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Hong H, Wang L, Qi Y. Characteristics of the oropharyngeal microbiota among infants with pneumonia and their effects on immune response and subsequent respiratory morbidity. Eur J Pediatr 2023; 182:3649-3658. [PMID: 37261548 DOI: 10.1007/s00431-023-05037-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 04/14/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. The present study aimed to analyze the oropharyngeal microbiota of infants with pneumonia and to explore the impact of disturbances of the microbiota on disease severity and long-term respiratory morbidities. The oropharyngeal microbiome was characterized using 16S ribosomal RNA-based sequencing, while serum immune mediators were assessed using cytometric bead array, and invariant natural killer T (iNKT) cells were detected using flow cytometry in infants with pneumonia < 6 months of age. Patients were followed up to 3 years of age, and clinical and respiratory morbidity data were collected. A total of 106 infants with pneumonia were enrolled in this study. Diversity of the respiratory microbiota was inversely correlated with the severity of pneumonia and length of hospitalization. Patients who experienced wheezing during pneumonia exhibited lower percentages of total iNKT cells, CD8-positive ( +), and CD4-CD8- subsets, and higher CD4 + subsets than those without. The relative abundances of Prevotella and Veillonella species were lower in patients with severe pneumonia. The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing than in those without wheezing. The relative abundance and total counts of Bifidobacterium, Lactobacillus, and Neisseria were higher in patients who did not experience subsequent recurrent wheezing. CONCLUSIONS Diversity of the respiratory microbiota was inversely associated with pneumonia severity, and the percentage of iNKT cells was associated with wheezing during pneumonia. Several species may be associated with subsequent respiratory morbidities and warrant further investigation. WHAT IS KNOWN • Early life airway microbiota symbiosis affects the severity of respiratory infection and the risk for the development of asthma. • Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. WHAT IS NEW • The diversity of the airway microbiome was inversely associated with the severity of pneumonia and length of hospitalization. • The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing.
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Affiliation(s)
- Huihui Hong
- Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Libo Wang
- Department of Respiratory Disease, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China
| | - Yuanyuan Qi
- Department of Respiratory Disease, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China.
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2
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Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H. Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients. J Med Virol 2023; 95:e28727. [PMID: 37185870 DOI: 10.1002/jmv.28727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.
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Affiliation(s)
- Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Department of AIDS and STD Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Liu
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Gengyan Luo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ming Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Minwu Peng
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Meiqi Cai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ying Jiang
- Environment Health Department, Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Chuming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guohui Chang
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Shenzhen, China
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3
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Rambliere L, Kermorvant-Duchemin E, de Lauzanne A, Collard JM, Herindrainy P, Vray M, Garin B, Zo AZ, Rasoanaivo F, Rakotoarimanana Feno Manitra J, Raheliarivao TB, Diouf JBN, Ngo V, Lach S, Long P, Borand L, Sok T, Abdou AY, Padget M, Madec Y, Guillemot D, Delarocque-Astagneau E, Huynh BT. Excess risk of subsequent infection in hospitalized children from a community cohort study in Cambodia and Madagascar. Int J Epidemiol 2022; 51:1421-1431. [PMID: 35333344 DOI: 10.1093/ije/dyac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/09/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Children in low- and middle-income countries are particularly vulnerable in the months following an initial health event (IHE), with increased risk of mortality caused mostly by infectious diseases. Due to exposure to a wide range of environmental stressors, hospitalization in itself might increase child vulnerability at discharge. The goal of this study was to disentangle the role of hospitalization on the risk of subsequent infection. METHODS Data from a prospective, longitudinal, international, multicenter mother-and-child cohort were analysed. The main outcome assessed was the risk of subsequent infection within 3 months of initial care at hospital or primary healthcare facilities. First, risk factors for being hospitalized for the IHE (Step 1) and for having a subsequent infection (Step 2) were identified. Then, inpatients were matched with outpatients using propensity scores, considering the risk factors identified in Step 1. Finally, adjusted on the risk factors identified in Step 2, Cox regression models were performed on the matched data set to estimate the effect of hospitalization at the IHE on the risk of subsequent infection. RESULTS Among the 1312 children presenting an IHE, 210 (16%) had a subsequent infection, mainly lower-respiratory infections. Although hospitalization did not increase the risk of subsequent diarrhoea or unspecified sepsis, inpatients were 1.7 (95% Confidence Intervals [1.0-2.8]) times more likely to develop a subsequent lower-respiratory infection than comparable outpatients. CONCLUSION For the first time, our findings suggest that hospitalization might increase the risk of subsequent lower-respiratory infection adjusted on severity and symptoms at IHE. This highlights the need for robust longitudinal follow-up of at-risk children and the importance of investigating underlying mechanisms driving vulnerability to infection.
