Changes Over Time in Nasopharyngeal Colonization in Children Under 2 Years of Age at the Time of Diagnosis of Acute Otitis Media (1999-2014)

Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection

Acute otitis media (AOM) is the most common childhood bacterial infectious disease requiring antimicrobial therapy. Most cases of AOM are caused by translocation of Streptococcus pneumoniae or Haemophilus influenzae from the nasopharynx to the middle ear during an upper respiratory tract infection (URI). Ongoing genomic surveillance of these pathogens is important for vaccine design and tracking of emerging variants, as well as for monitoring patterns of antibiotic resistance to inform treatment strategies and stewardship.In this work, we examined the ability of a genomics-based workflow to determine microbiological and clinically relevant information from cultured bacterial isolates obtained from patients with AOM or an URI. We performed whole genome sequencing (WGS) and analysis of 148 bacterial isolates cultured from the nasopharynx (N = 124, 94 AOM and 30 URI) and ear (N = 24, all AOM) of 101 children aged 6-35 months presenting with AOM or an URI. We then performed WGS-based sequence typing and antimicrobial resistance profiling of each strain and compared results to those obtained from traditional microbiological phenotyping.WGS of clinical isolates resulted in 71 S. pneumoniae genomes and 76 H. influenzae genomes. Multilocus sequencing typing (MSLT) identified 33 sequence types for S. pneumoniae and 19 predicted serotypes including the most frequent serotypes 35B and 3. Genome analysis predicted 30% of S. pneumoniae isolates to have complete or intermediate penicillin resistance. AMR predictions for S. pneumoniae isolates had strong agreement with clinical susceptibility testing results for beta-lactam and non beta-lactam antibiotics, with a mean sensitivity of 93% (86-100%) and a mean specificity of 98% (94-100%). MLST identified 29 H. influenzae sequence types. Genome analysis identified beta-lactamase genes in 30% of H. influenzae strains, which was 100% in agreement with clinical beta-lactamase testing. We also identified a divergent highly antibiotic-resistant strain of S. pneumoniae, and found its closest sequenced strains, also isolated from nasopharyngeal samples from over 15 years ago.Ultimately, our work provides the groundwork for clinical WGS-based workflows to aid in detection and analysis of H. influenzae and S. pneumoniae isolates.

Association Between Nasopharyngeal Colonization and Clinical Outcome in Children With Acute Otitis Media

BACKGROUND

Young children with acute otitis media (AOM) frequently exhibit nasopharyngeal colonization with either Streptococcus pneumoniae, Haemophilus influenzae or both pathogens. We aimed to determine if antibiotics could be spared or shortened in those without nasopharyngeal colonization with either pathogen.

METHODS

In 2 separate randomized clinical trials in children aged 6-23 months with stringently-diagnosed AOM, we performed bacterial cultures on nasopharyngeal specimens collected at the time of diagnosis. In the first trial, we compared the efficacy of amoxicillin/clavulanate (amox/clav) administered for 10 days vs. that of placebo, and in the second trial, we compared the efficacy of amox/clav administered for 10 days vs. 5 days. In each trial, we classified children as being colonized with both S. pneumoniae and H. influenzae, S. pneumoniae alone, H. influenzae alone, or neither pathogen, and as experiencing either clinical success or clinical failure at the end-of-therapy visit, based on previously reported a priori criteria.

RESULTS

We evaluated 796 children. Among children randomized to amox/clav, those colonized with either S. pneumoniae or H. influenzae or both were approximately twice as likely to experience clinical failure as children not colonized with either pathogen (odds ratio: 1.8; confidence intervals: 1.2-2.9). In contrast, among children randomized to placebo, clinical failure at the end-of-therapy visit was not associated with nasopharyngeal culture results at the time of diagnosis.

CONCLUSIONS

Children colonized with either S. pneumoniae or H. influenzae or both have a greater chance of treatment failure than children colonized with neither pathogen.

Nasopharyngeal rapid diagnostic testing to reduce unnecessary antibiotic use and individualize management of acute otitis media

Background

Acute otitis media (AOM) is the most common indication for antibiotics in children. The associated organism can influence the likelihood of antibiotic benefit and optimal treatment. Nasopharyngeal polymerase chain reaction can effectively exclude the presence of organisms in middle-ear fluid. We explored the potential cost-effectiveness and reduction in antibiotics with nasopharyngeal rapid diagnostic testing (RDT) to direct AOM management.

Methods

We developed 2 algorithms for AOM management based on nasopharyngeal bacterial otopathogens. The algorithms provide recommendations on prescribing strategy (ie, immediate, delayed, or observation) and antimicrobial agent. The primary outcome was the incremental cost-effectiveness ratio (ICER) expressed as cost per quality-adjusted life day (QALD) gained. We used a decision-analytic model to evaluate the cost-effectiveness of the RDT algorithms compared to usual care from a societal perspective and the potential reduction in annual antibiotics used.

