool. This paper indicates the need for further studies of microbiome and asthma, as in today's knowledge, there is no particular bacterium that discriminates the asthmatics from the healthy peers and can be used as a potential biological factor in the disease prevalence and treatment.
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Affiliation(s)
- Kamil Bar
- 1st Department and Clinic of Paediatrics, Allergology and Cardiology, Wroclaw Medical University, 50-367 Wroclaw, Poland
| | - Maja Litera-Bar
- University Clinical Hospital in Wroclaw, 50-556 Wroclaw, Poland
| | - Barbara Sozańska
- 1st Department and Clinic of Paediatrics, Allergology and Cardiology, Wroclaw Medical University, 50-367 Wroclaw, Poland
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Bloodworth JC, Hoji A, Wolff G, Mandal RK, Schmidt NW, Deshane JS, Morrow CD, Kloepfer KM, Cook-Mills JM. Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen. FRONTIERS IN ALLERGY 2023; 4:1135412. [PMID: 36970065 PMCID: PMC10036811 DOI: 10.3389/falgy.2023.1135412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.
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Affiliation(s)
- Jeffery C. Bloodworth
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Aki Hoji
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Garen Wolff
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rabindra K. Mandal
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nathan W. Schmidt
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kirsten M. Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Joan M. Cook-Mills
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
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Zhang J, Wu Y, Liu J, Yang Y, Li H, Wu X, Zheng X, Liang Y, Tu C, Chen M, Tan C, Chang B, Huang Y, Wang Z, Tian G, Ding T. Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203115. [PMID: 36031410 PMCID: PMC9661847 DOI: 10.1002/advs.202203115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Indexed: 05/09/2023]
Abstract
The oral and upper respiratory tracts are closely linked anatomically and physiologically with the lower respiratory tract and lungs, and the influence of oral and upper respiratory microbes on the lung microbiota is increasingly being recognized. However, the ecological process and individual heterogeneity of the oral and upper respiratory tract microbes shaping the lung microbiota remain unclear owing to the lack of controlled analyses with sufficient sample sizes. Here, the microbiomes of saliva, nasal cavity, oropharyngeal area, and bronchoalveolar lavage samples are profiled and the shaping process of multisource microbes on the lung microbiota is measured. It is found that oral and nasal microbial inputs jointly shape the lung microbiota by occupying different ecological niches. It is also observed that the spread of oral microbes to the lungs is heterogeneous, with more oral microbes entering the lungs being associated with decreased lung function and increased lung proinflammatory cytokines. These results depict the external shaping process of lung microbiota and indicate the great value of oral samples, such as saliva, in monitoring and assessing lung microbiota status in clinical settings.
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Affiliation(s)
- Jingxiang Zhang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiping Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Jing Liu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yongqiang Yang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Hui Li
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaorong Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaobin Zheng
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yingjian Liang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Changli Tu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Meizhu Chen
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Cuiyan Tan
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Bozhen Chang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiying Huang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Zhengguo Wang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Guo‐Bao Tian
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
- School of MedicineXizang Minzu UniversityXianyangShaanxi712082China
| | - Tao Ding
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
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8
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Ballas ZK. “Where are they now”? Catching up with the 2017 AAAAI Faculty Development Awardees. J Allergy Clin Immunol 2022; 150:583-584. [DOI: 10.1016/j.jaci.2022.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 10/16/2022]
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9
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Validation of nasal tracheal aspiration in children with lung disease. BMC Pulm Med 2022; 22:198. [PMID: 35581568 PMCID: PMC9112497 DOI: 10.1186/s12890-022-01992-2] [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: 09/20/2021] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Background Nasal tracheal aspiration (NTA) is a frequently used diagnostic method to assess of infections in the lower airways. However, the validity of the method has not previously been compared to bronchoalveolar lavage (BAL) in non-intubated children with a lung disease. We hypothesised that NTA performed by health professionals using the nares vocal cord distance to be placed at the entrance of the trachea, will result in same finding of bacteria in the lower airways as the gold standard of BAL. Methods In a prospective study, 173 paired samples of NTA and BAL were obtained between June 2016 to August 2018. Samples were collected from all patients undergoing bronchoscopy with spontaneous breathing during general anaesthesia. This study compares the microbiological results from the cultures obtained by investigating complete concordance i.e. identical pathogenic bacteria and coherence i.e. absence or presence of pathogenic bacteria growth between NTA and BAL. Results Samples were collected in 164 patients, 158 children between 21 days and 18 years of age and six young adults still treated at the paediatric department. The overall similarity (complete agreement) was found in 49% [41–56], sensitivity was 35% [27–45], specificity was 66% [55–76], positive predictive value was 36% [27–46] and negative predictive value was 64% [54–64] concerning complete pathogenic bacteria concordance. If we only considered coherence growth of pathogenic bacteria, similarity was 71% [63–79], sensitivity was 74% [64–81], specificity was 66% [55–76], positive predictive value was 75% [65–82] and negative predictive value was 65% [54–75]. Patients with cystic fibrosis showed a similarity of 88% [73–95], a sensitivity of 92% [76–99], a specificity of 71% [36–95], a positive predictive value of 92% [76–99] and a negative predictive value of 71% [36–95] concerning coherence growth of pathogenic bacteria. Conclusion The study indicates that NTA compared to BAL as the gold standard is not clinically useful to assess positive findings of specific bacteria in the lower airway tract. Statistically significantly increased sensitivity and positive predictive value were found in cystic fibrosis patients concerning coherence growth. The clinical usage of NTA remains important as negative findings are of clinical value. However, BAL continues to be preferred as a significantly superior diagnostic tool.
