Upper respiratory tract microbial communities, acute otitis media pathogens, and antibiotic use in healthy and sick children

The Nasopharyngeal and Gut Microbiota in Children in a Pediatric Otolaryngology Practice

BACKGROUND

The human microbiome evolves rapidly in early life with contributions from various factors such as diet, delivery mode, medical history, antibiotics exposure, genetics, immunomodulators and the environment. A high use of antibiotics in pediatric outpatient settings has been well documented, and improvement in antibiotic selection is required to reduce the risks of antibiotic resistance and disruption of the microbiome.

METHODS

We performed an exploratory study using 16S rRNA gene-based sequencing to characterize the gut and nasopharyngeal microbiome of children (n = 50) age 1-6 years of age in a pediatric otolaryngology practice.

RESULTS

Relative abundance of Haemophilus and Moraxella were higher in nasopharyngeal swabs, while Prevotella, Bacteroides, Porphyromonas and Faecalibacterium were highly abundant in rectal swabs. The gut microbiome composition in children <2 years old was different compared with children ≥2 years age. Gut bacterial diversity increased with an increase in age of the children. Children taking probiotics had a notable increase in abundance of potentially beneficial gut bacteria such as Bacteroides and Akkermansia. The nasopharyngeal microbiome differed between children who received antibiotics in the 3 months before sample collection compared with those that did not. Haemophilus spp. was highly abundant in children who received antibiotics 3 months before sampling.

CONCLUSIONS

The pediatric nasopharyngeal and rectal microbiomes differ in bacterial composition and diversity. The increased abundance of Haemophilus spp. in the nasopharyngeal microbiome of children who received antibiotics during the 3 months before sampling suggests a potential impact of antibiotics in colonization with the otopathogen and may be relevant to clinical practice.

Respiratory Bacterial Microbiota in Cattle: From Development to Modulation to Enhance Respiratory Health

The respiratory tract of cattle is colonized by complex bacterial ecosystems also known as bacterial microbiotas. These microbiotas evolve over time and are shaped by numerous factors, including maternal vaginal microbiota, environment, age, diet, parenteral antimicrobials, and stressful events. The resulting microbiota can be diverse and enriched with known beneficial bacteria that can provide colonization resistance against bacterial pathogens or, on the contrary, with opportunistic pathogens that can predispose cattle to respiratory disease. The respiratory microbiota can be modulated by nonantimicrobial approaches to promote health, creating new potential strategies for prevention and treatment of bovine respiratory disease.

The Ability of Respiratory Commensal Bacteria to Beneficially Modulate the Lung Innate Immune Response Is a Strain Dependent Characteristic

We investigated whether the ability of commensal respiratory bacteria to modulate the innate immune response against bacterial and viral pathogens was a shared or strain-specific characteristic. Bacterial strains belonging to the Corynebacterium pseudodiphtheriticum and Dolosigranulum pigrum species were compared by studying their influence in the Toll-like receptor (TLR)-2- and TLR3-triggered immune responses in the respiratory tract, as well as in the resistance to Respiratory Syncytial Virus (RSV) and Streptococcus pneumoniae infections. We demonstrated that nasally administered C. pseudodiphteriticum 090104 or D. pigrum 040417 were able to modulate respiratory immunity and increase the resistance against pathogens, while other strains of the same species did not influence the respiratory immune responses, demonstrating a clear strain-dependent immunomodulatory effect of respiratory commensal bacteria. We also reported here that bacterium-like particles (BLP) and cell walls derived from immunomodulatory respiratory commensal bacteria are an interesting alternative for the modulation of the respiratory immune system. Our study is a step forward in the positioning of certain strains of respiratory commensal bacteria as next-generation probiotics for the respiratory tract.

Season of Birth Impacts the Neonatal Nasopharyngeal Microbiota

Objective: Pathogenic airway bacteria colonizing the neonatal airway increase the risk of childhood asthma, but little is known about the determinants of the establishment and dynamics of the airway microbiota in early life. We studied associations between perinatal risk factors and bacterial richness of the commensal milieu in the neonatal respiratory tract. Methods: Three hundred and twenty-eight children from the Copenhagen Prospective Studies on Asthma in the Childhood2000 (COPSAC2000) at-risk birth cohort were included in this study. The bacterial richness in each of the nasopharynxes of the 1-month old, asymptomatic neonates was analyzed by use of a culture-independent technique (T-RFLP). Information on perinatal risk factors included predisposition to asthma, allergy and eczema; social status of family; maternal exposures during pregnancy; mode of delivery; and postnatal exposures. The risk factor analysis was done by conventional statistics and partial least square discriminant analysis (PLSDA). Results: The nasopharyngeal bacterial community at 1-month displayed an average of 35 (IQR: 14-55, range 1-161) phylogenetically different bacteria groups. Season of birth was associated with nasopharyngeal bacterial richness at 1-month of age with a higher bacterial richness (p = 0.003) and more abundant specific bacterial profiles representing Gram-negative alpha-proteobacteria and Gram-positive Bacilli in the nasopharynx of summer-born children. Conclusion: Early postnatal bacterial colonization of the upper airways is significantly affected by birth season, emphasizing a future focus on the seasonality aspect in modelling the impact of early dynamic changes in airway bacterial communities in relation to later disease development.

Sputum microbiome profiling in COPD: beyond singular pathogen detection

Culture-independent microbial sequencing techniques have revealed that the respiratory tract harbours a complex microbiome not detectable by conventional culturing methods. The contribution of the microbiome to chronic obstructive pulmonary disease (COPD) pathobiology and the potential for microbiome-based clinical biomarkers in COPD are still in the early phases of investigation. Sputum is an easily obtainable sample and has provided a wealth of information on COPD pathobiology, and thus has been a preferred sample type for microbiome studies. Although the sputum microbiome likely reflects the respiratory microbiome only in part, there is increasing evidence that microbial community structure and diversity are associated with disease severity and clinical outcomes, both in stable COPD and during the exacerbations. Current evidence has been limited to mainly cross-sectional studies using 16S rRNA gene sequencing, attempting to answer the question 'who is there?' Longitudinal studies using standardised protocols are needed to answer outstanding questions including differences between sputum sampling techniques. Further, with advancing technologies, microbiome studies are shifting beyond the examination of the 16S rRNA gene, to include whole metagenome and metatranscriptome sequencing, as well as metabolome characterisation. Despite being technically more challenging, whole-genome profiling and metabolomics can address the questions 'what can they do?' and 'what are they doing?' This review provides an overview of the basic principles of high-throughput microbiome sequencing techniques, current literature on sputum microbiome profiling in COPD, and a discussion of the associated limitations and future perspectives.

Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures

OBJECTIVE

To perform a comprehensive review of otitis media microbiome literature published between 1^st July 2015 and 30th June 2019.

DATA SOURCES

PubMed database, National Library of Medicine.

REVIEW METHODS

Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.

CONCLUSIONS

Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.

IMPLICATIONS FOR PRACTICE

Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.

Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis

Alloiococcus otitidis and Turicella otitidis are common bacteria of the human ear. They have frequently been isolated from the middle ear of children with otitis media (OM), though their potential role in this disease remains unclear and confounded due to their presence as commensal inhabitants of the external auditory canal. In this review, we summarize the current literature on these organisms with an emphasis on their role in OM. Much of the literature focuses on the presence and abundance of these organisms, and little work has been done to explore their activity in the middle ear. We find there is currently insufficient evidence available to determine whether these organisms are pathogens, commensals or contribute indirectly to the pathogenesis of OM. However, building on the knowledge currently available, we suggest future approaches aimed at providing stronger evidence to determine whether A. otitidis and T. otitidis are involved in the pathogenesis of OM. Such evidence will increase our understanding of the microbial risk factors contributing to OM and may lead to novel treatment approaches for severe and recurrent disease.

Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens

The relationship between antibiotic stewardship and population levels of antibiotic resistance remains unclear. In order to better understand shifts in selective pressure due to stewardship, we use publicly available data to estimate the effect of changes in prescribing on exposures to frequently used antibiotics experienced by potentially pathogenic bacteria that are asymptomatically colonizing the microbiome. We quantify this impact under four hypothetical stewardship strategies. In one scenario, we estimate that elimination of all unnecessary outpatient antibiotic use could avert 6% to 48% (IQR: 17% to 31%) of exposures across pairwise combinations of sixteen common antibiotics and nine bacterial pathogens. All scenarios demonstrate that stewardship interventions, facilitated by changes in clinician behavior and improved diagnostics, have the opportunity to broadly reduce antibiotic exposures across a range of potential pathogens. Concurrent approaches, such as vaccines aiming to reduce infection incidence, are needed to further decrease exposures occurring in ‘necessary’ contexts.

Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production

The composition of the human microbiome profoundly impacts human well-being. However, the mechanisms underlying microbiome maturation are poorly understood. The nasal microbiome is of particular importance as a source of many respiratory infections. Here, we performed a large sequencing and culture-based analysis of the human nasal microbiota from different age groups. We observed a significant decline of pathogenic bacteria before adulthood, with an increase of the commensal Staphylococcus epidermidis. In seniors, this effect was partially reversed. In vitro, many S. epidermidis isolates stimulated nasal epithelia to produce antimicrobial peptides, killing pathogenic competitors, while S. epidermidis itself proved highly resistant owing to its exceptional capacity to form biofilms. Furthermore, S. epidermidis isolates with high antimicrobial peptide-inducing and biofilm-forming capacities outcompeted pathogenic bacteria during nasal colonization in vivo. Our study identifies a pivotal role of S. epidermidis in healthy maturation of the nasal microbiome, which is achieved at least in part by symbiotic cooperation with innate host defense.

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling

The microbiota primes immune defences but the identity of specific commensal microorganisms that protect against infection is unclear. Conversely, how pathogens compete with the microbiota to establish their host niche is also poorly understood. In the present study, we investigate the antagonism between the microbiota and Klebsiella pneumoniae during colonization and transmission. We discover that maturation of the microbiota drives the development of distinct immune defence programmes in the upper airways and intestine to limit K. pneumoniae colonization within these niches. Immune protection in the intestine depends on the development of Bacteroidetes, interleukin (IL)-36 signalling and macrophages. This effect of Bacteroidetes requires the polysaccharide utilization locus of their conserved commensal colonization factor. Conversely, in the upper airways, Proteobacteria prime immunity through IL-17A, but K. pneumoniae overcomes these defences through encapsulation to effectively colonize this site. Ultimately, we find that host-to-host spread of K. pneumoniae occurs principally from its intestinal reservoir, and that commensal-colonization-factor-producing Bacteroidetes are sufficient to prevent transmission between hosts through IL-36. Thus, our study provides mechanistic insight into when, where and how commensal Bacteroidetes protect against K. pneumoniae colonization and contagion, providing insight into how these protective microorganisms could be harnessed to confer population-level protection against K. pneumoniae infection.

Recent Perspectives on Gene-Microbe Interactions Determining Predisposition to Otitis Media

A comprehensive understanding about the pathogenesis of otitis media (OM), one of the most common pediatric diseases, has the potential to alleviate a substantial disease burden across the globe. Advancements in genetic and bioinformatic detection methods, as well as a growing interest in the microbiome, has enhanced the capability of researchers to investigate the interplay between host genes, host microbiome, invading bacteria, and resulting OM susceptibility. Early studies deciphering the role of genetics in OM susceptibility assessed the heritability of the phenotype in twin and triplet studies, followed by linkage studies, candidate gene approaches, and genome-wide association studies that have helped in the identification of specific loci. With the advancements in techniques, various chromosomal regions and genes such as FBXO11, TGIF1, FUT2, FNDC1, and others have been implicated in predisposition to OM, yet questions still remain as to whether these implicated genes truly play a causative role in OM and to what extent. Meanwhile, 16S ribosomal RNA (rRNA) sequencing, microbial quantitative trait loci (mbQTL), and microbial genome-wide association studies (mGWAS) have mapped the microbiome of upper airways sites and therefore helped in enabling a more detailed study of interactions between host polymorphisms and host microbiome composition. Variants of specific genes conferring increased OM susceptibility, such as A2ML1, have also been shown to influence the microbial composition of the outer and middle ear in patients with OM, suggesting their role as mediators of disease. These interactions appear to impact the colonization of known otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), as well as Neisseria, Gemella, Porphyromonas, Alloprevotella, and Fusobacterium populations that have also been implicated in OM pathogenesis. Meanwhile, studies demonstrating an increased abundance of Dolosigranulum and Corynebacterium in healthy patients compared to those with OM suggest a protective role for these bacteria, thereby introducing potential avenues for future probiotic treatment. Incorporating insights from these genetic, microbiome, and host-pathogen studies will allow for a more robust, comprehensive understanding of OM pathogenesis that can ultimately facilitate in the development of exciting new treatment modalities.

Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children With Acute Otitis Media

Acute otitis media (AOM) is the most common pediatric infection for which antibiotics are prescribed in the United States. The role of the respiratory tract microbiome in pathogenesis and immune modulation of AOM remains unexplored. We sought to compare the nasopharyngeal (NP) microbiome of children 1 to 3 weeks prior to onset of AOM vs. at onset of AOM, and the NP microbiome with the microbiome in middle ear (ME). Six children age 6 to 24 months old were studied. Nasal washes (NW) were collected at healthy visits 1 to 3 weeks prior to AOM and at onset of AOM. The middle ear fluids (MEF) were collected by tympanocentesis at onset of AOM. Samples were stored in Trizol reagents or phosphate-buffered saline (PBS) at -80°C until use. The microbiome was characterized by 16S rRNA gene sequencing. Taxonomic designations and relative abundance of bacteria were determined using the RDP classifier tool through QIIME. Cumulative sum scaling normalization was applied before determining bacterial diversity and abundance. Shannon diversity index was calculated in Microsoft excel. The relative abundance of each bacteria species was compared via Mann-Whitney U test. We found that the NW microbiome of children during healthy state or at baseline was more diverse than microbiome during AOM. At AOM, no significant difference in microbiome diversity was found between NW and MEF, although some bacteria species appear to differ in MEF than in NW. The microbiome of samples stored in PBS had significant greater diversity than samples stored in Trizol reagent.

