EDITORIALS 7. Kerem E, Konstan MW, De Boeck K, Accurso FJ, Sermet-Gaudelus I, Wilschanski M, Elborn JS, Melotti P, Bronsveld I, Fajac I, et al.; Cystic Fibrosis Ataluren Study Group. Ataluren for the treatment of nonsense-mutation cystic fibrosis: a randomised, double-blind, placebo-controlled phase 3 trial. Lancet Respir Med 2014;2:539–547.
8. Mutyam V, Du M, Xue X, Keeling KM, White EL, Bostwick JR, Rasmussen L, Liu B, Mazur M, Hong JS, et al. Discovery of clinically approved agents that promote suppression of cystic fibrosis transmembrane conductance regulator nonsense mutations. Am J Respir Crit Care Med 2016;194:1092–1103.
Copyright © 2016 by the American Thoracic Society
Respiratory Syncytial Virus Bronchiolitis: Enter the Microbiome Most of the recent advances in the treatment of severe respiratory syncytial virus (RSV) bronchiolitis are related to reversing well-intended misadventures. Treatment of RSV bronchiolitis has included systemic corticosteroids, bronchodilators, nebulized hypertonic saline, antibiotics, anticholinergic agents, and oxygen. Reexamination of these strategies has shortened the list of recommended treatments to the provision of oxygen and respiratory support (1). Given that palivizumab is priced prohibitively high for general use and that an RSV vaccine remains a medical challenge, new insights into pathogenesis that can guide new modes of treatment are needed. Enter the microbiome. In this issue of the Journal, the study by de Steenhuijsen Piters and colleagues (pp. 1104–1115) was designed to test the hypothesis that the severity of RSV infection is influenced by modulation of the host immune response by the airway microbiome (2). The rationale for this study is that RSV causes bronchiolitis in only a subset of infected infants, and that known risk factors have poor predictive value for term infants. This suggests that other factors such as airway bacteria modify airway inflammation and the severity of illness during RSV infection. To test this hypothesis, the research team obtained nasal mucus samples from children with mild versus more severe RSV illnesses and used 16S ribosomal sequencing to characterize the microbiome. Analysis of bacterial genomics revealed five major bacterial communities characterized by their dominant organisms, and RSV infection and RSV hospitalization were positively associated with abundance of Haemophilus influenzae and Streptococcus and negatively associated with abundance of Staphylococcus aureus. In parallel, transcriptomic profiles of whole blood obtained during the illness revealed that RSV infection induced the expression of IFNrelated genes, whereas colonization with microbial communities dominated by H. influenzae or Streptococcus induced the expression of proinflammatory pathways including Toll-like receptors and neutrophil and macrophage activation. Thus, the RSV illness was related to microbial communities dominated by known bacterial pathogens, which in turn augmented systemic inflammatory responses. The authors concluded that these interactions between RSV and nasopharyngeal microbiota could contribute to the severity of clinical illness. This study builds on previous studies that have linked bronchiolitis and wheezing illnesses in early childhood to colonization with bacterial pathogens or the detection of microbial communities that are dominated by potential pathogens (3, 4). Previous studies suggest a sequence effect, in which the viral infection promotes proliferation of pathogens (5) and transient states of less diverse microbiomes dominated by pathogens (3). 1044
There may also be direct interactions between RSV and Streptococcus pneumoniae (6). The study by de Steenhuijsen Piters and colleagues adds new information about the interactions between RSV and the microbiome, and the transcriptomic analysis indicates that the systemic immune responses to viruses and bacteria are distinct and additive. The authors acknowledge that the study has limitations, including differences in the ages of cases and control subjects and the cross-sectional study design that precludes conclusions related to causality. Was the microbiome abnormal in the children destined for hospitalization even before the RSV infection? Furthermore, in this cross-sectional observational study, it cannot be determined whether the bacteria contributed to illness severity. This seems likely, however, given the observed inflammatory response associated with either Streptococcus or Haemophilus, and the growing evidence that these same bacterial communities contribute to severity of disease and airway dysfunction during other viral infections and even in other airway diseases such as asthma or chronic obstructive pulmonary disease (7, 8). Future studies would also benefit from the inclusion of children who are infected with RSV and yet develop little or no illness; what are the microbial or bacterial factors that are associated with resilience? Findings from the current study and others suggest a model in which viral infections and the airway microbiome both contribute to the pathogenesis of airway symptoms (Figure 1). Infections with Preexisting microbiome RSV infection Virus-altered microbiome: Dominated by pathogens? No
Yes
Limited virus-induced inflammation and cell destruction
More extensive virus- and bacteria-induced inflammation and cell destruction
Mediators of resilience
Mediators of airway obstruction
Asymptomatic infection or mild illness
Moderate or severe illness
Figure 1. Interactions among respiratory syncytial virus (RSV), the airway microbiome, and the severity of illness.