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10
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Zhang L, Ai T, Xie C, Xia W, Zhang Y, Liao H, Jia L, Fan Y, Xu J. Lower airway microbiome of children with recurrent wheezing: a clinical cohort study. Transl Pediatr 2022; 11:696-705. [PMID: 35685081 PMCID: PMC9173878 DOI: 10.21037/tp-22-165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/07/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Wheezing is one of the most common respiratory symptoms in childhood especially in infants. In recent years, the incidence of recurrent wheezing is on the rise worldwide. To investigate the lower airway microbiota in patients with recurrent wheezing and provide insights into clinical diagnosis and treatment. METHODS This study initially enrolled 45 hospitalised children with recurrent wheezing symptoms awaiting complete fiberoptic bronchoscopy. Of these, 13 children with tracheobronchomalacia were excluded. The final population included 32 participants (group A). The control group comprised 23 children who inhaled a foreign body and were admitted to the hospital for fiberoptic bronchoscopy within 24 hours (group B). Deoxyribonucleic acid (DNA) was extracted from the bronchoalveolar lavage fluid (BALF) and amplified for the 16S ribosomal Ribonucleic Acid (rRNA) gene, and sequencing of the microbiome was performed using the Illumina Nova Seq 6000 system. RESULTS There were significant differences in the gestational duration (P=0.0458), mode of delivery (P=0.0261), and allergy status (P=0.0000) between groups A and B, but they had similar richness (P=0.8574). There was also a marked difference in the diversity of flora composition between the two groups (P=0.0095). The three most common phyla of microbiota in the two groups were Proteobacteria, Firmicutes, and Bacteroidetes. Species with notably different phyla included Proteobacteria, Bacteroidota, Fusobacteriota, and Acidobacteriota. There was a significant enrichment in the of Proteobacteria and lower levels of Bacteroidota, Fusobacteriota, and Acidobacteriota in group A compared to that in group B. CONCLUSIONS Significant changes occur in the lower airway microbiota during recurrent wheezing in children. The discovery of beneficial airway bacteria may facilitate the prevention and treatment of recurrent wheezing or asthma in children.
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Affiliation(s)
- Lei Zhang
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Ai
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Xie
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wanmin Xia
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ying Zhang
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Huling Liao
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Liangqin Jia
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yinghong Fan
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jia Xu
- Department of Pediatric Pulmonology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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11
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Abstract
PURPOSE OF REVIEW Asthma is the most common chronic disease of childhood. Investigations of the lower and upper airway microbiomes have significantly progressed over recent years, and their roles in pediatric asthma are becoming increasingly clear. RECENT FINDINGS Early studies identified the existence of upper and lower airway microbiomes, including imbalances in both associated with pediatric asthma. The infant airway microbiome may offer predictive value for the development of asthma in later childhood, and it may also be influenced by external factors such as respiratory viral illness. The airway microbiome has also been associated with the clinical course of asthma, including rates of exacerbation and level of control. Advances in -omics sciences have enabled improved identification of the airway microbiome's relationships with host response and function in children with asthma. Investigations are now moving toward the application of the above findings to explore risk modification and treatment options. SUMMARY The airway microbiome provides an intriguing window into pediatric asthma, offering insights into asthma diagnosis, clinical course, and perhaps treatment. Further investigation is needed to solidify these associations and translate research findings into clinical practice.
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Affiliation(s)
- Rhia Shah
- Division of Pulmonary Medicine, Department of Pediatrics,
Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of
Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, NY
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12
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Cho HJ, Ha JG, Lee SN, Kim CH, Wang DY, Yoon JH. Differences and similarities between the upper and lower airway: focusing on innate immunity. Rhinology 2021; 59:441-450. [PMID: 34339483 DOI: 10.4193/rhin21.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The nose is the first respiratory barrier to external pathogens, allergens, pollutants, or cigarette smoke, and vigorous immune responses are triggered when external pathogens come in contact with the nasal epithelium. The mucosal epithelial cells of the nose are essential to the innate immune response against external pathogens and transmit signals that modulate the adaptive immune response. The upper and lower airways share many physiological and immunological features, but there are also numerous differences. It is crucial to understand these differences and their contribution to pathophysiology in order to optimize treatments for inflammatory diseases of the respiratory tract. This review summarizes important differences in the embryological development, histological features, microbiota, immune responses, and cellular subtypes of mucosal epithelial cells of the nose and lungs.