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Affiliation(s)
- Lison Rambliere
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
| | - Elsa Kermorvant-Duchemin
- Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Necker-Enfants Malades, Department of Neonatology and Université de Paris, Paris, France
| | - Agathe de Lauzanne
- Institut Pasteur du Cambodge, Epidemiology & Public Health Unit, Phnom Penh, 12201 Phnom Penh, Cambodia
| | - Jean-Marc Collard
- Institut Pasteur de Madagascar, Unité de bactériologie expérimentale, Antananarivo, Madagascar
| | - Perlinot Herindrainy
- Institut Pasteur de Madagascar, Unité d'épidémiologie et de Recherche Clinique, Antananarivo 101, Madagascar
| | - Muriel Vray
- Institut Pasteur de Dakar, Unité d'épidémiologie des Maladies Infectieuses, Dakar, Senegal
| | - Benoit Garin
- Laboratoire Hématologie-Immunologie/Secteur HLA, CHU Pointe-à-Pitre/Abymes, Pointe-à-Pitre, Guadeloupe
| | | | - Fanjalalaina Rasoanaivo
- Institut Pasteur de Madagascar, Unité d'épidémiologie et de Recherche Clinique, Antananarivo 101, Madagascar
| | | | | | | | - Véronique Ngo
- Institut Pasteur du Cambodge, Epidemiology & Public Health Unit, Phnom Penh, 12201 Phnom Penh, Cambodia
| | - Siyin Lach
- Institut Pasteur du Cambodge, Epidemiology & Public Health Unit, Phnom Penh, 12201 Phnom Penh, Cambodia
| | - Pring Long
- Institut Pasteur du Cambodge, Epidemiology & Public Health Unit, Phnom Penh, 12201 Phnom Penh, Cambodia
| | - Laurence Borand
- Institut Pasteur du Cambodge, Epidemiology & Public Health Unit, Phnom Penh, 12201 Phnom Penh, Cambodia
| | - Touch Sok
- Ministry of Health, Phnom Penh, Cambodia
| | - Armiya Youssouf Abdou
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
| | - Michael Padget
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
| | - Yoann Madec
- Institut Pasteur, Epidemiology of Emerging Disease, Paris, France
| | - Didier Guillemot
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France.,AP-HP. Paris Saclay, Public Health, Medical Information, Clinical Research, Le Kremlin-Bicêtre, France
| | - Elisabeth Delarocque-Astagneau
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France.,AP-HP. Paris Saclay, Public Health, Medical Information, Clinical Research, Le Kremlin-Bicêtre, France
| | - Bich-Tram Huynh
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-Infective Evasion and Pharmacoepidemiology Team, Montigny-le-Bretonneux, France
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4
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Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Clark JS, Woods CW, Kelly MS. Age-Related Changes in the Nasopharyngeal Microbiome Are Associated With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Symptoms Among Children, Adolescents, and Young Adults. Clin Infect Dis 2022; 75:e928-e937. [PMID: 35247047 PMCID: PMC8903463 DOI: 10.1093/cid/ciac184] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Children are less susceptible to SARS-CoV-2 infection and typically have milder illness courses than adults, but the factors underlying these age-associated differences are not well understood. The upper respiratory microbiome undergoes substantial shifts during childhood and is increasingly recognized to influence host defense against respiratory pathogens. Thus, we sought to identify upper respiratory microbiome features associated with SARS-CoV-2 infection susceptibility and illness severity. METHODS We collected clinical data and nasopharyngeal swabs from 285 children, adolescents, and young adults (<21 years) with documented SARS-CoV-2 exposure. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and evaluated for age-adjusted associations between microbiome characteristics and SARS-CoV-2 infection status and respiratory symptoms. RESULTS Nasopharyngeal microbiome composition varied with age (PERMANOVA, P < .001; R2 = 0.06) and between SARS-CoV-2-infected individuals with and without respiratory symptoms (PERMANOVA, P = .002; R2 = 0.009). SARS-CoV-2-infected participants with Corynebacterium/Dolosigranulum-dominant microbiome profiles were less likely to have respiratory symptoms than infected participants with other nasopharyngeal microbiome profiles (OR: .38; 95% CI: .18-.81). Using generalized joint attributed modeling, we identified 9 bacterial taxa associated with SARS-CoV-2 infection and 6 taxa differentially abundant among SARS-CoV-2-infected participants with respiratory symptoms; the magnitude of these associations was strongly influenced by age. CONCLUSIONS We identified interactive relationships between age and specific nasopharyngeal microbiome features that are associated with SARS-CoV-2 infection susceptibility and symptoms in children, adolescents, and young adults. Our data suggest that the upper respiratory microbiome may be a mechanism by which age influences SARS-CoV-2 susceptibility and illness severity.