American Journal of Respiratory and Critical Care Medicine Volume 194 Number 9 | November 1 2016
EDITORIALS RSV or other airway viruses can destabilize the airway microbiome to enable proliferation of pathogens. The combination of RSV infection and a pathogen-dominated microbiome increases the inflammatory response, accentuates damage to the airways, and results in airway obstruction and greater illness severity. It seems likely that the preexisting microbiome could also influence the severity of RSV infection and downstream events (4). This model of bacterial–viral interactions also raises additional questions. What bacterial or host factors promote stability versus instability of the microbiome during RSV infection? Early-life environmental exposure such as living on a dairy farm reduces the risk of early-life viral illnesses, likely through a mechanism involving alterations to the microbiome (9). Is there a role for vitamin D, breastfeeding, mode of delivery, and perhaps the family dog in preventing more severe RSV infection (10, 11)? In addition, how does the microbiome affect the airway response to RSV infection? Patterns of colonization are associated with distinct patterns of cytokines and chemokines in nasal fluid (12). Importantly, what mediators bridge the gap between observed changes in inflammation and airway obstruction, and are they of bacterial or host origin? Finally, will new information about the microbiome in RSV bronchiolitis inform new treatment strategies? Is there a role for antibiotics in the treatment of bronchiolitis? Despite recent studies showing some efficacy of azithromycin in the treatment of preschool wheeze (13, 14), previous studies of RSV do not support this approach (15). If bacteria are contributing to bronchiolitis, perhaps their effects start early in the course of the illness so that the window of opportunity has elapsed once lower-airway symptoms are present. In this case, treatment centering on antibacterial strategies would need to focus on prevention. Preventive intervention studies targeting the microbiome could focus on establishing a “healthy microbiome” in early life that prevents colonization with pathogenic bacteria through immunization or perhaps interrupts bacteria-induced inflammatory responses or downstream mediators that contribute to airway pathology. If the microbiome does contribute to RSV bronchiolitis, as implied by the study by de Steenhuijsen Piters and colleagues, there is a range of new therapeutic possibilities to be explored. n Author disclosures are available with the text of this article at www.atsjournals.org. James E. Gern, M.D. School of Medicine and Public Health University of Wisconsin-Madison Madison, Wisconsin
ORCID ID: 0000-0002-6667-4708 (J.E.G.).
References 1. Ralston SL, Lieberthal AS, Meissner HC, Alverson BK, Baley JE, Gadomski AM, Johnson DW, Light MJ, Maraqa NF, Mendonca EA, et al.; American Academy of Pediatrics. Clinical practice guideline: the diagnosis, management, and prevention of bronchiolitis. Pediatrics 2014;134:e1474–e1502.
Editorials
2. de Steenhuijsen Piters WAA, Heinonen S, Hasrat R, Bunsow E, Smith B, Suarez-Arrabal M-C, Chaussabel D, Cohen DM, Sanders EAM, Ramilo O, et al. Nasopharyngeal microbiota, host transcriptome, and disease severity in children with respiratory syncytial virus infection. Am J Respir Crit Care Med 2016;194:1104–1115. 3. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, Holt BJ, Hales BJ, Walker ML, Hollams E, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe 2015;17:704–715. 4. Vissing NH, Chawes BL, Bisgaard H. Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. Am J Respir Crit Care Med 2013;188:1246–1252. 5. Kloepfer KM, Lee WM, Pappas TE, Kang TJ, Vrtis RF, Evans MD, Gangnon RE, Bochkov YA, Jackson DJ, Lemanske RF, Jr, et al. Detection of pathogenic bacteria during rhinovirus infection is associated with increased respiratory symptoms and asthma exacerbations. J Allergy Clin Immunol 2014;133:1301–1307, e1–e3. 6. Smith CM, Sandrini S, Datta S, Freestone P, Shafeeq S, Radhakrishnan P, Williams G, Glenn SM, Kuipers OP, Hirst RA, et al. Respiratory syncytial virus increases the virulence of Streptococcus pneumoniae by binding to penicillin binding protein 1a: a new paradigm in respiratory infection. Am J Respir Crit Care Med 2014; 190:196–207. 7. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, et al. Disordered microbial communities in asthmatic airways. PLoS One 2010;5:e8578. 8. Molyneaux PL, Mallia P, Cox MJ, Footitt J, Willis-Owen SA, Homola D, Trujillo-Torralbo MB, Elkin S, Kon OM, Cookson WO, et al. Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2013;188:1224–1231. 9. Loss GJ, Depner M, Hose AJ, Genuneit J, Karvonen AM, Hyvarinen ¨ A, Roduit C, Kabesch M, Lauener R, Pfefferle PI, et al.; PASTURE (Protection against Allergy Study in Rural Environments) Study Group. The early development of wheeze: environmental determinants and genetic susceptibility at 17q21. Am J Respir Crit Care Med 2016;193: 889–897. 10. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, et al. Man’s best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol 2010;126:410–412. 11. Shilts MH, Rosas-Salazar C, Tovchigrechko A, Larkin EK, Torralba M, Akopov A, Halpin R, Peebles RS, Moore ML, Anderson LJ, et al. Minimally invasive sampling method identifies differences in taxonomic richness of nasal microbiomes in young infants associated with mode of delivery. Microb Ecol 2016;71:233–242. 12. Vissing NH, Larsen JM, Rasmussen MA, Chawes BL, Thysen AH, Bønnelykke K, Brix S, Bisgaard H. Susceptibility to lower respiratory infections in childhood is associated with perturbation of the cytokine response to pathogenic airway bacteria. Pediatr Infect Dis J 2016;35:561–566. 13. Stokholm J, Chawes BL, Vissing NH, Bjarnad ottir ´ E, Pedersen TM, Vinding RK, Schoos AM, Wolsk HM, Thorsteinsd ottir ´ S, Hallas HW, et al. Azithromycin for episodes with asthma-like symptoms in young children aged 1-3 years: a randomised, double-blind, placebo-controlled trial. Lancet Respir Med 2016; 4:19–26. 14. Bacharier LB, Guilbert TW, Mauger DT, Boehmer S, Beigelman A, Fitzpatrick AM, Jackson DJ, Baxi SN, Benson M, Burnham CA, et al.; National Heart, Lung, and Blood Institute’s AsthmaNet. Early administration of azithromycin and prevention of severe lower respiratory tract illnesses in preschool children with a history of such illnesses: a randomized clinical trial. JAMA 2015;314: 2034–2044. 15. Farley R, Spurling GK, Eriksson L, Del Mar CB. Antibiotics for bronchiolitis in children under two years of age. Cochrane Database Syst Rev 2014;10:CD005189.
Copyright © 2016 by the American Thoracic Society
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8. Mutyam V, Du M, Xue X, Keeling KM, White EL, Bostwick JR, Rasmussen L, Liu B, Mazur M, Hong JS, et al. Discovery of clinically approved agents that promote suppression of cystic fibrosis transmembrane conductance regulator nonsense mutations. Am J Respir Crit Care Med 2016;194:1092–1103.
Copyright © 2016 by the American Thoracic Society
Respiratory Syncytial Virus Bronchiolitis: Enter the Microbiome Most of the recent advances in the treatment of severe respiratory syncytial virus (RSV) bronchiolitis are related to reversing well-intended misadventures. Treatment of RSV bronchiolitis has included systemic corticosteroids, bronchodilators, nebulized hypertonic saline, antibiotics, anticholinergic agents, and oxygen. Reexamination of these strategies has shortened the list of recommended treatments to the provision of oxygen and respiratory support (1). Given that palivizumab is priced prohibitively high for general use and that an RSV vaccine remains a medical challenge, new insights into pathogenesis that can guide new modes of treatment are needed. Enter the microbiome. In this issue of the Journal, the study by de Steenhuijsen Piters and colleagues (pp. 1104–1115) was designed to test the hypothesis that the severity of RSV infection is influenced by modulation of the host immune response by the airway microbiome (2). The rationale for this study is that RSV causes bronchiolitis in only a subset of infected infants, and that known risk factors have poor predictive value for term infants. This suggests that other factors such as airway bacteria modify airway inflammation and the severity of illness during RSV infection. To test this hypothesis, the research team obtained nasal mucus samples from children with mild versus more severe RSV illnesses and used 16S ribosomal sequencing to characterize the microbiome. Analysis of bacterial genomics revealed five major bacterial communities characterized by their dominant organisms, and RSV infection and RSV hospitalization were positively associated with abundance of Haemophilus influenzae and Streptococcus and negatively associated with abundance of Staphylococcus aureus. In parallel, transcriptomic profiles of whole blood obtained during the illness revealed that RSV infection induced the expression of IFNrelated genes, whereas colonization with microbial communities dominated by H. influenzae or Streptococcus induced the expression of proinflammatory pathways including Toll-like receptors and neutrophil and macrophage activation. Thus, the RSV illness was related to microbial communities dominated by known bacterial pathogens, which in turn augmented systemic inflammatory responses. The authors concluded that these interactions between RSV and nasopharyngeal microbiota could contribute to the severity of clinical illness. This study builds on previous studies that have linked bronchiolitis and wheezing illnesses in early childhood to colonization with bacterial pathogens or the detection of microbial communities that are dominated by potential pathogens (3, 4). Previous studies suggest a sequence effect, in which the viral infection promotes proliferation of pathogens (5) and transient states of less diverse microbiomes dominated by pathogens (3). 1044