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Affiliation(s)
- H-J Cho
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - J G Ha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - S N Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea 2 Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea
| | - C-H Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - D-Y Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J-H Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
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13
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Cui J, Zhang Y, Zhao H, Sun X, Chen Z, Zhang Q, Yan C, Xue G, Li S, Feng Y, Liu H, Xie X, Yuan J. The Relationship Between Lower Respiratory Tract Microbiome and Allergic Respiratory Tract Diseases in Children. Front Microbiol 2021; 12:630345. [PMID: 34054744 PMCID: PMC8160472 DOI: 10.3389/fmicb.2021.630345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Similar to those in the upper respiratory tract, there are microbes present in the healthy human lower respiratory tract (LRT), including the lungs and bronchus. To evaluate the relationship between LRT microbiome and allergic respiratory diseases in children, we enrolled 68 children who underwent bronchoscopy from January 2018 to December 2018 in the affiliated hospital of the Capital Institute of Pediatrics. Using the total IgE (TIgE) values, children were divided into two groups: allergy sensitivity (AS) group and non-allergy sensitivity (NAS) group. Nucleic acid was extracted from samples of bronchoalveolar lavage fluid (BALF) from the two groups of children taken during bronchoscopy treatment and the 16S rDNA gene was sequenced and analyzed. The results showed that Haemophilus, Moraxella, Streptococcus, Prevotella, Neisseria, and Rothia were detected in all patients. There was a statistically significant difference in the composition and distribution of microbiota between the AS and NAS groups (p < 0.01). Analysis of the correlation of clinical indices and microbiome showed that TIgE was positively correlated with Bacteroidetes and negatively correlated with Streptococcus. Absolute lymphocyte count showed a relationship with Streptococcus, and the absolute neutrophil count or percentage of neutrophils showed a relationship with Cardiobacterium. The LRT microbiome functioned similarly to the intestinal microbiome. That is, the decrease in microbial diversity and the change in composition could lead to an increase in allergic symptoms. The microbiome of the LRT in children, especially that of Bacteriodetes and Streptococcus, showed a correlation with respiratory allergic diseases.
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Affiliation(s)
- Jinghua Cui
- Capital Institute of Pediatrics, Beijing, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | | | - Xuemei Sun
- Dongfeng Traditional Chinese Medicine Hospital, Jilin, China
| | - Zhen Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qun Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chao Yan
- Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Capital Institute of Pediatrics, Beijing, China
| | - Shaoli Li
- Capital Institute of Pediatrics, Beijing, China
| | | | - Han Liu
- Baicheng Medical College, Jilin, China
| | | | - Jing Yuan
- Capital Institute of Pediatrics, Beijing, China
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14
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Linnane B, Walsh AM, Walsh CJ, Crispie F, O’Sullivan O, Cotter PD, McDermott M, Renwick J, McNally P. The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study. Microorganisms 2021; 9:microorganisms9030492. [PMID: 33652802 PMCID: PMC7996874 DOI: 10.3390/microorganisms9030492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The cystic fibrosis (CF) lung harbours a diverse microbiome and reduced diversity in the CF lung has been associated with advancing age, increased inflammation and poorer lung function. Data suggest that the window for intervention is early in CF, yet there is a paucity of studies on the lung microbiome in children with CF. The objective of this study was to thoroughly characterise the lower airway microbiome in pre-school children with CF. Bronchoalveolar lavage (BAL) samples were collected annually from children attending the three clinical centres. Clinical and demographic data were collated on all subjects alongside BAL inflammatory markers. 16S rRNA gene sequencing was performed on the Illumina MiSeq platform. Bioinformatics and data analysis were performed using Qiime and R project software. Data on 292 sequenced BALs from 101 children with CF and 51 without CF show the CF lung microbiome, while broadly similar to that in non-CF children, is distinct. Alpha diversity between the two cohorts was indistinguishable at this early age. The CF diagnosis explained only 1.1% of the variation between the cohort microbiomes. However, several key genera were significantly differentially abundant between the groups. While the non-CF lung microbiome diversity increased with age, diversity reduced in CF with age. Pseudomonas and Staphylococcus were more abundant with age, while genera such as Streptococcus, Porphyromonas and Veillonella were less abundant with age. There was a negative correlation between alpha diversity and interleukin-8 and neutrophil elastase in the CF population. Neither current flucloxacillin or azithromycin prophylaxis, nor previous oral or IV antibiotic exposure, was correlated with microbiome diversity. Consecutive annual BAL samples over 5 years from a subgroup of children demonstrated diverse patterns of development in the first years of life.
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Affiliation(s)
- Barry Linnane
- Centre for Interventions in Infection, Inflammation and Immunity (4i) and Graduate Entry Medical School, University of Limerick, Limerick V94 T9PX, Ireland;
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin D12 N512, Ireland;
| | - Aaron M. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (A.M.W.); (C.J.W.); (F.C.); (O.O.); (P.D.C.)
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Calum J. Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (A.M.W.); (C.J.W.); (F.C.); (O.O.); (P.D.C.)
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (A.M.W.); (C.J.W.); (F.C.); (O.O.); (P.D.C.)
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (A.M.W.); (C.J.W.); (F.C.); (O.O.); (P.D.C.)
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (A.M.W.); (C.J.W.); (F.C.); (O.O.); (P.D.C.)
- APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
| | - Michael McDermott
- Pathology Department, Our Lady’s Children’s Hospital, Crumlin, Dublin D12 N512, Ireland;
| | - Julie Renwick
- Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland
- Correspondence: ; Tel.: +353-1-896-3791
| | - Paul McNally
- National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin D12 N512, Ireland;
- Department of Paediatrics, Royal College of Surgeons in Ireland, Our Lady’s Children’s Hospital Crumlin, Dublin D12 N512, Ireland
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15
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Gatcliffe C, Rao A, Brigger M, Dimmock D, Hansen C, Montgomery J, Schlaberg R, Coufal NG, Farnaes L. Metagenomic sequencing and evaluation of the host response in the pediatric aerodigestive population. Pediatr Pulmonol 2021; 56:516-524. [PMID: 33270378 DOI: 10.1002/ppul.25198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/30/2020] [Accepted: 11/19/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES To assess the diagnostic utility of metagenomic sequencing in pediatric aerodigestive clinic patients being evaluated for chronic aspiration. We hypothesize that using a metagenomics platform will aid in the identification of microbes not found on standard culture. STUDY DESIGN AND METHODS Twenty-four children referred to an aerodigestive clinic were enrolled in a prospective, single-site, cross-sectional cohort study. At the time of clinical evaluation under anesthesia, two samples were obtained: an upper airway sample and a sample from bronchoalveolar lavage (BAL). Samples were sent for routine culture and analyzed using Explify® Respiratory, a CLIA Laboratory Developed Test which identifies respiratory commensals and pathogens through RNA and DNA sequencing. Since RNA was sequenced in the course of the metagenomic analysis to identify organisms (RNA viruses and bacteria), the sequencing approach also captured host derived messenger RNA during sample analysis. This incidentally obtained host transcriptomic data were analyzed to evaluate the host immune response. The results of these studies were correlated with the clinical presentation of the research subjects. RESULTS In 10 patients, organisms primarily associated with oral flora were identified in the BAL. Standard culture was negative in three patients where clinical metagenomics led to a result with potential clinical significance. Transcriptomic data correlated with the presence or absence of dysphagia as identified on prior videofluoroscopic evaluation of swallowing. CONCLUSIONS Clinical metagenomics allows for simultaneous analysis of the microbiota and the host immune response from BAL samples. As the technologies in this field continue to advance, such testing may improve the diagnostic evaluation of patients with suspected chronic aspiration.
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Affiliation(s)
- Chelsea Gatcliffe
- Department of Pediatrics, Division of Pediatric Respiratory Medicine, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA.,Department of Surgery, Division of Pediatric Otolaryngology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | - Aparna Rao
- Department of Pediatrics, Division of Pediatric Respiratory Medicine, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | - Matthew Brigger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, San Diego, California, USA
| | - David Dimmock
- Department of Surgery, Division of Pediatric Otolaryngology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | - Christian Hansen
- Department of Surgery, Division of Pediatric Otolaryngology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | | | | | - Nicole G Coufal
- Department of Surgery, Division of Pediatric Otolaryngology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA.,Department of Pediatrics, Pediatric Critical Care, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | - Lauge Farnaes
- Department of Surgery, Division of Pediatric Otolaryngology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA.,Department of Pediatrics, Division of Pediatric Infectious Diseases, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
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16
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Saladié M, Caparrós-Martín JA, Agudelo-Romero P, Wark PAB, Stick SM, O'Gara F. Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. Front Microbiol 2020; 11:572504. [PMID: 33123104 PMCID: PMC7573210 DOI: 10.3389/fmicb.2020.572504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years the study of the commensal microbiota is driving a remarkable paradigm shift in our understanding of human physiology. However, intrinsic technical difficulties associated with investigating the Microbiomics of some body niches are hampering the development of new knowledge. This is particularly the case when investigating the functional role played by the human microbiota in modulating the physiology of key organ systems. A major hurdle in investigating specific Microbiome communities is linked to low bacterial density and susceptibility to bias caused by environmental contamination. To prevent such inaccuracies due to background processing noise, harmonized tools for Microbiomic and bioinformatics practices have been recommended globally. The fact that the impact of this undesirable variability is negatively correlated with the DNA concentration in the sample highlights the necessity to improve existing DNA isolation protocols. In this report, we developed and tested a protocol to more efficiently recover bacterial DNA from low volumes of bronchoalveolar lavage fluid obtained from infants and adults. We have compared the efficiency of the described method with that of a commercially available kit for microbiome analysis in body fluids. We show that this new methodological approach performs better in terms of extraction efficiency. As opposed to commercial kits, the DNA extracts obtained with this new protocol were clearly distinguishable from the negative extraction controls in terms of 16S copy number and Microbiome community profiles. Altogether, we described a cost-efficient protocol that can facilitate microbiome research in low-biomass human niches.