The bacteriome of otitis media with effusion: Does it originate from the adenoid?

OBJECTIVE

The aim of this study was to evaluate the composition and the diversity of bacteriome in middle ear effusion (MEE) and adenoid specimens of pediatric patients having otitis media with effusion (OME).

MATERIALS AND METHODS

Sample collection from children with OME followed by next generation sequencing. Seventeen adenoid and 43 middle ear effusion specimens from 25 children having OME were evaluated. Microbiome analysis was performed via Ion 16S rRNA metagenomics kit.

RESULTS

Twenty-two different bacterial species were identified from all of the samples analyzed. There were variations in the prevalence and relative abundance of the bacteriome observed between adenoid and MEE samples. MEE microbiome was significantly dominated by Alloicoccus otitis (44%), Turicella otitidis (6%), and Staphylococcus auricularis (3%). Whereas, Rothia mucilaginosa (39%), R. dentocariosa (11%), S. aureus (5%), Veillonella rogosae (2%), Granulicatella elegans (2%), Granulicatella adiacens (2%), Eikenella corrodens (1%), and Prevotella nanceiensis (1%) had significantly higher relative abundance in adenoid samples. Overall, there was no statistically significant difference in alpha diversity of MEE and adenoid samples, whereas adenoid samples constituted a cluster in the beta diversity graph.

CONCLUSION

Bacteriome of MEE is mostly dominated by A. otitis yet accompanied by other bacteria with lower relative abundances suggests that OME is likely to be a polymicrobial process. Despite similarities, significant differences in relative abundances of several predominant species between bacteriome in the MEE and adenoid put the theory that OME in children is originated from the adenoids under question.

Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies

The microbiota of the upper respiratory tract (URT) protects the host from bacterial pathogenic colonization by competing for adherence to epithelial cells and by immune response regulation that includes the activation of antimicrobial and (anti-)inflammatory components. However, environmental or host factors can modify the microbiota to an unstable community that predisposes the host to infection or inflammation. One of the URT diseases most often encountered in children is otitis media (OM). The role of pathogenic bacteria like Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in the pathogenesis of OM is well documented. Results from next-generation-sequencing (NGS) studies reveal other bacterial taxa involved in OM, such as Turicella and Alloiococcus Such studies can also identify bacterial taxa that are potentially protective against URT infections, whose beneficial action needs to be substantiated in relevant experimental models and clinical trials. Of note, lactic acid bacteria (LAB) are members of the URT microbiota and associated with a URT ecosystem that is deemed healthy, based on NGS and some experimental and clinical studies. These observations have formed the basis of this review, in which we describe the current knowledge of the molecular and clinical potential of LAB in the URT, which is currently underexplored in microbiome and probiotic research.

Temporal association of the development of oropharyngeal microbiota with early life wheeze in a population-based birth cohort

BACKGROUND

A critical window in infancy has been proposed, during which the microbiota may affect subsequent health. The longitudinal development of the oropharyngeal microbiota is under-studied and may be associated with early-life wheeze. We aimed to investigate the temporal association of the development of the oropharyngeal microbiota with early-life wheeze.

METHODS

A population-based birth cohort based in London, UK was followed for 24 months. We collected oropharyngeal swabs at six time-points. Microbiota was determined using sequencing of the V3-V5 region of the 16S rRNA-encoding gene. Medical records were reviewed for the outcome of doctor diagnosed wheeze. We used a time-varying model to investigate the temporal association between the development of microbiota and doctor-diagnosed wheeze.

FINDINGS

159 participants completed the study to 24 months and for 98 there was complete sequencing data at all timepoints and outcome data. Of these, 26 had doctor-diagnosed wheeze. We observed significant increase in the abundance of Neisseria between 9 and 24 months in children who developed wheeze (p = 0∙003), while in those without wheezing there was a significant increment in the abundance of Granulicatella (p = 0∙012) between 9 and 12 months, and of Prevotella (p = 0∙018) after 18 months.

INTERPRETATION

A temporal association between the respiratory commensal Granulicatella and also Prevotella with wheeze (negative), and between Neisseria and wheeze (positive) was identified in infants prior to one year of age. This adds to evidence for the proposed role of the microbiota in the development of wheeze. FUND: Research funding from the Winnicott Foundation, Meningitis Now and Micropathology Ltd.

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine

Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.

Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota

BACKGROUND

Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bovine microbiome is largely unknown. Therefore, we determined the longitudinal impact of two commonly administered veterinary antibiotics, oxytetracycline and tulathromycin, on the fecal and nasopharyngeal (NP) microbiota of beef cattle that were transported to a feedlot. We also report the effect these antibiotics have on several antibiotic resistance determinants in both the fecal and NP microbiome.

RESULTS

Oxytetracycline and tulathromycin perturbation of the bovine fecal and NP microbiota was greatest at days 2 and 5. Although the NP microbiota of the tulathromycin-treated cattle had recovered by day 12, the NP microbiota of the oxytetracycline-treated group remained altered through day 34. Overall, the NP microbiota appeared to be more sensitive to antibiotic treatment than the fecal microbiota. Members of the bacterial Microbacteriaceae family were most notably affected by antibiotic administration in the NP microbiota. Both antibiotics protected against Pasteurella spp. in the nasopharynx at days 2 and 5. Despite very similar diets at both locations, the largest shift in the fecal and NP microbiota occurred after transport to the feedlot (P < 0.05). Antibiotic resistance determinants in the NP microbiome were also affected more strongly by antibiotic treatment than those in the fecal microbiome. Oxytetracycline increased the proportion of erm(X), sul2, tet(H), tet(M), and tet(W) in NP samples and tet(M) and tet(W) in fecal samples, at day 12 (P < 0.05). The effect of tulathromycin on the relative abundance of resistance genes in the NP microbiome was greatest at day 34 as erm(X), sul2, and tet(M) were enriched (P < 0.05).

CONCLUSIONS

Administration of a single injection of oxytetracycline and tulathromycin resulted in significant changes in the NP and fecal microbiota during the first 5 days after treatment. Antibiotic treatment also increased the relative abundance of several antibiotic resistance determinants in the fecal and NP microbiome at either day 12 or 34.

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes

BACKGROUND

Acute otitis media (AOM) is one of the most common childhood infections, generally thought to be caused by ascension of bacteria from the nasopharynx (NP) to the middle ear. Using 16S ribosomal RNA-based sequencing, we evaluated the relationship between the NP and middle ear fluid (MEF) microbiota in children with AOM with tympanostomy tubes (AOMT) as a proxy for AOM and explored whether microbiota profiling predicts natural disease course.

METHODS

Microbiota profiles of paired NP and MEF samples of 94 children below 5 years of age with uncomplicated AOMT were determined.