Results

An RDT algorithm that used immediate prescribing, delayed prescribing, and observation based on pathogen (RDT-DP) had an ICER of $1,336.15 per QALD compared with usual care. At an RDT cost of $278.56, the ICER for RDT-DP exceeded the willingness to pay threshold; however, if the RDT cost was <$212.10, the ICER was below the threshold. The use of RDT was estimated to reduced annual antibiotic use, including broad-spectrum antimicrobial use, by 55.7% ($4.7 million for RDT vs $10.5 million for usual care).

Conclusion

The use of a nasopharyngeal RDT for AOM could be cost-effective and substantially reduce unnecessary antibiotic use. These iterative algorithms could be modified to guide management of AOM as pathogen epidemiology and resistance evolve.

Haemophilus influenzae Prevalence, Proportion of Capsulated Strains and Antibiotic Susceptibility During Colonization and Acute Otitis Media in Children, 2019-2020

BACKGROUND

The objective of this study was to determine the prevalence, proportion of encapsulated strains and antibiotic susceptibility of Haemophilus influenzae isolated from young children.

METHODS

Children, 6 months to 30 months old, were prospectively enrolled from September 2019 to September 2020 at Rochester, NY, pediatric clinics. H. influenzae isolates from nasopharynx (NP) at healthy visits and disease isolates from NP and middle ear fluid (MEF) at onset of acute otitis media (AOM) were characterized by capsular typing, β-lactamase production and antibiotic susceptibility.

RESULTS

Samples from 565 healthy visits and 130 AOM visits were collected. H. influenzae was detected 5.9% and 27% in the NP from healthy and AOM visits, respectively. In the MEF, H. influenzae was isolated in 43% of samples. Eight percent of H. influenzae isolates were encapsulated, 88% type f. Overall 39.7% of isolates were β-lactamase producing; 43% for MEF isolates. Ampicillin, trimethoprim/sulfamethoxazole, erythromycin and clarithromycin nonsusceptibility were found in more than 25% of isolates. None of the encapsulated H. influenzae isolates were positive for β-lactamase production or ampicillin nonsusceptibility. 9.2% of isolates were β-lactamase negative, ampicillin resistant (β-lactamase negative, ampicillin resistant + β-lactamase negative, ampicillin intermediate).

CONCLUSIONS

The prevalence of H. influenzae in the NP of young children is very low at times of health, but H. influenzae is highly prevalent in MEF at onset of AOM. Nontypeable H. influenzae accounts for >90% of all H. influenzae isolates. Type f predominated among encapsulated strains. β-lactamase production and antibiotic nonsusceptibility among H. influenzae strains isolated from the NP and MEF are common.

Decreased prevalence of Moraxella catarrhalis in addition to Streptococcus pneumoniae in children with upper respiratory tract infection after introduction of conjugated pneumococcal vaccine: a retrospective cohort study

OBJECTIVES

To study effects of the introduction of pneumococcal conjugate vaccines (PCV) on the interspecies dynamics of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in preschool children with respiratory tract infection.

METHODS

Nasopharyngeal samples from children aged ≤6 years with upper respiratory tract infection (n = 14 473) in South Sweden were analysed during 14 consecutive years, 5 years before and 9 years after PCV introduction. The yearly prevalence was calculated, and multivariate count regressions between prevalence and estimated yearly proportions of vaccinated children were performed. Associations between pneumococcal serotypes and the other pathogens were assessed.

RESULTS

When comparing the prevaccine period with the years after introduction, the prevalence of S. pneumoniae decreased by 65.2% (16.4 to 5.7 per 1000 individuals; p < 0.001), whereas M. catarrhalis and H. influenzae decreased by 52.1% (21.5 to 10.3 per 1000 individuals; p < 0.001) and 46.6% (13.6 to 7.3 per 1000 individuals; p < 0.001), respectively. In multivariate negative binomial regressions adjusted for yearly numbers of samples taken, S. pneumoniae and M. catarrhalis were significantly negatively associated with increasing vaccine coverage proportions (adjusted prevalence ratio (aPR) = 0.17; p < 0.001 and aPR = 0.48; p < 0.001, respectively), whereas H. influenzae (aPR = 0.75; p = 0.17) was not. In addition, the proportion of cultures positive for S. pneumoniae as well as M. catarrhalis was significantly lower in the postvaccine period compared to the prevaccine period, while this was not the case for H. influenzae. A significant positive association between certain PCV serotypes and simultaneous growth with M. catarrhalis was observed.

CONCLUSIONS

After introduction of PCV, the prevalence of M. catarrhalis in addition to S. pneumoniae in children with respiratory tract infection decreased; this was also the case after adjusting for reduced numbers of samples taken. This may partly be attributed to a positive association between PCV serotypes and M. catarrhalis.