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Affiliation(s)
- Montserrat Saladié
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Jose Antonio Caparrós-Martín
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Patricia Agudelo-Romero
- Telethon Kids Institute, Perth, WA, Australia.,ARC Centre for Plant Energy Biology, Faculty of Science, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Peter A B Wark
- Centre of Excellence in Severe Asthma and Priority Research, Centre for Healthy Lungs, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, WA, Australia
| | - Fergal O'Gara
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Telethon Kids Institute, Perth, WA, Australia.,BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
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17
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Which sample type is better for Xpert MTB/RIF to diagnose adult and pediatric pulmonary tuberculosis? Biosci Rep 2020; 40:225865. [PMID: 32701147 PMCID: PMC7403955 DOI: 10.1042/bsr20200308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 02/05/2023] Open
Abstract
Objective: This review aimed to identify proper respiratory-related sample types for adult and pediatric pulmonary tuberculosis (PTB), respectively, by comparing performance of Xpert MTB/RIF when using bronchoalveolar lavage (BAL), induced sputum (IS), expectorated sputum (ES), nasopharyngeal aspirates (NPAs), and gastric aspiration (GA) as sample. Methods: Articles were searched in Web of Science, PubMed, and Ovid from inception up to 29 June 2020. Pooled sensitivity and specificity were calculated, each with a 95% confidence interval (CI). Quality assessment and heterogeneity evaluation across included studies were performed. Results: A total of 50 articles were included. The respective sensitivity and specificity were 87% (95% CI: 0.84–0.89), 91% (95% CI: 0.90–0.92) and 95% (95% CI: 0.93–0.97) in the adult BAL group; 90% (95% CI: 0.88–0.91), 98% (95% CI: 0.97–0.98) and 97% (95% CI: 0.95–0.99) in the adult ES group; 86% (95% CI: 0.84–0.89) and 97% (95% CI: 0.96–0.98) in the adult IS group. Xpert MTB/RIF showed the sensitivity and specificity of 14% (95% CI: 0.10–0.19) and 99% (95% CI: 0.97–1.00) in the pediatric ES group; 80% (95% CI: 0.72–0.87) and 94% (95% CI: 0.92–0.95) in the pediatric GA group; 67% (95% CI: 0.62–0.72) and 99% (95% CI: 0.98–0.99) in the pediatric IS group; and 54% (95% CI: 0.43–0.64) and 99% (95% CI: 0.97–0.99) in the pediatric NPA group. The heterogeneity across included studies was deemed acceptable. Conclusion: Considering diagnostic accuracy, cost and sampling process, ES was a better choice than other sample types for diagnosing adult PTB, especially HIV-associated PTB. GA might be more suitable than other sample types for diagnosing pediatric PTB. The actual choice of sample types should also consider the needs of specific situations.
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18
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Chun Y, Do A, Grishina G, Grishin A, Fang G, Rose S, Spencer C, Vicencio A, Schadt E, Bunyavanich S. Integrative study of the upper and lower airway microbiome and transcriptome in asthma. JCI Insight 2020; 5:133707. [PMID: 32161195 PMCID: PMC7141394 DOI: 10.1172/jci.insight.133707] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/13/2020] [Indexed: 12/31/2022] Open
Abstract
Relatively little is known about interactions between the airway microbiome and airway host transcriptome in asthma. Since asthma affects and is affected by the entire airway, studying the upper (e.g., nasal) and lower (e.g., bronchial) airways together represents a powerful approach to understanding asthma. Here, we performed a systematic, integrative study of the nasal and bronchial microbiomes and nasal and bronchial host transcriptomes of children with severe persistent asthma and healthy controls. We found that (a) the microbiomes and host transcriptomes of asthmatic children are each distinct by site (nasal versus bronchial); (b) among asthmatic children, Moraxella and Alloiococcus are hub genera in the nasal microbiome, while there are no hubs among bronchial genera; (c) bronchial Actinomyces is negatively associated with bronchial genes for inflammation, suggesting Actinomyces may be protective; (d) compared with healthy children, asthmatic children express more nasal genes for ciliary function and harbor more nasal Streptococcus; and (e) nasal genera such as Corynebacterium are negatively associated with significantly more nasal genes for inflammation in healthy versus asthmatic children, suggesting a potentially stronger protective role for such nasal genera in healthy versus asthmatic children. Our systematic, integrative study provides a window into host-microbiome associations in asthma.
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Affiliation(s)
- Yoojin Chun
- Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences
| | - Anh Do
- Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, and
| | | | - Gang Fang
- Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences
| | - Samantha Rose
- Division of Pulmonary Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chantal Spencer
- Division of Pulmonary Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alfin Vicencio
- Division of Pulmonary Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric Schadt
- Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences
| | - Supinda Bunyavanich
- Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences
- Division of Allergy and Immunology, Department of Pediatrics, and
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19
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Durack J, Christophersen CT. Human Respiratory and Gut Microbiomes-Do They Really Contribute to Respiratory Health? Front Pediatr 2020; 8:528. [PMID: 33014929 PMCID: PMC7509439 DOI: 10.3389/fped.2020.00528] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
Human gastrointestinal and respiratory tracts are colonized by diverse polymicrobial communities shortly after birth, which are continuously molded by environmental exposure. The development of the resident microbiota in early life is a critical factor in the maturation of a healthy immune system. Disturbances to the intricate relationship between environmental exposure and maturation of the infant microbiome have been increasingly identified as a potential contributor to a range of childhood diseases. This review details recent evidence that implicates the contribution of gut and airway microbiome to pediatric respiratory health.