RESULTS

Local diversity (P < 0.001) and overall microbiota composition (P < 0.001) of NP and MEF samples differed significantly, although paired NP and MEF samples were much more similar than unpaired samples (P < 0.001). High qualitative agreement between the presence of individual bacteria in both niches was observed. Abundances of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Turicella otitidis, Klebsiella pneumoniae and Haemophilus spp. were strongly correlated between the 2 niches. Additionally, P. aeruginosa, S. aureus, T. otitidis and Streptococcus pneumoniae abundance in NP were predictive of the presence of a range of oral types of bacteria in MEF. Interestingly, there was no association between Moraxella catarrhalis in NP and MEF samples, which was highly present in NP but virtually absent in MEF. Finally, the NP microbiota composition could predict duration of AOMT, even better than MEF microbiota.

CONCLUSIONS

We observed substantial correlations between paired NP and MEF microbiota in children with AOMT. Our data also suggest that NP microbiota profiling deserves further exploration as tool for future treatment decisions.

Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children

Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time.

Contribution of the Mucosal Microbiota to Bovine Respiratory Health

Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock.

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.

Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study

Background

Lower respiratory tract infections (LRTIs) are a leading cause of childhood morbidity and mortality. Potentially pathogenic organisms are present in the respiratory tract in both symptomatic and asymptomatic children, but their presence does not necessarily indicate disease. We aimed to assess the concordance between upper and lower respiratory tract microbiota during LRTIs and the use of nasopharyngeal microbiota to discriminate LRTIs from health.

Methods

First, we did a prospective study of children aged between 4 weeks and 5 years who were admitted to the paediatric intensive care unit (PICU) at Wilhelmina Children's Hospital (Utrecht, Netherlands) for a WHO-defined LRTI requiring mechanical ventilation. We obtained paired nasopharyngeal swabs and deep endotracheal aspirates from these participants (the so-called PICU cohort) between Sept 10, 2013, and Sept 4, 2016. We also did a matched case-control study (1:2) with the same inclusion criteria in children with LRTIs at three Dutch teaching hospitals and in age-matched, sex-matched, and time-matched healthy children recruited from the community. Nasopharyngeal samples were obtained at admission for cases and during home visits for controls. Data for child characteristics were obtained by questionnaires and from pharmacy printouts and medical charts. We used quantitative PCR and 16S rRNA-based sequencing to establish viral and bacterial microbiota profiles, respectively. We did sparse random forest classifier analyses on the bacterial data, viral data, metadata, and the combination of all three datasets to distinguish cases from controls.

Findings

29 patients were enrolled in the PICU cohort. Intra-individual concordance in terms of viral microbiota profiles (96% agreement [95% CI 93–99]) and bacterial microbiota profiles (58 taxa with a median Pearson's r 0·93 [IQR 0·62–0·99]; p<0·05 for all 58 taxa) was high between nasopharyngeal and endotracheal aspirate samples, supporting the use of nasopharyngeal samples as proxy for lung microbiota during LRTIs. 154 cases and 307 matched controls were prospectively recruited to our case-control cohort. Individually, bacterial microbiota (area under the curve 0·77), viral microbiota (0·70), and child characteristics (0·80) poorly distinguished health from disease. However, a classification model based on combined bacterial and viral microbiota plus child characteristics distinguished children with LRTIs from their matched controls with a high degree of accuracy (area under the curve 0·92).

Interpretation

Our data suggest that the nasopharyngeal microbiota can serve as a valid proxy for lower respiratory tract microbiota in childhood LRTIs, that clinical LRTIs in children result from the interplay between microbiota and host characteristics, rather than a single microorganism, and that microbiota-based diagnostics could improve future diagnostic and treatment protocols.

Funding

Spaarne Gasthuis, University Medical Center Utrecht, and the Netherlands Organization for Scientific Research.

Nasal microbial composition and chronic otitis media with effusion: A case-control study

OBJECTIVES

Chronic otitis media with effusion (COME) in children can cause prolonged hearing loss, which is associated with an increased risk of learning delays and behavioural problems. Dispersal of bacterial pathogens from the nasal passages to the middle ear is implicated in COME. We sought to determine whether there is an association between nasal microbial composition and COME in children.

METHODS

A case-control study of children aged 3 and 4 years was conducted. Cases undergoing placement of tympanostomy tubes for COME were compared to healthy controls. Nasal swabs were collected and a questionnaire was administered. The V1-3 region of the 16S rRNA gene was amplified, and sequenced on the Illumina MiSeq.

RESULTS

73 children with COME had a lower Shannon diversity index than 105 healthy controls (1.62 [.80] versus 1.88 [.84], respectively; P = .046). The nasal microbiota of cases and controls differed in composition using Bray-Curtis dissimilarity (p = 0.002). Children with COME had a higher abundance of otopathogens and lower abundance of commensals including alpha haemolytic Streptococci and Lactococcus. Cluster analysis revealed 4 distinct nasal microbial profiles. Profiles that were Corynebacterium-dominated (aOR 4.18 [95%CI, 1.68-10.39], Streptococcus-dominated (aOR 3.12 [95%CI, 1.08-9.06], or Moraxella-dominated (aOR 4.70 [95%CI, 1.73-12.80] were associated with COME, compared to a more mixed microbial profile when controlling for age, ethnicity, and recent antibiotics use.

CONCLUSIONS

Children with COME have a less diverse nasal microbial composition with a higher abundance of pathogens, compared to healthy children who have a more mixed bacterial profile with a higher abundance of commensals. Further research is required to determine how nasal microbiota may relate to the pathogenesis or maintenance of COME, and whether modification of the nasal microbiota can prevent or treat children at risk of COME.

Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood

Background

Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants’ nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers.

Results

For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection.

Conclusions

Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1372-8) contains supplementary material, which is available to authorized users.

Probiotics in the treatment of otitis media. The past, the present and the future

Otitis media (OM) is one of the most common infectious diseases in children and the leading cause for medical consultations and antibiotic prescription in this population. The burden of disease associated with OM is greater in developing nations and indigenous populations where the associated hearing loss contributes to poor education and employment outcomes. Current treatment and prevention is largely focused on vaccination and antibiotics. However, rates of OM, particularly in indigenous populations, remain high. With growing concerns regarding antibiotic resistance and antibiotic-associated complications, an alternative, more effective treatment is required. Administration of probiotics, both locally and systemically have been investigated for their ability to treat and prevent OM in children. This review explores the theoretical bases of probiotics, successful application of probiotics in medicine, and their use in the treatment and prevention of OM. We conclude that local administration of niche-specific probiotic bacteria that demonstrates the ability to inhibit the growth of otopathogens in vitro shows promise in the prevention and treatment of OM and warrants further investigation.

Monitoring and evaluation of the immune status of female Kunming mice maintained in different biosafety level laboratories

High-level biosafety laboratories (BSL), such as BSL-3 and BSL-4, which deal with high infectivity and virulence pathogens, have become indispensable. Mice are frequently used in animal BSL (ABSL) to establish animal models for infection and to evaluate in vivo immune responses. A project of monitoring and evaluation on the physiology and immune status of mice housed in different ABSL labs was performed in the ABSL-2/3/4 labs of Kunming National High-level Biosafety Research Center, China. Female Kunming mice were housed in the ABSL-2/3/4 labs for 1 month, and mouse behavior, body physiology/immune status, pulmonary immune status and respiratory bacteria composition were evaluated and compared among mice from the different labs. Mice settled in their new housing environment of the different labs after transfer and gained weight steadily. Blood hematology testing, serum cytokine/chemokine profiles and blood/spleen lymphocyte constitutions were comparable between the ABSL-2/3/4 labs. The numbers of different pulmonary leukocytes in the bronchoalveolar lavage fluid were at baseline levels in mice from the ABSL-2/3/4 labs. Diversity and dominance of mice respiratory bacteria were semblable among the ABSL-2/3/4 labs. Our results confirm the stability of physiology and immune status of Kunming mice maintained in different ABSL-2/3/4 labs for at least 1 month.