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Affiliation(s)
| | | | - Jhoanna N Aquino
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Javier Rodriguez
- Children’s Clinical Research Unit, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sarah M Heston
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Debra J Lugo
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandre T Rotta
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas A Turner
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Trevor S Pfeiffer
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thaddeus C Gurley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Anthony Moody
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA,Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USAand
| | - James S Clark
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Matthew S Kelly
- Correspondence: M. S. Kelly, 2301 Erwin Road, Durham, NC 27710 USA ()
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5
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Tarquinio KM, Karsies T, Shein SL, Beardsley A, Khemani R, Schwarz A, Smith L, Flori H, Karam O, Cao Q, Haider Z, Smirnova E, Serrano MG, Buck GA, Willson DF. Airway microbiome dynamics and relationship to ventilator-associated infection in intubated pediatric patients. Pediatr Pulmonol 2022; 57:508-518. [PMID: 34811963 PMCID: PMC8809006 DOI: 10.1002/ppul.25769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/31/2021] [Accepted: 11/20/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Little is known about the airway microbiome in intubated mechanically ventilated children. We sought to characterize the airway microbiome longitudinally and in association with clinical variables and possible ventilator-associated infection (VAI). METHODS Serial tracheal aspirate samples were prospectively obtained from mechanically ventilated subjects under 3 years old from eight pediatric intensive care units in the United States from June 2017 to July 2018. Changes in the tracheal microbiome were analyzed by sequencing bacterial 16S ribosomal RNA gene relative to subject demographics, diagnoses, clinical parameters, outcomes, antibiotic treatment, and the Ventilator-Associated InfectioN (VAIN) score. RESULTS A total of 221 samples from 58 patients were processed and 197 samples met the >1000 reads criteria (89%), with an average of 43,000 reads per sample. The median number of samples per subject was 3 (interquartile range [IQR]: 2-5), with a median VAIN score of 2 (IQR: 1-3). Proteobacteria was the highest observed phyla throughout the intubation period, followed by Firmicutes and Actinobacteria. Alpha diversity was negatively associated with days of intubation (p = .032) and VAIN score (p = .016). High VAIN scores were associated with a decrease of Mycobacterium obuense, and an increase of Streptococcus peroris, Porphyromonadaceae family (unclassified species), Veillonella atypica, and several other taxa. No specific pattern of microbiome composition related to clinically diagnosed VAIs was observed. CONCLUSIONS Our data demonstrate decreasing alpha diversity with increasing VAIN score and days of intubation. No specific microbiome pattern was associated with clinically diagnosed VAI.