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Affiliation(s)
- Juliana Durack
- Symbiome Inc., San Francisco, CA, United States.,Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Claus T Christophersen
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.,WA Human Microbiome Collaboration Centre, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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20
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Kloepfer KM, Ross SE, Hemmerich CM, Slaven JE, Rusch DB, Davis SD. Increased microbiota diversity associated with higher FEV 0.5 in infants. Pediatr Pulmonol 2020; 55:27-29. [PMID: 31859450 PMCID: PMC7709493 DOI: 10.1002/ppul.24559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/21/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Kirsten M Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sydney E Ross
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Christopher M Hemmerich
- Center of Genomics and Bioinformatics, Department of Biology, Indiana University Bloomington, Indiana
| | - James E Slaven
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Douglas B Rusch
- Center of Genomics and Bioinformatics, Department of Biology, Indiana University Bloomington, Indiana
| | - Stephanie D Davis
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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21
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Espuela-Ortiz A, Lorenzo-Diaz F, Baez-Ortega A, Eng C, Hernandez-Pacheco N, Oh SS, Lenoir M, Burchard EG, Flores C, Pino-Yanes M. Bacterial salivary microbiome associates with asthma among african american children and young adults. Pediatr Pulmonol 2019; 54:1948-1956. [PMID: 31496123 PMCID: PMC6851413 DOI: 10.1002/ppul.24504] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/21/2019] [Indexed: 02/01/2023]
Abstract
Several studies have shown that the airways of asthma patients contain higher diversity of bacteria and are enriched in pathogenic species. However, sampling the airways in children is challenging. Here we aimed to identify differences in the salivary bacterial composition between African Americans children with and without asthma. Saliva samples from 57 asthma cases and 57 healthy controls were analyzed by means of 16S ribosomal RNA amplicon profiling. Measurements of bacterial diversity and genus relative abundance were compared between cases and controls using the nonparametric Wilcoxon test and multivariate regression models. A total of five phyla and a mean of 56 genera were identified. Among them, 15 genera had a relative abundance greater than 1%, being Prevotella, Haemophilus, Streptococcus, and Veillonella the most abundant genera. Differences between cases and controls were found in terms of diversity, as well as in relative abundance for Streptococcus genus (13.0% in cases vs 18.3% in controls; P = .003) and Veillonella genus (11.1% in cases vs 8.0% in controls; P = .002). These differences remained significant after correction for multiple comparisons and when potential confounders were taken into account in logistic regression models. In conclusion, we identified changes in the salivary microbiota associated with asthma among African Americans.
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Affiliation(s)
- Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Adrian Baez-Ortega
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Natalia Hernandez-Pacheco
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sam S. Oh
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | | | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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22
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Loughlin CE, Muston HN, Pena MA, Ren CL, Yilmaz O, Noah TL. Pediatric Pulmonology year in review 2018: Asthma, physiology/pulmonary function testing, and respiratory infections. Pediatr Pulmonol 2019; 54:1508-1515. [PMID: 31237426 DOI: 10.1002/ppul.24420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 11/06/2022]
Abstract
Pediatric Pulmonology publishes original research, reviews, and case reports related to a wide range of children's respiratory disorders. In our "Year in Review" series, we summarize publications in our major topic areas from 2018, in the context of selected literature in these areas from other journals relevant to our discipline. This review covers selected articles on asthma, physiology/lung function testing, and respiratory infections.
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Affiliation(s)
- Ceila E Loughlin
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Heather N Muston
- Department of Pediatrics, Riley Children's Hospital, Indiana University School of Medicine, Indianapolis, Indiana
| | - Michael A Pena
- Department of Pediatrics, Riley Children's Hospital, Indiana University School of Medicine, Indianapolis, Indiana
| | - Clement L Ren
- Department of Pediatrics, Riley Children's Hospital, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ozge Yilmaz
- Department of Pediatrics, Pediatric Allergy and Pulmonology, Celal Bayar University, Manisa, Turkey
| | - Terry L Noah
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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23
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Kirst ME, Baker D, Li E, Abu-Hasan M, Wang GP. Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation. PLoS One 2019; 14:e0222323. [PMID: 31536536 PMCID: PMC6752789 DOI: 10.1371/journal.pone.0222323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/28/2019] [Indexed: 12/21/2022] Open
Abstract
Objective Airways of children with cystic fibrosis (CF) harbor complex polymicrobial communities which correlates with pulmonary disease progression and use of antibiotics. Throat swabs are widely used in young CF children as a surrogate to detect potentially pathogenic microorganisms in lower airways. However, the relationship between upper and lower airway microbial communities remains poorly understood. This study aims to determine (1) to what extent oropharyngeal microbiome resembles the lung microbiome in CF children and (2) if lung microbiome composition correlates with airway inflammation. Method Throat swabs and bronchoalveolar lavage (BAL) were obtained concurrently from 21 CF children and 26 disease controls. Oropharyngeal and lung microbiota were analyzed using 16S rRNA deep sequencing and correlated with neutrophil counts in BAL and antibiotic exposure. Results Oropharyngeal microbial communities clustered separately from lung communities and had higher microbial diversity (p < 0.001). CF microbiome differed significantly from non-CF controls, with a higher abundance of Proteobacteria in both upper and lower CF airways. Neutrophil count in the BAL correlated negatively with the diversity but not richness of the lung microbiome. In CF children, microbial genes involved in bacterial motility proteins, two-component system, flagella assembly, and secretion system were enriched in both oropharyngeal and lung microbiome, whereas genes associated with synthesis and metabolism of nucleic acids and protein dominated the non-CF controls. Conclusions This study identified a unique microbial profile with altered microbial diversity and metabolic functions in CF airways which is significantly affected by airway inflammation. These results highlight the limitations of using throat swabs as a surrogate to study lower airway microbiome and metagenome in CF children.
