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Objectives We compared age-stratified SARS-CoV-2 symptomatology of wild-type/Alpha vs Omicron BA.1/BA.2 variant infected individuals and the impact of COVID-19 booster vaccination on Omicron symptom burden. Methods Data from three European prospective household cohorts were used (April 2020 to April 2021 and January to March 2022). Standardized outbreak protocols included (repeated) polymerase chain reaction testing, paired serology, and daily symptom scoring for all household members. Comparative analyses were performed on 346 secondary household cases from both periods. Results Children P≤0.01). In adults, Omicron disease duration and severity were reduced (P≤ 0.095). Omicron was associated with lower odds for loss of smell or taste (adjusted odds ratio [aOR]: 0.14; 95% CI 0.03-0.50) and higher but non-significant odds for upper respiratory symptoms, fever, and fatigue (aORs: 1.85-2.23). No differences were observed in disease severity or duration between primary vs booster series vaccinated adults (P≥0.12). Conclusion The Omicron variant causes higher symptom burden in children compared with wild-type/Alpha and lower in adults, possibly due to previous vaccination. A shift in symptoms occurred with reduction in loss of smell/taste for Omicron. No additional effect of booster vaccination on Omicron symptom burden was observed.

Invasive group A streptococcal (iGAS) disease cases increased in the first half of 2022 in the Netherlands, with a remarkably high proportion of emm4 isolates. Whole-genome sequence analysis of 66 emm4 isolates, 40 isolates from the pre-coronavirus disease 2019 (COVID-19) pandemic period 2009-2019 and 26 contemporary isolates from 2022, identified a novel Streptococcus pyogenes lineage (M4NL22), which accounted for 85 % of emm4 iGAS cases in 2022. Surprisingly, we detected few isolates of the emm4 hypervirulent clone, which has replaced nearly all other emm4 in the USA and the UK. M4NL22 displayed genetic differences compared to other emm4 strains, although these were of unclear biological significance. In publicly available data, we identified a single Norwegian isolate belonging to M4NL22, which was sampled after the isolates from this study, possibly suggesting export of M4NL22 to Norway. In conclusion, our study identified a novel S. pyogenes emm4 lineage underlying an increase of iGAS disease in early 2022 in the Netherlands and the results have been promptly communicated to public health officials.

Early-life microbiota seeding and subsequent development is crucial to future health. Cesarean-section (CS) birth, as opposed to vaginal delivery, affects early mother-to-infant transmission of microbes. Here, we assess mother-to-infant microbiota seeding and early-life microbiota development across six maternal and four infant niches over the first 30 days of life in 120 mother-infant pairs. Across all infants, we estimate that on average 58.5% of the infant microbiota composition can be attributed to any of the maternal source communities. All maternal source communities seed multiple infant niches. We identify shared and niche-specific host/environmental factors shaping the infant microbiota. In CS-born infants, we report reduced seeding of infant fecal microbiota by maternal fecal microbes, whereas colonization with breastmilk microbiota is increased when compared with vaginally born infants. Therefore, our data suggest auxiliary routes of mother-to-infant microbial seeding, which may compensate for one another, ensuring that essential microbes/microbial functions are transferred irrespective of disrupted transmission routes.

Pneumococcal conjugate vaccines reduce pneumococcal colonization via serotype-specific immunoglobulin G (IgG) at mucosal surfaces. The infant immunization schedule with the ten-valent pneumococcal conjugate vaccine (PCV10) changed from a 3 + 1 schedule (2-3-4-11 months) to a 2 + 1 schedule (2-4-11 months) in The Netherlands in 2013. We compared anti-pneumococcal IgG concentrations in saliva between the schedules. IgG was measured using a fluorescent bead-based multiplex immunoassay at the ages of 6 (post-primary) and 12 (post-booster) months in 51 infants receiving the 3 + 1 schedule and 68 infants receiving the 2 + 1 schedule. Post-primary IgG geometric mean concentrations (GMCs) were comparable between schedules for all vaccine serotypes. Post-booster IgG GMCs were significantly lower after the 2 + 1 schedule for serotypes 4 (p = 0.035), 7F (p = 0.048) and 23F (p = 0.0056). This study shows small differences in mucosal IgG responses between a 3 + 1 and a 2 + 1 PCV10 schedule. Future studies should establish correlates of protection against pneumococcal colonization for mucosal antibodies.