Peptide Ligands of AmiA, AliA, and AliB Proteins Determine Pneumococcal Phenotype

The Ami-AliA/AliB oligopeptide permease of Streptococcus pneumoniae has been suggested to play a role in environmental sensing and colonisation of the nasopharynx by this human bacterial pathogen by binding peptides derived from bacterial neighbours of other species in the microbiota. Here, we investigated the effects of the peptide ligands of the permease’s substrate binding proteins AmiA, AliA, and AliB on pneumococcal phenotype. AmiA and AliA ligands reduced pneumococcal growth, increased biofilm production and reduced capsule size. In contrast, AliB ligand increased growth and greatly increased bacterial chain length. A decrease in transformation rate was observed in response to all three peptides. Changes in protein expression were also observed, particularly those associated with metabolism and cell wall synthesis. Understanding interspecies bacterial communication and its effect on development of colonising versus invasive phenotypes has the potential to reveal new targets to tackle and prevent pneumococcal infections.

Distinct Nasopharyngeal and Oropharyngeal Microbiota of Children with Influenza A Virus Compared with Healthy Children

BACKGROUND

Influenza A virus (IAV) has had the highest morbidity globally over the past decade. A growing number of studies indicate that the upper respiratory tract (URT) microbiota plays a key role for respiratory health and that a dysfunctional respiratory microbiota is associated with disease; but the impact of microbiota during influenza is understudied.

METHODS

We recruited 180 children, including 121 IAV patients and 59 age-matched healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected to conduct 16S rDNA sequencing and compare microbiota structures in different individuals.

RESULTS

Both NP and OP microbiota in IAV patients differed from those in healthy individuals. The NP dominated genera in IVA patients, such as Moraxella, Staphylococcus, Corynebacterium, and Dolosigranulum, showed lower abundance than in healthy children. The Streptococcus significantly enriched in patients' NP and Phyllobacterium could be generally detected in patients' NP microbiota. The most abundant genera in OP microbiota showed a decline tendency in patients, including Streptococcus, Neisseria, and Haemophilus. The URT's bacterial concurrence network changed dramatically in patients. NP and OP samples were clustered into subgroups by different dominant genera; and NP and OP microbiota provided the precise indicators to distinguish IAV patients from healthy children.

CONCLUSION

This is the first respiratory microbiome analysis on pediatric IAV infection which reveals distinct NP and OP microbiota in influenza patients. It provides a new insight into IAV research from the microecology aspect and promotes the understanding of IAV pathogenesis.

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media

BACKGROUND

Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic review of the literature exploring the upper airway and middle ear microbiota in relation to OM in indigenous children.

METHODS

Papers targeting microbiota in relation to OM in children < 18 years indigenous to Australia, New Zealand, North America, and Greenland were sought. MEDLINE, CINAHL, EMBASE, Cochrane Library, and Informit databases were searched using key words. Two independent reviewers screened titles, abstracts, and then full-text papers against inclusion criteria according to PRISMA guidelines.

RESULTS

Twenty-five papers considering indigenous Australian, Alaskan, and Greenlandic children were included. There were high rates of nasopharyngeal colonization with the three main otopathogens (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) in indigenous children with OM. Middle ear samples had lower rates of otopathogen detection, although detection rates increased when molecular methods were used. Pseudomonas aeruginosa and Staphylococcus aureus were commonly detected in middle ear discharge of children with chronic suppurative OM. There was a significant heterogeneity between studies, particularly in microbiological methods, which were largely limited to culture-based detection of the main otopathogens.

CONCLUSIONS

There are high rates of otopathogen colonization in indigenous children with OM. Chronic suppurative OM appears to be associated with a different microbial profile. Beyond the main otopathogens, the data are limited. Further research is required to explore the entire upper respiratory tract/middle ear microbiota in relation to OM, with the inclusion of healthy indigenous peers as controls.

Probiotics for the airways: Potential to improve epithelial and immune homeostasis

Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefit on the host. The therapeutic effects of probiotics have been mostly studied in the gastrointestinal tract, but recent evidence points toward the potential of these bacteria to prevent and/or treat chronic airway diseases. In this review, possible mechanisms of action of probiotics in the airways are described, with a particular focus on their capacity to modulate the epithelial barrier function and their mode of interaction with the immune system. Indeed, probiotic bacteria, mostly lactobacilli, can promote the expression and regulation of tight junctions and adherence junctions, resulting in the restoration of a defective epithelial barrier. These bacteria interact with the epithelial barrier and immune cells through pattern recognition receptors, such as Toll-like receptors, which upon activation can stimulate or suppress various immune responses. Finally, the clinical potential of probiotics to treat inflammatory diseases of the upper and lower respiratory tract, and the difference between their mode of application (eg, oral or nasal) are discussed here.

Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle

The objective was to study effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of feedlot cattle. Two groups of 30 Angus-cross heifers were studied from weaning to 28 d after arrival at a feedlot. For each group, half the heifers were either transported directly to a feedlot after weaning (RANC) or transported to and co-mingled at an auction market for 24 h before being placed in a feedlot (AUCT). Deep nasal swabs (DNS) and trans-tracheal aspirates (TTA) were collected at weaning (d0) and at on-arrival processing at the feedlot (d2). At 7 (d9) and 28 d (d30) after arrival, DNS were repeated. The DNA was extracted from DNS and TTA and the V4 region of the 16S rRNA gene sequenced (MiSeq). Alpha diversity analysis did not reveal differences between AUCT and RANC. However, bacterial diversity decreased over time in the nasopharynx, especially at d9. Although beta-diversity was not different between AUCT and RANC, interval after arrival and feedlot where heifers were placed affected composition of the nasopharyngeal bacterial communities. In both groups, a large increase in Mycoplasma was observed after arrival; in one group, Mycoplasma bovis was dominant at d9 and remained dominant until d30. However, in the other group, Mycoplasma dispar dominated at d9 and was replaced by Moraxella at d30. We concluded that transportation to and co-mingling at an auction market for 24 h did not significantly influence diversity or composition of nasopharyngeal or tracheal bacterial communities.

A guide to polarized airway epithelial models for studies of host-pathogen interactions

Mammalian lungs are organs exhibiting the cellular and spatial complexity required for gas exchange to support life. The respiratory epithelium internally lining the airways is susceptible to infections due to constant exposure to inhaled microbes. Biomedical research into respiratory bacterial infections in humans has been mostly carried out using small mammalian animal models or two-dimensional, submerged cultures of undifferentiated epithelial cells. These experimental model systems have considerable limitations due to host specificity of bacterial pathogens and lack of cellular and morphological complexity. This review describes the in vitro differentiated and polarized airway epithelial cells of human origin that are used as a model to study respiratory bacterial infections. Overall, these models recapitulate key aspects of the complexity observed in vivo and can help in elucidating the molecular details of disease processes observed during respiratory bacterial infections.