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Affiliation(s)
- Mariana E. Kirst
- Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Dawn Baker
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Eric Li
- Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Mutasim Abu-Hasan
- Department of Pediatrics, Division of Pediatric Pulmonology, University of Florida College of Medicine, Gainesville, FL, United States of America
| | - Gary P. Wang
- Department of Medicine, Division of Infectious Diseases and Global Medicine, University of Florida College of Medicine, Gainesville, FL, United States of America
- Medical Service, Infectious Disease Section, North Florida/South Georgia Veterans Health System, Gainesville, FL, United States of America
- * E-mail:
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24
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Hare KM, Chang AB, Smith-Vaughan HC, Bauert PA, Spain B, Beissbarth J, Grimwood K. Do combined upper airway cultures identify lower airway infections in children with chronic cough? Pediatr Pulmonol 2019; 54:907-913. [PMID: 31006971 DOI: 10.1002/ppul.24336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/11/2019] [Accepted: 03/07/2019] [Indexed: 01/20/2023]
Abstract
BACKGROUND Obtaining lower airway specimens is important for guiding therapy in chronic lung infection but is difficult in young children unable to expectorate. While culture-based studies have assessed the diagnostic accuracy of nasopharyngeal or oropharyngeal specimens for identifying lower airway infection, none have used both together. We compared respiratory bacterial pathogens cultured from nasopharyngeal and oropharyngeal swabs with bronchoalveolar lavage (BAL) cultures as the "gold standard" to better inform the diagnosis of lower airway infection in children with chronic wet cough. METHODS Nasopharyngeal and oropharyngeal swabs and BAL fluid specimens were collected concurrently from consecutive children undergoing flexible bronchoscopy for chronic cough and cultured for bacterial pathogens. RESULTS In cultures from 309 children (median age, 2.3 years) with chronic endobronchial suppuration, all main pathogens detected (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) were more prevalent in nasopharyngeal than oropharyngeal swabs (37%, 34%, and 23% vs 21%, 6.2%, and 3.2%, respectively). Positive and negative predictive values for lower airway infection by any of these three pathogens were 63% (95% confidence interval [95% CI] 55, 70) and 85% (95% CI, 78, 91) for nasopharyngeal swabs, 65% (95% CI, 54, 75), and 66% (95% CI, 59, 72) for oropharyngeal swabs, and 61% (95% CI, 54,68), and 88% (95% CI, 81, 93) for both swabs, respectively. CONCLUSIONS Neither nasopharyngeal nor oropharyngeal swabs, alone or in combination, reliably predicted lower airway infection in children with chronic wet cough. Although upper airway specimens may be useful for bacterial carriage studies and monitoring antimicrobial resistance, their clinical utility in pediatric chronic lung disorders of endobronchial suppuration is limited.
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Affiliation(s)
- Kim M Hare
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,Department of Respiratory Medicine, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Paul A Bauert
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Brian Spain
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Keith Grimwood
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia
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25
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Toivonen L, Hasegawa K, Waris M, Ajami NJ, Petrosino JF, Camargo CA, Peltola V. Early nasal microbiota and acute respiratory infections during the first years of life. Thorax 2019; 74:592-599. [PMID: 31076501 DOI: 10.1136/thoraxjnl-2018-212629] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/16/2019] [Accepted: 04/08/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Emerging evidence shows that airway microbiota may modulate local immune responses, thereby contributing to the susceptibility and severity of acute respiratory infections (ARIs). However, there are little data on the longitudinal relationships between airway microbiota and susceptibility to ARIs in children. OBJECTIVE We aimed to investigate the association of early nasal microbiota and the subsequent risk of ARIs during the first years of life. METHODS In this prospective population-based birth-cohort study in Finland, we followed 839 healthy infants for ARIs from birth to age 24 months. Nasal microbiota was tested using 16S rRNA gene sequencing at age 2 months. We applied an unsupervised clustering approach to identify early nasal microbiota profiles, and examined the association of profiles with the rate of ARIs during age 2-24 months. RESULTS We identified five nasal microbiota profiles dominated by Moraxella, Streptococcus, Dolosigranulum, Staphylococcus and Corynebacteriaceae, respectively. Incidence rate of ARIs was highest in children with an early Moraxella-dominant profile and lowest in those with a Corynebacteriaceae-dominant profile (738 vs 552/100 children years; unadjusted incidence rate ratio (IRR), 1.34; 95% CI 1.16 to 1.54; p < 0.001). After adjusting for nine potential confounders, the Moraxella-dominant profile-ARI association persisted (adjusted IRR (aIRR), 1.19; 95% CI 1.04 to 1.37; p = 0.01). Similarly, the incidence rate of lower respiratory tract infections (a subset of all ARIs) was significantly higher in children with an early Moraxella-dominant profile (aIRR, 2.79; 95% CI 1.04 to 8.09; p = 0.04). CONCLUSION Moraxella-dominant nasal microbiota profile in early infancy was associated with an increased rate of ARIs during the first 2 years of life.