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Affiliation(s)
- Keiko M. Tarquinio
- Division of Pediatric Critical Care, Children’s Healthcare of Atlanta, Emory University, Atlanta, Georgia, USA
| | - Todd Karsies
- Division of Pediatric Critical Care, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Steven L. Shein
- Division of Pediatric Critical Care, Rainbow Babies and Children’s Hospital, Cleveland, Ohio, USA
| | - Andrew Beardsley
- Division of Pediatric Critical Care, Riley Hospital for Children, Indianapolis, Indiana, USA
| | - Robinder Khemani
- Division of Pediatric Critical Care, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Adam Schwarz
- Division of Pediatric Critical Care, Children’s Hospital of Orange Country, Mission Viejo, California, USA
| | - Lincoln Smith
- Division of Pediatric Critical Care, Seattle Children’s Hospital, Seattle, Washington, USA
| | - Heidi Flori
- Division of Pediatric Critical Care, CS Mott Children’s Hospital, University of Michigan, Ann Arbor, Michigan, USA
| | - Oliver Karam
- Division of Pediatric Critical Care, Children’s Hospital of Richmond at VCU, Richmond, Virginia, USA
| | - Quy Cao
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Hershey, Pennsylvania, USA
| | - Zainab Haider
- Department of Bioinformatics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Ekaterina Smirnova
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Douglas F. Willson
- Division of Pediatric Critical Care, Children’s Hospital of Richmond at VCU, Richmond, Virginia, USA
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6
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Henares D, Rocafort M, Brotons P, de Sevilla MF, Mira A, Launes C, Cabrera-Rubio R, Muñoz-Almagro C. Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease. Front Cell Infect Microbiol 2021; 11:744727. [PMID: 34712623 PMCID: PMC8546175 DOI: 10.3389/fcimb.2021.744727] [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: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Muntsa Rocafort
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
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7
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Salbutamol Transport and Deposition in the Upper and Lower Airway with Different Devices in Cats: A Computational Fluid Dynamics Approach. Animals (Basel) 2021; 11:ani11082431. [PMID: 34438888 PMCID: PMC8388725 DOI: 10.3390/ani11082431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Administration of inhaled salbutamol via metered-dose inhalers can effectively treat bronchoconstriction. Different devices are used for the delivery of this drug in cats, either in the hospital or at home, for long-term treatment. Effective drug administration may depend on the drug delivery device as well as patient cooperation. By using non-invasive computational fluid dynamics techniques, the impact of these devices on the deposition and transport of salbutamol particles in the cat airways was simulated and assessed. The results confirm a variable drug distribution depending on the device used. The percentage of particles reaching the lung was reduced when using spacers and increased when applied directly into an endotracheal tube. Abstract Pressurized metered-dose inhalers (pMDI) with or without spacers are commonly used for the treatment of feline inflammatory airway disease. During traditional airways treatments, a substantial amount of drugs are wasted upstream of their target. To study the efficiency of commonly used devices in the transport of inhaled salbutamol, different computational models based on two healthy adult client-owned cats were developed. Computed tomographic images from one cat were used to generate a three-dimensional geometry, and two masks (spherical and conical shapes) and two spacers (10 and 20 cm) completed the models. A second cat was used to generate a second model having an endotracheal tube (ETT) with and without the same spacers. Airflow, droplet spray transport, and deposition were simulated and studied using computational fluid dynamics techniques. Four regions were evaluated: device, upper airways, primary bronchi, and downstream lower airways/parenchyma (“lung”). Regardless of the model, most salbutamol is deposited in devices and/or upper airways. In general, particles reaching the lung varied between 5.8 and 25.8%. Compared with the first model, pMDI application through the ETT with or without a spacer had significantly higher percentages of particles reaching the lung (p = 0.006).
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8
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Cunha AJLA, Santos AC, Medronho RA, Barros H. Use of antibiotics during pregnancy is associated with infection in children at four years of age in Portugal. Acta Paediatr 2021; 110:1911-1915. [PMID: 33368616 DOI: 10.1111/apa.15733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022]
Abstract
AIM To assess the association between taking antibiotics in pregnancy and the occurrence of infections in children at four years of age. METHODS We studied children who participated in the follow-up of the birth cohort Generation XXI, Porto-Portugal, at the age of four years. We evaluated the associations between the use of antibiotics by the mother at any time in pregnancy with the occurrence of infections. Data were analysed using logistic regression, controlling for potential confounding variables. RESULTS We studied 7459 children (50.7% boys). The use of antibiotics at any stage of pregnancy, and not only in the third trimester, was associated with the occurrence of tonsillitis at four years, even after controlling for potential confounders (OR 1.19, 95% CI 1.03-1.38). Other infections did not show association. CONCLUSION Maternal use of antibiotics during pregnancy was associated with an increased risk of tonsillitis reported at four years of age. Antibiotics could favour the potential transmission of an unfavourable microbiome from mother to child.
