Nader Shaikh

Introduction: Few qualitative studies have examined parents’ experiences in the days following their child’s acute otitis media (AOM) diagnosis. This qualitative study explored challenges faced by parents and probed parents about how these challenges could be mitigated. Methods: Interviews took place from October 2022 to July 2024 with parents from four pediatric practices. Recruitment was limited to parents of children 3-24 months of age who were recently diagnosed with AOM. Transcripts were analyzed using template analysis. Results: We conducted 19 interviews. Major concerns identified by parents were failure of symptom improvement, missed sleep/work, and issues related to antimicrobial treatment. The experience of parents of children with multiple AOM episodes differed from that of less experienced parents. Parents identified areas physicians could improve parental experiences such as setting expectations for the recovery period and offering optional follow-up visits at the end of the treatment period. Discussion and Conclusions: This study provides insights into challenges parents face in the days following diagnosis of AOM. Our findings suggest parents may benefit from additional physician counseling at the time of diagnosis, including a detailed discussion of what to expect during the recovery period and review of indications for follow-up.

Background: Limited data exist on whether the timing or duration of treatment for acute otitis media (AOM) affects nasopharyngeal carriage. We studied the eradication of pathogens ( Streptococcus pneumoniae , Haemophilus influenzae and Moraxella catarrhalis ) in relation to timing (immediate vs. delayed) and duration (5 vs. 10 days) of antibiotic treatment. Methods: A secondary analysis of 3 randomized clinical trials: the Turku antibiotic versus placebo trial, the Pittsburgh antibiotic versus placebo trial and the Pittsburgh 5- versus 10-day trial (ClinicalTrials.gov registration numbers NCT00299455, NCT00377260 and NCT01511107, respectively). We investigated the change in AOM pathogen colonization rate in relation to timing (immediate vs. delayed antibiotic initiation) and duration (5 vs. 10 days) of antibiotic treatment for AOM. We included children aged 6–35 months with AOM who had nasopharyngeal samples collected both before and after treatment. Results: Antibiotic treatment with amoxicillin-clavulanate significantly reduced the carriage of S. pneumoniae and M. catarrhalis but had very little effect on the carriage of H. influenzae. The timing of treatment did not affect the eradication rates of nasopharyngeal pathogens. Antibiotic treatment eradicated S. pneumoniae and M. catarrhalis in 78% (95% confidence interval [CI], 72–83) and 85% (95% CI, 72–95) of cases, while H. influenzae was eradicated in only 20% (95% CI, 12–29) of cases. Conclusions: In most cases, H. influenzae carriage in the nasopharynx persisted despite antibiotic treatment with amoxicillin-clavulanate. This should be considered when choosing antibiotic treatment for children with a relapse of AOM.

The human nasopharynx is colonized by a diverse community of commensal microbiota linked to many respiratory diseases, yet their associations with the host remain unclear. In this study, we introduced a dual-transcriptomics analysis strategy, which can characterize the host transcriptome and microbiome from nasal samples simultaneously. We applied this workflow to a local SARS-CoV-2 cohort with 76 asymptomatic infected patients, among whom 52 (68.42%) developed symptomatic infection during a 1-week follow-up period. Nasal swabs were collected from all 76 patients at enrollment and from 73 patients at one-week later follow-up. We detected a median of 8.94% reads that did not map to the human genome across all 149 samples, among which around half (median 49.68%) were successfully mapped to microbiome genome. Meta-transcriptomic analysis detected significantly higher SARS-related coronavirus loads in samples from the symptomatic group at enrollment (P = 0.004), and both groups showed decreased loads one week later (symptomatic, P = 0.001; asymptomatic, P = 0.035). Compared with benchmarking 16 S rRNA sequencing on 53 samples, our computational strategy showed high correlation of relative abundance in all top 20 genera (median Rho = 0.90, P_max < 0.001). A total of 670 bacteria species were identified to show a relative abundance ≥ 0.01% in at least 10% samples. Differential abundance analysis identified 76 species (DASs) from six phyla with significantly decreased abundance in samples from the symptomatic group (log₂(fold change or FC) < -1 and adjusted P < 0.05) compared to the asymptomatic group at enrollment. Integrating these symptom-associated DASs with host's gene expression using an expression quantitative trait bacteria (eQTB) model, we found 45 symptom-associated DASs identified at enrollment were significantly associated with one to 14 genes (adjusted P < 0.05). GSEA showed a series of symptom-associated DASs were significantly correlated with pathways related to olfactory function, keratinocyte differentiation, and DNA methylation. In summary, our dual-transcriptomic analysis strategy effectively characterized host-microbiome associations, offering insights into microbial contributions to respiratory diseases.