ImportanceIn the early COVID-19 pandemic, SARS-CoV-2 testing was only accessible and recommended for symptomatic persons or adults. This restriction hampered assessment of the true incidence of SARS-CoV-2 infection in children as well as detailed characterization of the SARS-CoV-2 disease spectrum and how this spectrum compared with that of other common respiratory illnesses.ObjectiveTo estimate the community incidence of SARS-CoV-2 infection in children and parents and to assess the symptoms and symptom severity of respiratory illness episodes involving SARS-CoV-2–positive test results relative to those with SARS-CoV-2–negative test results.Design, Setting, and ParticipantsThis cohort study randomly selected Dutch households with at least 1 child younger than 18 years. A total of 1209 children and adults from 307 households were prospectively followed up between August 25, 2020, and July 29, 2021, covering the second and third waves of the COVID-19 pandemic. Participation included SARS-CoV-2 screening at 4- to 6-week intervals during the first 23 weeks of participation (core study period; August 25, 2020, to July 29, 2021). Participants in all households finishing the core study before July 1, 2021, were invited to participate in the extended follow-up and to actively report respiratory symptoms using an interactive app until July 1, 2021. At new onset of respiratory symptoms or a SARS-CoV-2 positive test result, a household outbreak study was initiated, which included daily symptom recording, repeated polymerase chain reaction testing (nose-throat swabs and saliva and fecal samples), and SARS-CoV-2 antibody measurement (paired dried blood spots) in all household members. Outbreaks, households, and episodes of respiratory illness were described as positive or negative depending on SARS-CoV-2 test results. Data on participant race and ethnicity were not reported because they were not uniformly collected in the original cohorts and were therefore not representative or informative.ExposuresSARS-CoV-2–positive and SARS-CoV-2–negative respiratory illness episodes.Main Outcomes and MeasuresAge-stratified incidence rates, symptoms, and symptom severity for SARS-CoV-2–positive and SARS-CoV-2–negative respiratory illness episodes.ResultsAmong 307 households including 1209 participants (638 female [52.8%]; 403 [33.3%] aged P Conclusions and RelevanceIn this cohort study, during the first pandemic year when mostly partial or full in-person learning occurred, the SARS-CoV-2 incidence rate in children was substantially higher than estimated from routine testing or seroprevalence data and was similar to that of adult household members. Unlike in unvaccinated adults, SARS-CoV-2 symptoms and symptom severity in children were similar to other common respiratory illnesses. These findings may prove useful when developing pediatric COVID-19 vaccine recommendations.

Background Respiratory syncytial virus (RSV) is a major cause of hospitalization in infants. Early detection of RSV can optimize clinical management and minimize use of antibiotics. BinaxNOW RSV (BN) is a rapid antigen detection test that is widely used. We aimed to validate the sensitivity of BN in hospitalized and nonhospitalized infants against the gold standard of molecular diagnosis. Methods We evaluated the performance of BN in infants with acute respiratory tract infections with different degrees of disease severity. Diagnostic accuracy of BN test results were compared with molecular diagnosis as reference standard. Results One hundred sixty-two respiratory samples from 148 children from October 2017 to February 2019 were studied. Sixty-six (40.7%) samples tested positive for RSV (30 hospitalizations, 31 medically attended episodes not requiring hospitalization, and 5 nonmedically attended episodes). Five of these samples tested positive with BN, leading to an overall sensitivity of BN of 7.6% (95% confidence interval [CI], 3.3%–16.5%) and a specificity of 100% (95% CI, 96.2%–100%). Sensitivity was low in all subgroups. Conclusions We found a low sensitivity of BN for point-of-care detection of RSV infection. BinaxNOW RSV should be used and interpreted with caution.

Pneumococcal conjugate vaccines reduce pneumococcal colonization via serotype-specific immunoglobulin G (IgG) at mucosal surfaces. The infant immunization schedule with the ten-valent pneumococcal conjugate vaccine (PCV10) changed from a 3+1 schedule (2-3-4-11 months) to a 2+1 schedule (2-4-11 months) in The Netherlands in 2013. We compared anti-pneumococcal IgG concentrations in saliva between the schedules. IgG was measured using a fluorescent bead-based multiplex immunoassay, at the ages of 6 (post-primary) and 12 (post-booster) months in 51 infants receiving the 3+1 schedule and 68 infants receiving the 2+1 schedule. Post-primary IgG geometric mean concentrations (GMCs) were comparable between schedules for all vaccine serotypes. Post-booster IgG GMCs were significantly lower after the 2+1 schedule for serotypes 4 (p=0.035), 7F (p=0.048) and 23F (p=0.0056). This study shows small differences in mucosal IgG responses between a 3+1 and a 2+1 PCV10 schedule. Future studies should establish correlates of protection against pneumococcal colonization for mucosal antibodies.Key words: PCV10; mucosal immunity; immunoglobulin G; infant; vaccination schedule.