There may also be direct interactions between RSV and Streptococcus pneumoniae (6). The study by de Steenhuijsen Piters and colleagues adds new information about the interactions between RSV and the microbiome, and the transcriptomic analysis indicates that the systemic immune responses to viruses and bacteria are distinct and additive. The authors acknowledge that the study has limitations, including differences in the ages of cases and control subjects and the cross-sectional study design that precludes conclusions related to causality. Was the microbiome abnormal in the children destined for hospitalization even before the RSV infection? Furthermore, in this cross-sectional observational study, it cannot be determined whether the bacteria contributed to illness severity. This seems likely, however, given the observed inflammatory response associated with either Streptococcus or Haemophilus, and the growing evidence that these same bacterial communities contribute to severity of disease and airway dysfunction during other viral infections and even in other airway diseases such as asthma or chronic obstructive pulmonary disease (7, 8). Future studies would also benefit from the inclusion of children who are infected with RSV and yet develop little or no illness; what are the microbial or bacterial factors that are associated with resilience? Findings from the current study and others suggest a model in which viral infections and the airway microbiome both contribute to the pathogenesis of airway symptoms (Figure 1). Infections with Preexisting microbiome RSV infection Virus-altered microbiome: Dominated by pathogens? No
Yes
Limited virus-induced inflammation and cell destruction
More extensive virus- and bacteria-induced inflammation and cell destruction
Mediators of resilience
Mediators of airway obstruction
Asymptomatic infection or mild illness
Moderate or severe illness
Figure 1. Interactions among respiratory syncytial virus (RSV), the airway microbiome, and the severity of illness.
American Journal of Respiratory and Critical Care Medicine Volume 194 Number 9 | November 1 2016
EDITORIALS RSV or other airway viruses can destabilize the airway microbiome to enable proliferation of pathogens. The combination of RSV infection and a pathogen-dominated microbiome increases the inflammatory response, accentuates damage to the airways, and results in airway obstruction and greater illness severity. It seems likely that the preexisting microbiome could also influence the severity of RSV infection and downstream events (4). This model of bacterial–viral interactions also raises additional questions. What bacterial or host factors promote stability versus instability of the microbiome during RSV infection? Early-life environmental exposure such as living on a dairy farm reduces the risk of early-life viral illnesses, likely through a mechanism involving alterations to the microbiome (9). Is there a role for vitamin D, breastfeeding, mode of delivery, and perhaps the family dog in preventing more severe RSV infection (10, 11)? In addition, how does the microbiome affect the airway response to RSV infection? Patterns of colonization are associated with distinct patterns of cytokines and chemokines in nasal fluid (12). Importantly, what mediators bridge the gap between observed changes in inflammation and airway obstruction, and are they of bacterial or host origin? Finally, will new information about the microbiome in RSV bronchiolitis inform new treatment strategies? Is there a role for antibiotics in the treatment of bronchiolitis? Despite recent studies showing some efficacy of azithromycin in the treatment of preschool wheeze (13, 14), previous studies of RSV do not support this approach (15). If bacteria are contributing to bronchiolitis, perhaps their effects start early in the course of the illness so that the window of opportunity has elapsed once lower-airway symptoms are present. In this case, treatment centering on antibacterial strategies would need to focus on prevention. Preventive intervention studies targeting the microbiome could focus on establishing a “healthy microbiome” in early life that prevents colonization with pathogenic bacteria through immunization or perhaps interrupts bacteria-induced inflammatory responses or downstream mediators that contribute to airway pathology. If the microbiome does contribute to RSV bronchiolitis, as implied by the study by de Steenhuijsen Piters and colleagues, there is a range of new therapeutic possibilities to be explored. n Author disclosures are available with the text of this article at www.atsjournals.org. James E. Gern, M.D. School of Medicine and Public Health University of Wisconsin-Madison Madison, Wisconsin
ORCID ID: 0000-0002-6667-4708 (J.E.G.).