Microbiota Composition in Upper Respiratory Tracts of Healthy Children in Shenzhen, China, Differed with Respiratory Sites and Ages

The upper respiratory tract (URT) is home to various microbial commensals, which function as competitors to pathogens and help train the immune system. However, few studies have reported the normal microbiota carriage in the URT of healthy Chinese children. In this study, we performed a 16S rDNA gene sequencing analysis of 83 anterior nares (ANs), 60 nasopharynx (NP), and 97 oropharynx (OP) samples from 98 healthy children in Shenzhen, China (≤12 years of age). The microbiota in ANs and NP is the same at different ages and typical species in these sites include Moraxella, Staphylococcus, Corynebacterium, Streptococcus, and Dolosigranulum. By contrast, the OP is primarily colonized by Streptococcus, Prevotella, Neisseria, Veillonella, Rothia, Leptotrichia, and Haemophilus. Streptococcus and Rothia keep low abundance in OP microbiota of children ≤1 year old, whereas Prevotella, Neisseria, Haemophilus, and Leptotrichia amass significantly in individuals >1 year old. This work furnishes an important reference for understanding microbial dysbiosis in the URT of Chinese paediatric patients.

Bacterial biogeography of adult airways in atopic asthma

BACKGROUND

Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will require large longitudinal studies, for which bronchoscopy is poorly suited. Studies of samples obtained by sputum induction and nasopharyngeal brushing or lavage have also reported asthma-associated microbiota characteristics. It remains unknown, however, whether the microbiota detected in these less-invasive sample types reflect the composition of bronchial microbiota in asthma.

RESULTS

Bacterial microbiota in paired protected bronchial brushings (BB; n = 45), induced sputum (IS; n = 45), oral wash (OW; n = 45), and nasal brushings (NB; n = 27) from adults with mild atopic asthma (AA), atopy without asthma (ANA), and healthy controls (HC) were profiled using 16S rRNA gene sequencing. Though microbiota composition varied with sample type (p < 0.001), compositional similarity was greatest for BB-IS, particularly in AAs and ANAs. The abundance of genera detected in BB correlated with those detected in IS and OW (r median [IQR] 0.869 [0.748-0.942] and 0.822 [0.687-0.909] respectively), but not with those in NB (r = 0.004 [- 0.003-0.011]). The number of taxa shared between IS-BB and NB-BB was greater in AAs than in HCs (p < 0.05) and included taxa previously associated with asthma. Of the genera abundant in NB, only Moraxella correlated positively with abundance in BB; specific members of this genus were shared between the two compartments only in AAs. Relative abundance of Moraxella in NB of AAs correlated negatively with that of Corynebacterium but positively with markers of eosinophilic inflammation in the blood and BAL fluid. The genus, Corynebacterium, trended to dominate all NB samples of HCs but only half of AAs (p = 0.07), in whom abundance of this genus was negatively associated with markers of eosinophilic inflammation.

CONCLUSIONS

Induced sputum is superior to nasal brush or oral wash for assessing bronchial microbiota composition in asthmatic adults. Although compositionally similar to the bronchial microbiota, the microbiota in induced sputum are distinct, reflecting enrichment of oral bacteria. Specific bacterial genera are shared between the nasal and the bronchial mucosa which are associated with markers of systemic and bronchial inflammation.

Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia

Specific nasopharyngeal bacterial communities can provide colonization resistance against respiratory pathogens in cattle. However, the role of bacterial communities of the lower airways in respiratory health remains largely unknown. Therefore, our objective was to compare nasopharyngeal and tracheal bacterial communities between healthy feedlot cattle and those with bronchopneumonia (BP). Deep nasal swabs and trans-tracheal aspiration samples were collected from steers with (n = 60) and without (n = 60) BP at 4 feedlots in Western Canada. After DNA extraction, 16S rRNA gene (V4) was amplified and sequenced. Alpha-diversity analysis revealed a lower bacterial diversity in the nasopharynx and trachea of steers with BP compared to healthy pen-mates. Bacterial communities present within the airways clustered into 4 distinct metacommunities that were associated with sampling locations and health status. Metacommunity 1, enriched with Mycoplasma bovis, Mannheimia haemolytica and Pasteurella multocida, was dominant in the nasopharynx and trachea of steers with BP. In contrast, metacommunity 3, enriched with Mycoplasma dispar, Lactococcus lactis and Lactobacillus casei, was mostly present in the trachea of healthy steers. Metacommunity 4, enriched with Corynebacterium, Jeotgalicoccus, Psychrobacter and Planomicrobium, was present in the nasopharynx only. Metacommunity 2, enriched with Histophilus somni, Moraxella and L. lactis, was present in both healthy and sick steers, but was primarily detected in one feedlot. We concluded that distinct bacterial metacommunities inhabited the nasopharynx and trachea of healthy feedlot cattle and those with BP. Because L. lactis and L. casei can inhibit M. haemolytica growth in vitro, their presence in healthy steers may have provided colonization resistance against bacterial respiratory pathogens.

Multifactorial inhibition of lactobacilli against the respiratory tract pathogen Moraxella catarrhalis

Probiotics, mainly lactic acid bacteria (LAB), are widely focused on gastrointestinal applications. However, recent microbiome studies indicate that LAB can be endogenous members of other human body sites such as the upper respiratory tract (URT). Interestingly, DNA-based microbiome research suggests an inverse correlation between the presence of LAB and the occurrence of potential pathogens, such as Moraxella catarrhalis, an important URT pathogen linked to otitis media, sinusitis and chronic obstructive pulmonary disease. However, a direct interaction between these microbes has not been explored in detail. This study investigated the direct antipathogenic effects of Lactobacillus species, including several well-documented probiotic strains, on M. catarrhalis using agar-based assays, time course analysis, biofilm assays and minimal inhibitory concentration (MIC) testing. These assays were performed using spent culture supernatans (SCS) at two pHs (4.3 and 7) and D- and/or L-lactic acid at three pHs (2, 4 and 7). In addition, cell line assays for adhesion competition and immunomodulation were used to substantiate the inhibitory effect of lactobacilli against M. catarrhalis. A proportion of Lactobacillus strains, including the model probiotic Lactobacillus rhamnosus GG, showed a strong and direct activity against M. catarrhalis. Screening of the activity of the SCS after different treatments demonstrated that lactic acid has an important antimicrobial activity against this pathogen – at least in vitro – with mean MIC values for D- and L-lactic acid varying between 0.5 and 27 g/l depending on the pH. Furthermore, L. rhamnosus GG also decreased the adhesion of M. catarrhalis to human airway epithelial Calu-3 cells with more than 50%, and the expression of mucin MUC5AC, pro-inflammatory cytokines interleukin (IL)-8, IL-1β, and tumor necrosis factor-α at least 1.2 fold. This study suggests that several lactobacilli and their key metabolite lactic acid are possible candidates for probiotic therapeutic interventions against URT infections.