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Affiliation(s)
| | | | - Roberto A. Medronho
- Faculdade de Medicina Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Henrique Barros
- Instituto de Saúde Pública Universidade do Porto Porto Portugal
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9
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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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10
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Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Woods CW, Kelly MS. Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.20.21252680. [PMID: 33791716 PMCID: PMC8010748 DOI: 10.1101/2021.03.20.21252680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Children are less susceptible to SARS-CoV-2 and typically have milder illness courses than adults. We studied the nasopharyngeal microbiomes of 274 children, adolescents, and young adults with SARS-CoV-2 exposure using 16S rRNA gene sequencing. We find that higher abundances of Corynebacterium species are associated with SARS-CoV-2 infection and SARS-CoV-2-associated respiratory symptoms, while higher abundances of Dolosigranulum pigrum are present in SARS-CoV-2-infected individuals without respiratory symptoms. We also demonstrate that the abundances of these bacteria are strongly, and independently, associated with age, suggesting that the nasopharyngeal microbiome may be a potentially modifiable mechanism by which age influences SARS-CoV-2 susceptibility and severity. SUMMARY Evaluation of nasopharyngeal microbiome profiles in children, adolescents, and young adults with a SARS-CoV-2-infected close contact identified specific bacterial species that vary in abundance with age and are associated with SARS-CoV-2 susceptibility and the presence of SARS-CoV-2-associated respiratory symptoms.
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11
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Cardiorespiratory performance capacity and airway microbiome in patients following primary repair of esophageal atresia. Pediatr Res 2021; 90:66-73. [PMID: 33159185 PMCID: PMC8370877 DOI: 10.1038/s41390-020-01222-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/04/2020] [Accepted: 10/11/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Patients following repair of an esophageal atresia (EA) or tracheoesophageal fistula (TEF) carry an increased risk of long-term cardiopulmonary malaise. The role of the airway microbiome in EA/TEF patients remains unclear. METHODS All EA/TEF patients treated between 1980 and 2010 were invited to a prospective clinical examination, spirometry, and spiroergometry. The airway microbiome was determined from deep induced sputum by 16 S rRNA gene sequencing. The results were compared to a healthy age- and sex-matched control group. RESULTS Nineteen EA/TEF patients with a mean age of 24.7 ± 7 years and 19 age- and sex-matched controls were included. EA/TEF patients showed a significantly lower muscle mass, lower maximum vital capacity (VCmax), and higher rates of restrictive ventilation disorders. Spiroergometry revealed a significantly lower relative performance capacity and lower peak VO2 in EA/TEF patients. Alpha- and beta-diversity of the airway microbiome did not differ significantly between the two groups. Linear discriminant effect size analysis revealed significantly enriched species of Prevotella_uncultured, Streptococcus_anginosus, Prevotella_7_Prevotella_enoeca, and Mogibacterium_timidum. CONCLUSION EA/TEF patients frequently suffer from restrictive ventilation disorders and impaired cardiopulmonary function associated with minor alterations of the airway microbiome. Long-term examinations of EA/TEF patients seem to be necessary in order to detect impaired cardiopulmonary function. IMPACT The key messages of the present study are a significantly decreased VCmax and exercise performance, as well as airway microbiome differences in EA/TEF patients. This study is the first to present parameters of lung function and exercise performance in combination with airway microbiome analysis with a mean follow-up of 24 years in EA/TEF patients. Prospective, long-term studies are needed to unravel possible interactions between alterations of the airway microbiome and impaired pulmonary function in EA/TEF patients.
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12
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Jia Q, Tong XM. [A review on the characteristics of microbiome and their association with diseases in preterm infants]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1240-1244. [PMID: 33172562 PMCID: PMC7666391 DOI: 10.7499/j.issn.1008-8830.2005131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
The microbiome in neonates is affected by many factors such as mode of birth and feeding pattern, and homeostasis or disorder of microbiome is associated with various neonatal diseases. Preterm infants have a gestational age of <37 weeks at birth, with immature development and different colonization of bacteria from full-term infants. The research on the characteristics of microbiome and their association with diseases in preterm infants can provide new ideas for the treatment of neonatal diseases. This article reviews the characteristics of intrauterine microbiome, dermal microbiome, oral microbiome, stomach microbiome, intestinal microbiome, and environmental microbiome and their association with common diseases in preterm infants.
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Affiliation(s)
- Qiong Jia
- Department of Pediatrics, Peking University Third Hospital, Beijing 100191, China.