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Affiliation(s)
- Laura Toivonen
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA .,Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Matti Waris
- Virology Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
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26
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Tan XL, Liu HY, Long J, Jiang Z, Luo Y, Zhao X, Cai S, Zhong X, Cen Z, Su J, Zhou H. Septic patients in the intensive care unit present different nasal microbiotas. Future Microbiol 2019; 14:383-395. [PMID: 30803270 PMCID: PMC6479279 DOI: 10.2217/fmb-2018-0349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIM The primary objective of this study was to evaluate correlations among mortality, intensive care unit (ICU) length of stay and airway microbiotas in septic patients. MATERIALS & METHODS A deep-sequencing analysis of the 16S rRNA gene V4 region was performed. RESULTS The nasal microbiota in septic patients was dominated by three nasal bacterial types (Corynebacterium, Staphylococcus and Acinetobacter). The Acinetobacter type was associated with the lowest diversity and longest length of stay (median: 9 days), and the Corynebacterium type was associated with the shortest length of stay. We found that the Acinetobacter type in the >9-day group was associated with the highest mortality (33%). CONCLUSION Septic patients have three nasal microbiota types, and the nasal microbiota is related to the length of stay and mortality.
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Affiliation(s)
- Xi-Lan Tan
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, PR China.,Division of Infection Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Hai-Yue Liu
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jun Long
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Zhaofang Jiang
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Yuemei Luo
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, PR China.,State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Xin Zhao
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Shumin Cai
- Department of Intensive Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Xiaozhu Zhong
- Division of Infection Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Zhongran Cen
- Division of Intensive Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Jin Su
- Chronic Airways Diseases Laboratory, Department of Respiratory & Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Hongwei Zhou
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, PR China.,State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
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27
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Chang AB, Grimwood K. Contemporary Concise Review 2018: Bronchiectasis. Respirology 2019; 24:382-389. [PMID: 30743310 DOI: 10.1111/resp.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/27/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Anne B Chang
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,Centre for Children's Health Research, Queensland University of Technology, Brisbane, QLD, Australia.,Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia.,Department of Infectious Diseases, Gold Coast Health, Gold Coast, QLD, Australia.,Department of Paediatrics, Gold Coast Health, Gold Coast, QLD, Australia
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28
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Differences in the lower airway microbiota of infants with and without cystic fibrosis. J Cyst Fibros 2018; 18:646-652. [PMID: 30580994 DOI: 10.1016/j.jcf.2018.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/23/2018] [Accepted: 12/06/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cystic fibrosis (CF) lung disease commences in infancy, and understanding the role of the microbiota in disease pathogenesis is critical. This study examined and compared the lower airway microbiota of infants with and without CF and its relationship to airway inflammation in the first months of life. METHODS Infants newly-diagnosed with CF were recruited into a single-centre study in Melbourne, Australia from 1992 to 2001. Bronchoalveolar lavage was performed at study entry. Healthy infants undergoing bronchoscopy to investigate chronic stridor acted as controls. Quantitative microbiological culture was performed and inflammatory markers were measured contemporaneously. 16S ribosomal RNA gene analysis was performed on stored samples. RESULTS Thirteen bronchoalveolar samples from infants with CF and nine from control infants, collected at median ages of 1.8-months (25th-75th percentile 1.5 to 3.1-months) and 5-months (25th-75th percentile 2.9 to 8.2-months) respectively, provided 16S rRNA gene data. Bacterial biomass was positively associated with inflammation. Alpha diversity was reduced in infants with CF and between-group compositional differences were apparent. These differences were driven by increased Staphylococcus and decreased Fusobacterium and were most apparent in symptomatic infants with CF. CONCLUSION In CF lung disease, differences in lower airway microbial community composition and structure are established by age 6-months.
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29
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Early-Life Formation of the Microbial and Immunological Environment of the Human Airways. Cell Host Microbe 2018; 24:857-865.e4. [DOI: 10.1016/j.chom.2018.10.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/15/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
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30
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An SQ, Warris A, Turner S. Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples. Pediatr Pulmonol 2018; 53:921-928. [PMID: 29727521 DOI: 10.1002/ppul.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/30/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The study of the community of microorganisms (the microbiota) in the lower airways in children is restricted to opportunistic sampling in children undergoing elective general anaesthetic. Here we tested the hypothesis that induced sputum is a valid alternative to directly sampling the lower airways to study lower airway microbiota. METHODS Children scheduled for elective operations were recruited. Pre-operatively a sample of induced sputum was obtained. After anaesthesia was induced, a bronchial brushing and swabs of the upper respiratory tract were obtained. Bacterial community analysis was performed by amplification of the V3-V4 16S rRNA gene region. RESULTS Twenty children were recruited, mean age 10.7 years. Induced sputum samples were obtained from 12 children, bronchial brushing from 14 and nasal, mouth, and throat samples in 15, 16, and 17 children. The profile of bacterial communities was similar in the mouth, throat, and sputum samples with the nose and bronchial samples being different. Actinobacteria species dominated the nose and mouth, Fusobacteria were the dominant species in the throat and sputum while Proteobacteria species dominated in bronchial samples. Forty-one percent of detected bacteria in bronchial samples were unclassified. Bacterial communities from the mouth, throat, and induced sputum were tightly clustered and were distinct from nose and those found in bronchial communities. CONCLUSIONS Induced sputum may not be a valid surrogate for microbiome assessment of the lower airways in all individuals. Many bacteria in bronchial samples were not recognized by standard testing, suggesting that our understanding of the lower airway microbiota in children remains rudimentary.
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Affiliation(s)
- Shi-Qi An
- Division of Molecular Microbiology, University of Dundee, Belfast, UK.,Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Adilia Warris
- Department of Child Health, University of Aberdeen, Aberdeen, UK.,MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, UK
| | - Steve Turner
- Department of Child Health, University of Aberdeen, Aberdeen, UK
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