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites

Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site.

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Background

Recurrent acute otitis media (rAOM, recurrent ear infection) is a common childhood disease caused by bacteria termed otopathogens, for which current treatments have limited effectiveness. Generic probiotic therapies have shown promise, but seem to lack specificity. We hypothesised that healthy children with no history of AOM carry protective commensal bacteria that could be translated into a specific probiotic therapy to break the cycle of re-infection. We characterised the nasopharyngeal microbiome of these children (controls) in comparison to children with rAOM (cases) to identify potentially protective bacteria. As some children with rAOM do not appear to carry any of the known otopathogens, we also hypothesised that characterisation of the middle ear microbiome could identify novel otopathogens, which may also guide the development of more effective therapies.

Results

Middle ear fluids, middle ear rinses and ear canal swabs from the cases and nasopharyngeal swabs from both groups underwent 16S rRNA gene sequencing. The nasopharyngeal microbiomes of cases and controls were distinct. We observed a significantly higher abundance of Corynebacterium and Dolosigranulum in the nasopharynx of controls. Alloiococcus, Staphylococcus and Turicella were abundant in the middle ear and ear canal of cases, but were uncommon in the nasopharynx of both groups. Gemella and Neisseria were characteristic of the case nasopharynx, but were not prevalent in the middle ear.

Conclusions

Corynebacterium and Dolosigranulum are characteristic of a healthy nasopharyngeal microbiome. Alloiococcus, Staphylococcus and Turicella are possible novel otopathogens, though their rarity in the nasopharynx and prevalence in the ear canal means that their role as normal aural flora cannot be ruled out. Gemella and Neisseria are unlikely to be novel otopathogens as they do not appear to colonise the middle ear in children with rAOM.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1154-3) contains supplementary material, which is available to authorized users.

Establishment of the nasal microbiota in the first 18 months of life: Correlation with early-onset rhinitis and wheezing

BACKGROUND

Dynamic establishment of the nasal microbiota in early life influences local mucosal immune responses and susceptibility to childhood respiratory disorders.

OBJECTIVE

The aim of this case-control study was to monitor, evaluate, and compare development of the nasal microbiota of infants with rhinitis and wheeze in the first 18 months of life with those of healthy control subjects.

METHODS

Anterior nasal swabs of 122 subjects belonging to the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) birth cohort were collected longitudinally over 7 time points in the first 18 months of life. Nasal microbiota signatures were analyzed by using 16S rRNA multiplexed pair-end sequencing from 3 clinical groups: (1) patients with rhinitis alone (n = 28), (2) patients with rhinitis with concomitant wheeze (n = 34), and (3) healthy control subjects (n = 60).

RESULTS

Maturation of the nasal microbiome followed distinctive patterns in infants from both rhinitis groups compared with control subjects. Bacterial diversity increased over the period of 18 months of life in control infants, whereas infants with rhinitis showed a decreasing trend (P < .05). An increase in abundance of the Oxalobacteraceae family (Proteobacteria phylum) and Aerococcaceae family (Firmicutes phylum) was associated with rhinitis and concomitant wheeze (adjusted P < .01), whereas the Corynebacteriaceae family (Actinobacteria phylum) and early colonization with the Staphylococcaceae family (Firmicutes phylum; 3 weeks until 9 months) were associated with control subjects (adjusted P < .05). The only difference between the rhinitis and control groups was a reduced abundance of the Corynebacteriaceae family (adjusted P < .05). Determinants of nasal microbiota succession included sex, mode of delivery, presence of siblings, and infant care attendance.

CONCLUSION

Our results support the hypothesis that the nasal microbiome is involved in development of early-onset rhinitis and wheeze in infants.

Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children

Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.

The respiratory microbiome and respiratory infections

Despite advances over the past ten years lower respiratory tract infections still comprise around a fifth of all deaths worldwide in children under five years of age with the majority in low- and middle-income countries. Known risk factors for severe respiratory infections and poor chronic respiratory health do not fully explain why some children become sick and others do not. The respiratory tract hosts bacteria that can cause respiratory infections but also normal commensal bacteria. Together, this microbial population is called the microbiome. The composition of the respiratory microbiome in the first few months of life is likely influenced by external factors such as environment, mode of delivery and infant feeding practices, which are also associated with susceptibility to respiratory infections and wheezing illness/asthma. Recently, multiple studies have shown that respiratory microbiota profiles early in life are associated with an increased risk and frequency of subsequent respiratory infections, disease severity and occurrence of wheeze in later childhood. Early interactions between infectious agents such as viruses and the respiratory microbiome have shown to modulate host immune responses potentially affecting the course of the disease and future respiratory health. Deeper understanding of these interactions will help the development of new therapeutic agents or preventive measures that may modify respiratory health outcomes and help us to stratify at risk populations to better target our current interventional approaches.

Streptococcus pneumoniae Proteins AmiA, AliA, and AliB Bind Peptides Found in Ribosomal Proteins of Other Bacterial Species

The nasopharynx is frequently colonized by both commensal and pathogenic bacteria including Streptococcus pneumoniae (pneumococcus). Pneumococcus is an important pathogen responsible for bacterial meningitis and community acquired pneumonia but is also commonly an asymptomatic colonizer of the nasopharynx. Understanding interactions between microbes may provide insights into pathogenesis. Here, we investigated the ability of the three oligopeptide-binding proteins AmiA, AliA, and AliB of an ATP-binding cassette transporter of pneumococcus to detect short peptides found in other bacterial species. We found three possible peptide ligands for AmiA and four each for AliA and AliB of which two for each protein matched ribosomal proteins of other bacterial species. Using synthetic peptides we confirmed the following binding: AmiA binds peptide AKTIKITQTR, matching 50S ribosomal subunit protein L30, AliA binds peptide FNEMQPIVDRQ, matching 30S ribosomal protein S20, and AliB binds peptide AIQSEKARKHN, matching 30S ribosomal protein S20, without excluding the possibility of binding of the other peptides. These Ami-AliA/AliB peptide ligands are found in multiple species in the class of Gammaproteobacteria which includes common colonizers of the nostrils and nasopharynx. Binding such peptides may enable pneumococcus to detect and respond to neighboring species in its environment and is a potential mechanism for interspecies communication and environmental surveillance.

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis

BACKGROUND

The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes.

RESULTS

Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01).