BackgroundRespiratory syncytial virus (RSV) causes significant morbidity and mortality in infants worldwide. Although prematurity and cardiopulmonary disease are risk factors for severe disease, the majority of infants hospitalized with RSV are previously healthy. Various vaccines and therapeutics are under development and expected to be available in the near future. To inform the use of these new vaccines and therapeutics, it is necessary to determine the burden of RSV disease in Europe. We will prospectively follow-up a birth cohort to obtain incidence data on RSV acute respiratory tract infection (ARTI).MethodsMulticenter prospective study of a birth cohort consisting of 10 000 healthy infants, recruited during 3 consecutive years. RSV associated hospitalization in the first year of life will be determined by questionnaires and hospital chart reviews. A nested cohort of 1000 infants will be actively followed. In case of ARTI, a respiratory sample will be collected for RSV molecular diagnosis.ResultsThe primary outcome is the incidence rate of RSV-associated hospitalization in the first year of life. In the active cohort the primary outcome is RSV associated ARTI and MA-ARTI.ConclusionsWe will provide key information to fill the gaps in knowledge about the burden of RSV disease in healthy infants.Clinical Trials RegistrationNCT03627572.

The original version of this Article contained an error in the number of unique bacterial taxa identified by whole genome shotgun sequencing, which was incorrectly given as 137 instead of 119. This has been corrected in both the PDF and HTML versions of the Article.

BACKGROUND: In the Netherlands, preterm infants receive the immunisations at the same chronological age as recommended for term infants without correction for gestational age (GA). The aim of this paper was to describe the timeliness of the routine Dutch national immunisation schedule in preterm infants in their first year of life and to evaluate possible determinants of delay. METHODS: Preterm infants were prospectively recruited between October 2015 and October 2017 and stratified according to GA (

BACKGROUND: Perinatal asphyxia and resulting hypoxic-ischemic encephalopathy is a major cause of death and long-term disability in term born neonates. Up to 20,000 infants each year are affected by HIE in Europe and even more in regions with lower level of perinatal care. The only established therapy to improve outcome in these infants is therapeutic hypothermia. Allopurinol is a xanthine oxidase inhibitor that reduces the production of oxygen radicals as superoxide, which contributes to secondary energy failure and apoptosis in neurons and glial cells after reperfusion of hypoxic brain tissue and may further improve outcome if administered in addition to therapeutic hypothermia. METHODS: This study on the effects of ALlopurinol in addition to hypothermia treatment for hypoxic-ischemic Brain Injury on Neurocognitive Outcome (ALBINO), is a European double-blinded randomized placebo-controlled parallel group multicenter trial (Phase III) to evaluate the effect of postnatal allopurinol administered in addition to standard of care (including therapeutic hypothermia if indicated) on the incidence of death and severe neurodevelopmental impairment at 24 months of age in newborns with perinatal hypoxic-ischemic insult and signs of potentially evolving encephalopathy. Allopurinol or placebo will be given in addition to therapeutic hypothermia (where indicated) to infants with a gestational age ≥ 36 weeks and a birth weight ≥ 2500 g, with severe perinatal asphyxia and potentially evolving encephalopathy. The primary endpoint of this study will be death or severe neurodevelopmental impairment versus survival without severe neurodevelopmental impairment at the age of two years. Effects on brain injury by magnetic resonance imaging and cerebral ultrasound, electric brain activity, concentrations of peroxidation products and S100B, will also be studied along with effects on heart function and pharmacokinetics of allopurinol after iv-infusion. DISCUSSION: This trial will provide data to assess the efficacy and safety of early postnatal allopurinol in term infants with evolving hypoxic-ischemic encephalopathy. If proven efficacious and safe, allopurinol could become part of a neuroprotective pharmacological treatment strategy in addition to therapeutic hypothermia in children with perinatal asphyxia. TRIAL REGISTRATION: NCT03162653, www.ClinicalTrials.gov , May 22, 2017. ispartof: BMC PEDIATRICS vol:19 issue:1 ispartof: location:England status: published