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13
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Hahn A, Whiteson K, Davis TJ, Phan J, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Bean HD. Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study. Front Cell Infect Microbiol 2020; 10:174. [PMID: 32411616 PMCID: PMC7198769 DOI: 10.3389/fcimb.2020.00174] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 04/01/2020] [Indexed: 01/15/2023] Open
Abstract
The identification of 16S rDNA biomarkers from respiratory samples to describe the continuum of clinical disease states within persons having cystic fibrosis (CF) has remained elusive. We sought to combine 16S, metagenomics, and metabolomics data to describe multiple transitions between clinical disease states in 14 samples collected over a 12-month period in a single person with CF. We hypothesized that each clinical disease state would have a unique combination of bacterial genera and volatile metabolites as a potential signature that could be utilized as a biomarker of clinical disease state. Taxonomy identified by 16S sequencing corroborated clinical culture results, with the majority of the 109 PCR amplicons belonging to the bacteria grown in clinical cultures (Escherichia coli and Staphylococcus aureus). While alpha diversity measures fluctuated across disease states, no significant trends were present. Principle coordinates analysis showed that treatment samples trended toward a different community composition than baseline and exacerbation samples. This was driven by the phylum Bacteroidetes (less abundant in treatment, log2 fold difference -3.29, p = 0.015) and the genus Stenotrophomonas (more abundant in treatment, log2 fold difference 6.26, p = 0.003). Across all sputum samples, 466 distinct volatile metabolites were identified with total intensity varying across clinical disease state. Baseline and exacerbation samples were rather uniform in chemical composition and similar to one another, while treatment samples were highly variable and differed from the other two disease states. When utilizing a combination of the microbiome and metabolome data, we observed associations between samples dominated Staphylococcus and Escherichia and higher relative abundances of alcohols, while samples dominated by Achromobacter correlated with a metabolomics shift toward more oxidized volatiles. However, the microbiome and metabolome data were not tightly correlated; examining both the metagenomics and metabolomics allows for more context to examine changes across clinical disease states. In our study, combining the sputum microbiome and metabolome data revealed stability in the sputum composition through the first exacerbation and treatment episode, and into the second exacerbation. However, the second treatment ushered in a prolonged period of instability, which after three additional exacerbations and treatments culminated in a new lung microbiome and metabolome.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, United States.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, United States
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Trenton J Davis
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Joann Phan
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Emergency Medicine, Children's National Health System, Washington, DC, United States
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Heather D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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14
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15
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Chen J, Liu X, Du W, Srivastava R, Fu J, Zheng M, Zhou J, McGrath E. Pulmonary Function Testing in Pediatric Pneumonia Patients With Wheezing Younger Than 3 Years of Age. Glob Pediatr Health 2019; 6:2333794X19840357. [PMID: 31008153 PMCID: PMC6457021 DOI: 10.1177/2333794x19840357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 01/23/2019] [Accepted: 03/05/2019] [Indexed: 11/16/2022] Open
Abstract
Background. Wheezing symptoms are one of the risk factors in
young pneumonia patients that often leads to asthma development. Infant
pulmonary function test (iPFT) is potentially a useful tool to help identify and
manage these high-risk pneumonia patients. Methods. To examine
whether patients with wheezing symptoms are more likely to have poorer pulmonary
function and treatment outcomes, and also to explore the clinical benefit of
iPFT in young pneumonia patients, we conducted a retrospective analysis of 1005
pneumonia inpatients <3 years of age who had undergone iPFT testing in 2016
at Liuzhou Maternity and Child Healthcare Hospital in Guang-Xi, China.
Results. We identified from the hospital database 505
pneumonia patients who presented with wheezing and 500 without wheezing.
Univariate analysis showed that wheezing symptoms, viral infection, age <1
year, female gender, and prematurity were significantly associated with poorer
iPFT results. After adjusting for confounders, patients with wheezing showed
significantly poorer pulmonary function. Patients with wheezing had longer
length of stay (7.9 ± 3.9 days vs 6.5 ± 2.6 days; P < .001)
and lower percent with no residual clinical symptoms at discharge (58% vs 98%;
P < .001) when compared with those of non-wheezing
patients. In addition, 81% of patients with viral infection as compared with 43%
of patients with nonviral infection presented with wheezing symptoms
(P < .001). Conclusion. Wheezing
symptoms were associated with poorer iPFT measures and treatment outcomes for
pneumonia inpatients <3 years of age. Patients with wheezing had poorer
treatment outcomes. iPFT can be useful in assessing and monitoring young
patients with high risk of developing asthma or chronic lung disease later in
life.
