Abstract
IntroductionAntibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure.MethodsWe investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene.ResultsMain epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics.ConclusionOur results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
Highlights
Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae
NPA was collected before receiving antibiotics or within the first 24 h of antibiotic intake in 27 patients, and were assigned to the group not exposed to antibiotics
We have demonstrated clear differences in nasopharyngeal microbiota composition of hospitalized children with IPD exposed to antibiotics compared to those not exposed
Summary
Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Antibiotics have been described to perturb the balanced microbiota with shortand long-term effects on children’s health. The side effects of antibiotics have been described on the gut microbiota, including transient or profound loss of specific bacterial species, reduction of microbial diversity, and loss of colonization resistance (Kim et al, 2017). Even long-term effects on children’s health including obesity or diabetes have been linked to aberrant microbiomes altered by antibiotics (Boursi et al, 2015; Tai et al, 2015). Young children are subjected to a high number of short-term antibiotic prescriptions, especially for treating acute respiratory infections (Fleming-Dutra et al, 2016; Orlando et al, 2020) such as invasive pneumococcal disease (IPD)
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