Consortia for the ALBINO Study Group: Axel R. Franz, Mario Rüdiger, Christian F. Poets, Manon Benders, Frank van Bel, Karel Allegaert, Gunnar Naulaers, Dirk Bassler, Katrin Klebermaß-Schrehof, Maximo Vento, Hercilia Guimarães, Tom Stiris, Luigi Cattarossi, Marjo Metsäranta, Sampsa Vanhatalo, Jan Mazela, Tuuli Metsvaht, Cees van Veldhuizen, Corinna Engel, Christian A. Maiwald, Gabriele von Oldershausen, Iris Bergmann, Monika Weiss, Caroline J. B. R. Wichera, Andreas Eichhorn, Michael Raubuch, Birgit Schuler, Cees K. W. van Veldhuizen, Bas Laméris, Yannique Jacobs, Roselinda van der Vlught-Meijer, Elke Griesmaier, Johannes Brandner, Marie Tackoen, Ruth Reibel, Chantal Lecart, Luc Cornette, Genevieve Malfilatre, Renaud Viellevoye, Tuuli Metsvaht, Mari-Liis Ilmoja, Pille Saik, Ruth Käär, Pille Andresson, Marjo Metsaranta, Axel R. Franz, Rolf Schloesser, Torsten Ott, Stefan Winkler, Thomas Hoehn, Norbert Teig, Michael Schroth, Ulrich H. Thome, Harald Ehrhardt, Luigi Cattarossi, Isabella Mauro, Eugenio Baraldi, Virgilio Carnielli, Giuseppe Paterlini, Marcello Napolitano, Paola Francesca Faldini, Gianluca Lista, Gianluca Visintin, Mario Barbarini, Laura Pagani, Emmanuele Mastretta, Giovanni Vento, Monica Fumagalli, Marco Binotti, Mirjam M. van Weissenbruch, Henrica L. M. van Straaten, Manon J. N. L. Benders, Kim V. Annink, Frank van Bel, Jeroen Dudink, Jan B. Derks, Inge P. de Boer, Clemens B. Meijssen, Timo R. de Haan, Linda G. van Rooij, Jacqueline L. van Hillegersberg, Minouche van Dongen, Jos Bruinenberg, Koen P. Dijkman, Marlies A. van Houten, Sophie R. D. van der Schoor, Tom Stiris, Bodil Salvesen, Moritz Schneider, Eirik Nestaas, Britt Nakstad, Jan Mazela, Lukas Karpinski, Ewa Gulczynska, Barbara Królak-Olejnik, Renata Bokiniec, Ana I. Vilan, Liliana Flores de Pinho, Claudia Ferraz, Almerinda Pereira, Rosalina Barroso, André Mendes da Graça, Teresa Tomé, Filomena Pinto, Maximo Vento, Juan Martínez Rodilla, Simón Lubián, Marta Campubri Camprubí, José Antonio Hurtado Suazo, Eva Valverde, José Ramón Fernández Lorenzo, José Martinez Orgado, Héctor Boix, Francisco Jimenez Parrilla, Maria Teresa Moral-Pumarega, Julia Maletzki, Claudia Knoepfli, Cornelia Hagmann, Sven Schulzke, Martin Stocker, André Birkenmaier, Thomas Riedel, Hans-Jörg Ehni, Annie Janvier & Georg Marckmann., [Background]: Perinatal asphyxia and resulting hypoxic-ischemic encephalopathy is a major cause of death and long-term disability in term born neonates. Up to 20,000 infants each year are affected by HIE in Europe and even more in regions with lower level of perinatal care. The only established therapy to improve outcome in these infants is therapeutic hypothermia. Allopurinol is a xanthine oxidase inhibitor that reduces the production of oxygen radicals as superoxide, which contributes to secondary energy failure and apoptosis in neurons and glial cells after reperfusion of hypoxic brain tissue and may further improve outcome if administered in addition to therapeutic hypothermia., [Methods]: This study on the effects of ALlopurinol in addition to hypothermia treatment for hypoxic-ischemic Brain Injury on Neurocognitive Outcome (ALBINO), is a European double-blinded randomized placebo-controlled parallel group multicenter trial (Phase III) to evaluate the effect of postnatal allopurinol administered in addition to standard of care (including therapeutic hypothermia if indicated) on the incidence of death and severe neurodevelopmental impairment at 24 months of age in newborns with perinatal hypoxic-ischemic insult and signs of potentially evolving encephalopathy. Allopurinol or placebo will be given in addition to therapeutic hypothermia (where indicated) to infants with a gestational age ≥ 36 weeks and a birth weight ≥ 2500 g, with severe perinatal asphyxia and potentially evolving encephalopathy. The primary endpoint of this study will be death or severe neurodevelopmental impairment versus survival without severe neurodevelopmental impairment at the age of two years. Effects on brain injury by magnetic resonance imaging and cerebral ultrasound, electric brain activity, concentrations of peroxidation products and S100B, will also be studied along with effects on heart function and pharmacokinetics of allopurinol after iv-infusion., [Discussion]: This trial will provide data to assess the efficacy and safety of early postnatal allopurinol in term infants with evolving hypoxic-ischemic encephalopathy. If proven efficacious and safe, allopurinol could become part of a neuroprotective pharmacological treatment strategy in addition to therapeutic hypothermia in children with perinatal asphyxia., [Trial registration]: NCT03162653, www.ClinicalTrials.gov, May 22, 2017., This study is funded under the Horizon 2020 Framework Program of the European Union, call H2020-PHC-2015-two-stage, grant 667224. Publication of this manuscript was supported by Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of the University of Tuebingen.