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Affiliation(s)
- Jichang Chen
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Xin Liu
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Wei Du
- Children's Hospital of Michigan, Detroit, MI, USA.,Wayne State University, Detroit, MI, USA
| | - Ruma Srivastava
- Children's Hospital of Michigan, Detroit, MI, USA.,Wayne State University, Detroit, MI, USA
| | - Jinjian Fu
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Min Zheng
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Jin Zhou
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Eric McGrath
- Children's Hospital of Michigan, Detroit, MI, USA.,Wayne State University, Detroit, MI, USA
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16
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Hahn A, Fanous H, Jensen C, Chaney H, Sami I, Perez GF, Koumbourlis AC, Louie S, Bost JE, van den Anker JN, Freishtat RJ, Zemanick ET, Crandall KA. Changes in microbiome diversity following beta-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis. Sci Rep 2019; 9:2534. [PMID: 30796252 PMCID: PMC6385179 DOI: 10.1038/s41598-019-38984-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/04/2019] [Indexed: 01/10/2023] Open
Abstract
In persons with cystic fibrosis (CF), decreased airway microbial diversity is associated with lower lung function. Conflicting data exist on the impact of short-term antibiotics for treatment of acute pulmonary exacerbations. However, whether differences in antibiotic exposure impacts airway microbiome changes has not been studied. We hypothesized that subtherapeutic beta-lactam antibiotic exposure, determined by the pharmacokinetics and pharmacodynamics (PK/PD) after intravenous (IV) antibiotic administration, would be associated with different patterns of changes in CF airway microbial diversity. Eligible children were enrolled when well; study assessments were performed around the time of pulmonary exacerbation. Plasma drug concentrations and bacterial minimum inhibitory concentrations (MICs) were used to determine therapeutic versus subtherapeutic beta-lactam antibiotic exposure. Respiratory samples were collected from children, and extracted bacterial DNA was amplified for the V4 region of the 16S rRNA gene. Twenty children experienced 31 APEs during the study; 45% (n = 14) of antibiotic courses were deemed therapeutic. Those in the therapeutic group had more significant decreases in alpha diversity at end of treatment and post-recovery compared to baseline than those in the subtherapeutic group. Therapeutic and subtherapeutic beta-lactam use is associated with different patterns of changes in CF airway microbial diversity following antibiotic administration.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System (CNHS), 111 Michigan Ave NW, Washington DC, 20010, USA.
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA.
| | - Hani Fanous
- Division of Pulmonary and Sleep Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Caroline Jensen
- GWU School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
| | - Hollis Chaney
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Pulmonary and Sleep Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Iman Sami
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Pulmonary and Sleep Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Geovanny F Perez
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Pulmonary and Sleep Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Pulmonary and Sleep Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Stan Louie
- Department of Clinical Pharmacy, University of Southern California School of Pharmacy, 1985 Zonal Ave, Los Angeles, CA, 90089, USA
| | - James E Bost
- Division of Biostatistics and Study Methodology, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - John N van den Anker
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Clinical Pharmacology, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University (GWU) School of Medicine and Health Sciences, 2300 Eye Street NW, Washington DC, 20037, USA
- Division of Emergency Medicine, CNHS, 111 Michigan Ave NW, Washington DC, 20010, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, 13123 E. 16th Ave, Aurora, CO, 80045, USA
| | - Keith A Crandall
- Computational Biology Institute, GWU, 45085 University Drive, Ashburn, VA, 20147, USA
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17
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Bhandari V, Walsh MC. Bronchopulmonary dysplasia or chronic lung disease: an appeal to standardize nomenclature. Pediatr Res 2018; 84:589-590. [PMID: 30143779 DOI: 10.1038/s41390-018-0152-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 01/27/2023]
Abstract
Authors tend to use the nomenclature bronchopulmonary dysplasia (BPD) interchangeably with chronic lung disease (CLD). We propose that the preferred term be BPD and explain the rationale for the same in the attached commentary.