CONCLUSIONS

While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance

Beef cattle in North America that are deemed to be at high risk of developing bovine respiratory disease (BRD) are frequently administered a metaphylactic antibiotic injection to control the disease. Cattle may also receive in-feed antimicrobials to prevent specific diseases and ionophores to improve growth and feed efficiency. Presently, attempts to evaluate the effects that these medications have on antibiotic resistance in the bovine nasopharyngeal microbiota have been focused on culturable bacteria that are associated with BRD. Therefore, we assessed the effects of injectable antibiotics on the nasopharyngeal microbiota of commercial feedlot cattle in Alberta, Canada, through the first 60 d on feed. Although all cattle in the study were also receiving in-feed chlortetracycline and monensin, the administration of a single injection of either oxytetracycline or tulathromycin at feedlot placement altered the nasopharyngeal microbiota in comparison with the cattle receiving only in-feed antibiotics. Oxytetracycline significantly (P < 0.05) reduced the relative abundance of Mannheimia spp. from feedlot entry to exit (≥60 d) and both oxytetracycline and tulathromycin treated cattle had a significantly lower relative abundance of Mycoplasma spp. at feedlot exit compared with the in-feed antibiotic only group. The proportion of the tetracycline resistance gene tet(H) was significantly increased following oxytetracycline injection (P < 0.05). Oxytetracycline also reduced both the number of OTUs and the Shannon diversity index in the nasopharyngeal microbiota (P < 0.05). These results demonstrate that in feedlot cattle receiving subtherapeutic in-feed antimicrobials, the administration of a single injection of either oxytetracycline or tulathromycin resulted in measurable changes to the nasopharyngeal microbiota during the first 60 d following feedlot placement.

The nasopharyngeal microbiome

Human microbiomes have received increasing attention over the last 10 years, leading to a pervasiveness of hypotheses relating dysbiosis to health and disease. The respiratory tract has received much less attention in this respect than that of, for example, the human gut. Nevertheless, progress has been made in elucidating the immunological, ecological and environmental drivers that govern these microbial consortia and the potential consequences of aberrant microbiomes. In this review, we consider the microbiome of the nasopharynx, a specific niche of the upper respiratory tract. The nasopharynx is an important site, anatomically with respect to its gateway position between upper and lower airways, and for pathogenic bacterial colonisation. The dynamics of the latter are important for long-term respiratory morbidity, acute infections of both invasive and non-invasive disease and associations with chronic airway disease exacerbations. Here, we review the development of the nasopharyngeal (NP) microbiome over the life course, examining it from the early establishment of resilient profiles in neonates through to perturbations associated with pneumonia risk in the elderly. We focus specifically on the commensal, opportunistically pathogenic members of the NP microbiome that includes Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Moraxella catarrhalis. In addition, we consider the role of relatively harmless genera such as Dolosigranulum and Corynebacterium. Understanding that the NP microbiome plays such a key, beneficial role in maintaining equilibrium of commensal species, prevention of pathogen outgrowth and host immunity enables future research to be directed appropriately.

Bacterial microbiota of the nasal passages across the span of human life

The human nasal passages host major human pathogens. Recent research suggests that the microbial communities inhabiting the epithelial surfaces of the nasal passages are a key factor in maintaining a healthy microenvironment by affecting both resistance to pathogens and immunological responses. The nasal bacterial microbiota shows distinct changes over the span of human life and disruption by environmental factors might be associated with both short- and long-term health consequences, such as susceptibility to viral and bacterial infections and disturbances of the immunological balance. Because infants and older adults experience a high burden of morbidity and mortality from respiratory tract infections, we review recent data on the bacterial nasal microbiota composition in health and acute respiratory infection in these age groups.

Streptococcus pneumoniae Colonization Is Required To Alter the Nasal Microbiota in Cigarette Smoke-Exposed Mice

Smokers have nasal microbiota dysbiosis, with an increased frequency of colonizing bacterial pathogens. It is possible that cigarette smoke increases pathogen acquisition by perturbing the microbiota and decreasing colonization resistance. However, it is difficult to disentangle microbiota dysbiosis due to cigarette smoke exposure from microbiota changes caused by increased pathogen acquisition in human smokers. Using an experimental mouse model, we investigated the impact of cigarette smoke on the nasal microbiota in the absence and presence of nasal pneumococcal colonization. We observed that cigarette smoke exposure alone did not alter the nasal microbiota composition. The microbiota composition was also unchanged at 12 h following low-dose nasal pneumococcal inoculation, suggesting that the ability of the microbiota to resist initial nasal pneumococcal acquisition was not impaired in smoke-exposed mice. However, nasal microbiota dysbiosis occurred as a consequence of established high-dose nasal pneumococcal colonization at day 3 in smoke-exposed mice. Similar to clinical reports on human smokers, an enrichment of potentially pathogenic bacterial genera such as Fusobacterium, Gemella, and Neisseria was observed. Our findings suggest that cigarette smoke exposure predisposes to pneumococcal colonization independent of changes to the nasal microbiota and that microbiota dysbiosis observed in smokers may occur as a consequence of established pathogen colonization.

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study

A few studies have highlighted the importance of the respiratory microbiome in modulating the frequency and outcome of viral respiratory infections. However, there are insufficient data on the use of microbial signatures as prognostic biomarkers to predict respiratory disease outcomes. In this study, we aimed to evaluate whether specific bacterial community compositions in the nasopharynx of children at the time of hospitalization are associated with different influenza clinical outcomes. We utilized retrospective nasopharyngeal (NP) samples (n=36) collected at the time of hospital arrival from children who were infected with influenza virus and had been symptomatic for less than 2 days. Based on their clinical course, children were classified into two groups: patients with mild influenza, and patients with severe respiratory or neurological complications. We implemented custom 16S rRNA gene sequencing, metagenomic sequencing and computational analysis workflows to classify the bacteria present in NP specimens at the species level. We found that increased bacterial diversity in the nasopharynx of children was strongly associated with influenza severity. In addition, patients with severe influenza had decreased relative abundance of Staphylococcus aureus and increased abundance of Prevotella (including P. melaninogenica), Streptobacillus, Porphyromonas, Granulicatella (including G. elegans), Veillonella (including V. dispar), Fusobacterium and Haemophilus in their nasopharynx. This pilot study provides proof-of-concept data for the use of microbial signatures as prognostic biomarkers of influenza outcomes. Further large prospective cohort studies are needed to refine and validate the performance of such microbial signatures in clinical settings.

The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya

Background

Respiratory diseases cause substantial morbidity and mortality worldwide, with sub-Saharan Africa bearing the greatest burden. Identifying etiologies of respiratory disease is important to inform cost effective treatment, prevention and control strategies. Testing for all of the different pathogens that are potentially associated with respiratory illnesses is challenging. We piloted the use of a multi-pathogen respiratory Taqman Array Cards (TAC) to identify pathogens in respiratory samples collected from non-fatal and fatal cases and their matched asymptomatic controls.

Methods

This is a case control study comparing viral and bacterial pathogens detected among non-fatal and fatal cases to those detected among age and time matched asymptomatic controls. We used McNemar’s test to compare proportions of pathogens detected among cases (non-fatal and fatal) to their matched asymptomatic controls. We used Mann-Whitney test to compare the distribution of median Cycle threshold (Ct) values among non-fatal and fatal cases to their corresponding asymptomatic controls.

Results

There were 72 fatal and 72 non-fatal cases matched to 72 controls. We identified at least one pathogen in 109/144 (76%) cases and 59/72 (82%) controls. For most pathogens, the median Ct values were lower among cases (fatal and non-fatal) compared to asymptomatic controls.

Conclusions

Similar rates of pathogen detection among cases and controls make interpretation of results challenging. Ct-values might be helpful in interpreting clinical relevance of detected pathogens using multi-pathogen diagnostic tools.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2694-0) contains supplementary material, which is available to authorized users.