Rationale: Perinatal and postnatal influences are presumed important drivers of the early-life respiratory microbiota composition. We hypothesized that the respiratory microbiota composition and development in infancy is affecting microbiota stability and thereby resistance against respiratory tract infections (RTIs) over time. Objectives: To investigate common environmental drivers, including birth mode, feeding type, antibiotic exposure, and crowding conditions, in relation to respiratory tract microbiota maturation and stability, and consecutive risk of RTIs over the first year of life. Methods: In a prospectively followed cohort of 112 infants, we characterized the nasopharyngeal microbiota longitudinally from birth on (11 consecutive sample moments and the maximum three RTI samples per subject; in total, n = 1,121 samples) by 16S-rRNA gene amplicon sequencing. Measurements and Main Results: Using a microbiota-based machine-learning algorithm, we found that children experiencing a higher number of RTIs in the first year of life already demonstrate an aberrant microbial developmental trajectory from the first month of life on as compared with the reference group (0-2 RTIs/yr). The altered microbiota maturation process coincided with decreased microbial community stability, prolonged reduction of Corynebacterium and Dolosigranulum, enrichment of Moraxella very early in life, followed by later enrichment of Neisseria and Prevotella spp. Independent drivers of these aberrant developmental trajectories of respiratory microbiota members were mode of delivery, infant feeding, crowding, and recent antibiotic use. Conclusions: Our results suggest that environmental drivers impact microbiota development and, consequently, resistance against development of RTIs. This supports the idea that microbiota form the mediator between early-life environmental risk factors for and susceptibility to RTIs over the first year of life.

Background Respiratory syncytial virus (RSV) causes a substantial burden in older adults. Viral load in RSV-infected adults is generally lower compared to young children, which could result in suboptimal sensitivity of RSV diagnostics. Although the Xpert® Xpress Flu/RSV assay has been used in routine clinical care, its sensitivity to diagnose RSV infection in older adults is largely unknown. We aimed to compare the performance of the Xpert® Xpress Flu/RSV assay with real-time reverse-transcription polymerase chain reaction (RT-PCR) in home-dwelling older adults (≥60 years of age). Methods Nasopharyngeal swabs were tested with Xpert® Xpress Flu/RSV and compared to RSV RT-PCR in older adults with acute respiratory tract infections with different levels of disease severity. Results We studied 758 respiratory samples from 561 older adults from 2 consecutive RSV seasons. Thirty-five (4.6%) samples tested positive for RSV by at least 1 of the assays, of which 2 samples were negative by Xpert® Xpress Flu/RSV and 3 samples by real-time RT-PCR. The positive percentage agreement (PPA) was 90.9% (95% confidence interval [CI], 76.4%–96.8%) and negative percentage agreement was 99.7% (95% CI, 99.0%–99.9%). Viral loads were low (≤103 copies/mL or cycle threshold value ≥34) in all cases with discordant results for the 2 assays. Conclusions The PPA of Xpert® Xpress Flu/RSV compared to routine RT-PCR is high for RSV detection in home-dwelling older adults. The assay is fast and easy to use at the point of care. Clinical Trials Registration NCT03621930.