References 1. Ralston SL, Lieberthal AS, Meissner HC, Alverson BK, Baley JE, Gadomski AM, Johnson DW, Light MJ, Maraqa NF, Mendonca EA, et al.; American Academy of Pediatrics. Clinical practice guideline: the diagnosis, management, and prevention of bronchiolitis. Pediatrics 2014;134:e1474–e1502.
Editorials
2. de Steenhuijsen Piters WAA, Heinonen S, Hasrat R, Bunsow E, Smith B, Suarez-Arrabal M-C, Chaussabel D, Cohen DM, Sanders EAM, Ramilo O, et al. Nasopharyngeal microbiota, host transcriptome, and disease severity in children with respiratory syncytial virus infection. Am J Respir Crit Care Med 2016;194:1104–1115. 3. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, Holt BJ, Hales BJ, Walker ML, Hollams E, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe 2015;17:704–715. 4. Vissing NH, Chawes BL, Bisgaard H. Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. Am J Respir Crit Care Med 2013;188:1246–1252. 5. Kloepfer KM, Lee WM, Pappas TE, Kang TJ, Vrtis RF, Evans MD, Gangnon RE, Bochkov YA, Jackson DJ, Lemanske RF, Jr, et al. Detection of pathogenic bacteria during rhinovirus infection is associated with increased respiratory symptoms and asthma exacerbations. J Allergy Clin Immunol 2014;133:1301–1307, e1–e3. 6. Smith CM, Sandrini S, Datta S, Freestone P, Shafeeq S, Radhakrishnan P, Williams G, Glenn SM, Kuipers OP, Hirst RA, et al. Respiratory syncytial virus increases the virulence of Streptococcus pneumoniae by binding to penicillin binding protein 1a: a new paradigm in respiratory infection. Am J Respir Crit Care Med 2014; 190:196–207. 7. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, et al. Disordered microbial communities in asthmatic airways. PLoS One 2010;5:e8578. 8. Molyneaux PL, Mallia P, Cox MJ, Footitt J, Willis-Owen SA, Homola D, Trujillo-Torralbo MB, Elkin S, Kon OM, Cookson WO, et al. Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2013;188:1224–1231. 9. Loss GJ, Depner M, Hose AJ, Genuneit J, Karvonen AM, Hyvarinen ¨ A, Roduit C, Kabesch M, Lauener R, Pfefferle PI, et al.; PASTURE (Protection against Allergy Study in Rural Environments) Study Group. The early development of wheeze: environmental determinants and genetic susceptibility at 17q21. Am J Respir Crit Care Med 2016;193: 889–897. 10. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, et al. Man’s best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol 2010;126:410–412. 11. Shilts MH, Rosas-Salazar C, Tovchigrechko A, Larkin EK, Torralba M, Akopov A, Halpin R, Peebles RS, Moore ML, Anderson LJ, et al. Minimally invasive sampling method identifies differences in taxonomic richness of nasal microbiomes in young infants associated with mode of delivery. Microb Ecol 2016;71:233–242. 12. Vissing NH, Larsen JM, Rasmussen MA, Chawes BL, Thysen AH, Bønnelykke K, Brix S, Bisgaard H. Susceptibility to lower respiratory infections in childhood is associated with perturbation of the cytokine response to pathogenic airway bacteria. Pediatr Infect Dis J 2016;35:561–566. 13. Stokholm J, Chawes BL, Vissing NH, Bjarnad ottir ´ E, Pedersen TM, Vinding RK, Schoos AM, Wolsk HM, Thorsteinsd ottir ´ S, Hallas HW, et al. Azithromycin for episodes with asthma-like symptoms in young children aged 1-3 years: a randomised, double-blind, placebo-controlled trial. Lancet Respir Med 2016; 4:19–26. 14. Bacharier LB, Guilbert TW, Mauger DT, Boehmer S, Beigelman A, Fitzpatrick AM, Jackson DJ, Baxi SN, Benson M, Burnham CA, et al.; National Heart, Lung, and Blood Institute’s AsthmaNet. Early administration of azithromycin and prevention of severe lower respiratory tract illnesses in preschool children with a history of such illnesses: a randomized clinical trial. JAMA 2015;314: 2034–2044. 15. Farley R, Spurling GK, Eriksson L, Del Mar CB. Antibiotics for bronchiolitis in children under two years of age. Cochrane Database Syst Rev 2014;10:CD005189.
Copyright © 2016 by the American Thoracic Society
1045