Bacterial urinary tract infections (UTIs) are prevalent in childhood and adolescence. Paediatric UTIs present unique challenges with respect to diagnosis, prevention and management, and the potential for adverse sequelae. Uropathogenic Escherichia coli (UPEC) accounts for the majority of UTIs and is the best studied uropathogen. Novel discoveries have advanced our understanding of host–pathogen interactions, cellular and molecular mechanisms of host defence, and risk factors for UTI recurrence. Emerging evidence also highlights an association of the gut, vaginal and urinary microbiota in influencing UTI risk and recurrence. Yet, key knowledge gaps persist regarding UTI pathogenesis, host susceptibility, optimal diagnostic and management strategies and prevention of UTI recurrence and sequelae, especially in paediatric populations. The development of standardized clinical pathways offers an opportunity to improve care consistency and outcomes by integrating evidence-based practices into routine management. As technologies evolve and understanding deepens, future efforts must integrate host, microbial and clinical insights to optimize UTI prevention and treatment in paediatric populations.

The upper respiratory tract (URT) microbiome has emerged as a key component of acute otitis media (AOM) pathophysiology; however, few studies conducted to date have evaluated URT microbiome composition in children with recurrent AOM (rAOM). We collected serial nasopharyngeal samples from a cohort of 58 children, 6 to 35 months of age, over a one-year period. Samples were analyzed using 16S rRNA sequencing and PCR-based assays for common otopathogens and respiratory viruses. Age was strongly associated with differential abundance of specific genera, including increased abundance of genera associated with respiratory health (e.g., Dolosigranulum , Corynebacterium ). In contrast, samples collected during AOM episodes or within 30 days of receipt of an antibiotic had a lower relative abundance of these genera. Further, the number of antibiotic-free days prior to sample collection was associated with global changes in microbiome composition. Unsupervised clustering identified three microbiome profiles that differed by incidence of AOM, bacterial otopathogen burden, symptom score, and number of antibiotic-free days prior to sample collection. Increasing age was associated with transition to profiles characterized by lower incidence of AOM and bacterial otopathogen burden, while antibiotic use was associated with transition to a profile associated with greater incidence of AOM. Our findings indicate that alterations of the microbiome associated with aging may contribute to decreased incidence of AOM as children age, while systemic antibiotic use may induce dysbiosis, thereby enhancing AOM susceptibility. IMPORTANCE: Ear infections are the most common bacterial infection among young children and the leading cause of healthcare visits and antibiotic prescriptions. This study explores the connection between the microbiome of the nose—the community of microorganisms that live in different areas of the human body—and recurrent ear infections in young children. An analysis of nasal swabs collected from 58 children over a year showed that as children age, they tend to have fewer bacterial pathogens and more species that are associated with a healthy state in their microbiomes. These more mature microbiomes were associated with fewer ear infections. In contrast, recent use of antibiotics was associated with microbiomes that had more bacterial pathogens and that were associated with greater ear infection incidence. Overall, these findings indicate that the microbiome may be a key factor in reduced ear infections as children age.

Background: Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response. Methods: Here, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections. Results: RNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs. By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays. Conclusions: Our study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.

Aim: To determine if short‐ (2–5 days) course antimicrobials are as effective as standard‐ (6–14 days) course antimicrobials in the treatment of symptomatic UTI in children.Methods: MEDLINE and EMBASE were searched from their origin to January 2024. We only considered randomised controlled trials in children <18 years of age. The main outcomes of interest were UTI or bacteriuria at the end of therapy.Results: Nine studies were included. Compared to children treated with a standard course of antimicrobials, those treated with shortened courses of antimicrobials did not have significantly different risks of UTI at the end of therapy (risk difference 2.2%, CI: 0.0–4.3). Risk of bacteriuria at end of therapy (RD = 8.7%, CI: 5.3–12.2) was slightly higher in children treated with shorter courses. In children with fever at baseline (two studies), there was no significant difference in risk between short and standard duration treatment (RD = 0.4%, CI: −2.8 to 3.6).Conclusion: In children without fever at the time of presentation, treatment with shorter courses of antimicrobials appears reasonable. More studies of febrile children are needed before shorter courses could be recommended for febrile children.