Respiratory tract infections remain a leading cause of childhood morbidity and mortality worldwide. In this thesis, we have demonstrated that in childhood AOMT the nasopharyngeal microbiota considerably resembles and predicts the middle ear microbiota. We found evidence suggesting that the nasopharyngeal microbiota not only seeds the middle ear with bacteria including potential pathogens that might have initiated inflammation and infection, but also seem to determine recovery to health. Moreover, in children with LRTIs, the microbiota of the nasopharynx are strong biomarkers in case of lung disease. We identified specific viruses and bacterial taxa that were strongly associated with infection, and on the other hand consistently found a consortium of bacteria that were associated with health. Combining these viral and bacterial findings with data on the host, made it possible to classify health from disease with an unprecedented accuracy. Surprisingly, the microbial differences associated with childhood LRTI were disease phenotype-independent: we therefore postulate that treatment with targeted antibiotics should be based on predicted disease severity rather that clinical presentation per se. Furthermore, prophylaxis against the most common severe viral infection in infancy, RSV, was associated with persistent effects on the respiratory microbiota composition in early childhood that in turn was associated with reversible airway obstruction at age six suggesting the complexity of early life microbiota interventions. Finally, we show that early life loss of upper respiratory tract microbial topography, which among others seems determined by absence of certain keystone commensals, is associated with higher susceptibility to RTIs. This loss of topography was further driven by the influx of oral taxa in the nasopharynx. These data suggest that the infant respiratory microbiota play a pivotal role in maintaining the equilibrium that determines childhood respiratory health and disease. Humans are born in a microbial cloud and growing up as a child, simultaneously shaping your own personal microbiome, can be regarded an incredible ecological event. During our explorations, we discovered that the nasopharyngeal microbial community forms the boundary between the environment and the respiratory tract including ears and lungs, and that it has major promise for future diagnosis, treatment and prevention of childhood respiratory tract infections.

Respiratory tract infections (RTIs), such as pneumonia, are responsible for a large burden of disease, with the highest incidence and mortality in young children and elderly adults. Yearly, approximately 900,000 children die because of pneumonia globally, making up for ~15% of all deaths in children under the age of 5 years worldwide. Respiratory tract infections are also a major reason for (inappropriate) antibiotic prescriptions, which further underscores the relevance of RTIs. These infections have long been considered in isolation and viewed within the Koch’s one-host one-pathogen paradigm. However, the human body is colonized by vast numbers of specialised bacterial communities, conjointly referred to as the bacterial microbiome. The advent of next-generation sequencing techniques enabled us to characterise the entirety of the microbial community (microbiota) and its functional capacity (microbiome). Among others, the microbiome appears involved in steering immune development, setting an individual on a trajectory towards or away from disease. In addition, diverse resident bacterial communities provide us with ‘colonization resistance’, therewith protecting the human host from incoming or blooming pathogens. In this thesis, we study the role of the (upper) respiratory tract microbiota in health and in respiratory disease. In chapter 3, we characterise the healthy respiratory tract microbiota development in a cohort of healthy, unselected children over the first year of life. We demonstrate that microbiota changes within the first month of life are associated with long term susceptibility to respiratory infections. In chapter 4 and chapter 5 we study dynamics of nasal carriage of Streptococcus pneumoniae, in the context of the live-attenuated influenza vaccine. S. pneumoniae is a commensal with pathogenic potential, being able to cause severe lower RTIs, including pneumonia. Using an experimental human challenge model, we found that vaccination prior to pneumococcal inoculation increases pneumococcal carriage rate and density. Furthermore we found that the nasal microbiota present before pneumococcal challenge/vaccination determined pneumococcal receptiveness. We identified a new host phenotype of low-dense pneumococcal carriers, who seem to be able to control pneumococcal carriage well, resulting in the least microbial perturbations over time. In chapter 7 we studied the oropharyngeal microbiota in pneumonia and healthy adults and elderly, showing that particularly the absence of a group of harmless commensals is associated with pneumonia, more than the presence of pathogens. In chapter 8 we characterise the nasopharyngeal microbiota and host immune response in healthy children and children with a mild or severe infection with respiratory syncytial virus (RSV). Our data suggested that interactions between RSV and nasopharyngeal microbiota might modulate the host immune response, potentially impacting disease severity. Combined, these studies demonstrated the likely role of respiratory microbial communities in carriage of pathogens and susceptibility to RTIs. Furthermore, we also found differences in microbial communities during RTI that might drive inflammation and thereby severity of disease. Further studies are needed to further unravel cause-effect relationships in more detail, however we believe the studies presented in this thesis underline the importance of the respiratory tract microbiota as gatekeeper to respiratory health.