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Affiliation(s)
- Vineet Bhandari
- Section of Neonatology, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA.
| | - Michele C Walsh
- Division of Neonatology, Department of Pediatrics, University Hospitals Rainbow Babies and Children's Hospital, Case Western Reserve University, Cleveland, OH, USA
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18
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Pérez-Losada M, Authelet KJ, Hoptay CE, Kwak C, Crandall KA, Freishtat RJ. Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas. MICROBIOME 2018; 6:179. [PMID: 30286807 PMCID: PMC6172741 DOI: 10.1186/s40168-018-0564-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/25/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pediatric asthma is the most common chronic childhood disease in the USA, currently affecting ~ 7 million children. This heterogeneous syndrome is thought to encompass various disease phenotypes of clinically observable characteristics, which can be statistically identified by applying clustering approaches to patient clinical information. Extensive evidence has shown that the airway microbiome impacts both clinical heterogeneity and pathogenesis in pediatric asthma. Yet, so far, airway microbiotas have been consistently neglected in the study of asthma phenotypes. Here, we couple extensive clinical information with 16S rRNA high-throughput sequencing to characterize the microbiota of the nasal cavity in 163 children and adolescents clustered into different asthma phenotypes. RESULTS Our clustering analyses identified three statistically distinct phenotypes of pediatric asthma. Four core OTUs of the pathogenic genera Moraxella, Staphylococcus, Streptococcus, and Haemophilus were present in at least 95% of the studied nasal microbiotas. Phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) and genera (Moraxella, Corynebacterium, Dolosigranulum, and Prevotella) abundances, community composition, and structure varied significantly (0.05 < P ≤ 0.0001) across asthma phenotypes and one of the clinical variables (preterm birth). Similarly, microbial networks of co-occurrence of bacterial genera revealed different bacterial associations across asthma phenotypes. CONCLUSIONS This study shows that children and adolescents with different clinical characteristics of asthma also show different nasal bacterial profiles, which is indicative of different phenotypes of the disease. Our work also shows how clinical and microbial information could be integrated to validate and refine asthma classification systems and develop biomarkers of disease.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health,, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA 20147 USA
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052 USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Kayla J Authelet
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, 20010 USA
| | - Claire E Hoptay
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, 20010 USA
| | - Christine Kwak
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, 20010 USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health,, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA 20147 USA
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052 USA
| | - Robert J Freishtat
- Division of Emergency Medicine, Children’s National Medical Center, Washington, DC, 20010 USA
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19
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Hahn A, Burrell A, Fanous H, Chaney H, Sami I, Perez GF, Koumbourlis AC, Freishtat RJ, Crandall KA. Antibiotic multidrug resistance in the cystic fibrosis airway microbiome is associated with decreased diversity. Heliyon 2018; 4:e00795. [PMID: 30238064 PMCID: PMC6143701 DOI: 10.1016/j.heliyon.2018.e00795] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/30/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Cystic fibrosis (CF) is associated with significant morbidity and early mortality due to recurrent acute and chronic lung infections. The chronic use of multiple antibiotics increases the possibility of multidrug resistance (MDR). Antibiotic susceptibility determined by culture-based techniques may not fully represent the resistance profile. The study objective was to detect additional antibiotic resistance using molecular methods and relate the presence of MDR to airway microbiome diversity and pulmonary function. Methods Bacterial DNA was extracted from sputum samples and amplified for the V4 region of the 16S rRNA gene. An qPCR array was used to detect antibiotic resistance genes. Clinical culture results and pulmonary function were also noted for each encounter. Results Six study participants contributed samples from 19 encounters. Those samples with MDR (n = 7) had significantly lower diversity measured by inverse Simpson's index than those without (n = 12) (2.193 ± 0.427 vs 6.023 ± 1.564, p = 0.035). Differential abundance showed that samples with MDR had more Streptococcus (p = 0.002) and Alcaligenaceae_unclassified (p = 0.002). Pulmonary function was also decreased when MDR was present (FEV1, 51 ± 22.9 vs 77 ± 26.7, p = 0.054; FVC, 64.5 ± 22.7 vs 91.6 ± 27.7, p = 0.047). Conclusions The presence of MDR within the CF airway microbiome was associated with decreased microbial diversity, the presence of Alcaligenes, and decreased pulmonary function.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, USA.,Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Aszia Burrell
- Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA
| | - Hani Fanous
- Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Hollis Chaney
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Geovanny F Perez
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA
| | - Robert J Freishtat
- Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Emergency Medicine, Children's National Health System, Washington, DC, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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