Multicentric Analysis of Erythromycin Resistance Determinants in Invasive Streptococcus pneumoniae; Associated Serotypes and Sequence Types in India

Streptococcus pneumoniae serotype distribution in low- and middle-income countries of South Asia: Do we need to revisit the pneumococcal vaccine strategy?

S. pneumoniae serotypes responsible for pneumococcal disease differ with respect to disease severity, invasiveness, antimicrobial susceptibility, geographies, immunization history, age groups, and with time. Although PCVs have blunted the pneumococcal disease burden, they are plagued with numerous challenges, especially the emergence of NVTs. In this review, we show that there are diverse serotypes, especially NVTs, responsible for causing pneumococcal diseases in LMICs of South Asia across different studies conducted between 2012 and 2024. We propose that pharmaceutical/biotech companies should tailor/customize the PCVs as per the region-specific serotype prevalence based on surveillance data. Furthermore, protein-based vaccines, or WCVs, have been explored and can serve as viable alternatives to address the limitations associated with PCVs. However, robust studies are warranted in different geographies to demonstrate its efficacy and safety in clinical trials as well as the real-world effectiveness of these promising candidates.

Burden of Pneumococcal Disease in Young Children Due to Serotypes Contained in Different Pneumococcal Conjugate Vaccines in Eight Asian Countries and Territories

BACKGROUND

Pneumococcal disease (PD) is a major cause of morbidity and mortality in young children in Asia and globally. Pneumococcal conjugate vaccines (PCVs) have significantly reduced the burden of PD when included in pediatric national immunization programs (NIPs). This study estimates the clinical and economic burden of PD due to serotypes contained in different PCVs in children aged < 5 years in eight Asian countries/territories.

METHODS

Based on published data, a cohort-based decision analytic model was used to estimate annual PD cases, deaths, and direct medical costs associated with serotypes contained in PCV10, PCV13, PCV15, and PCV20.

RESULTS

PD incidence rates were lower in regions with PCV13 in their NIP than those without. Serotypes contained in higher but not lower valency PCVs resulted in a significant incremental clinical and economic burden, although the difference between PCV13 and PCV15 serotypes was generally small. Moving from PCV13 to PCV20 was estimated to result in greater clinical and economic burden reductions.

CONCLUSIONS

This study demonstrates the remaining and incremental burden of PD from PCV10 to PCV20 serotypes in young children in selected Asian regions. Extending NIP access to higher-valency PCVs with broader serotype coverage and improving vaccine uptake will help prevent morbidity and deaths and save healthcare costs.

Pan-Genome-Wide Association Study of Serotype 19A Pneumococci Identifies Disease-Associated Genes

Despite the widespread implementation of pneumococcal vaccines, hypervirulent Streptococcus pneumoniae serotype 19A is endemic worldwide. It is still unclear whether specific genetic elements contribute to complex pathogenicity of serotype 19A isolates. We performed a large-scale pan-genome-wide association study (pan-GWAS) of 1,292 serotype 19A isolates sampled from patients with invasive disease and asymptomatic carriers. To address the underlying disease-associated genotypes, a comprehensive analysis using three methods (Scoary, a linear mixed model, and random forest) was performed to compare disease and carriage isolates to identify genes consistently associated with disease phenotype. By using three pan-GWAS methods, we found consensus on statistically significant associations between genotypes and disease phenotypes (disease or carriage), with a subset of 30 consistently significant disease-associated genes. The results of functional annotation revealed that these disease-associated genes had diverse predicted functions, including those that participated in mobile genetic elements, antibiotic resistance, virulence, and cellular metabolism. Our findings suggest the multifactorial pathogenicity nature of this hypervirulent serotype and provide important evidence for the design of novel protein-based vaccines to prevent and control pneumococcal disease. IMPORTANCE It is important to understand the genetic and pathogenic characteristics of S. pneumoniae serotype 19A, which may provide important information for the prevention and treatment of pneumococcal disease. This global large-sample pan-GWAS study has identified a subset of 30 consistently significant disease-associated genes that are involved in mobile genetic elements, antibiotic resistance, virulence, and cellular metabolism. These findings suggest the multifactorial pathogenicity nature of hypervirulent S. pneumoniae serotype 19A isolates and provide implications for the design of novel protein-based vaccines.

Increase of Macrolide-Resistance in Streptococcus pneumoniae Strains After the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine in Lima, Peru

Streptococcus pneumoniae upper respiratory infections and pneumonia are often treated with macrolides, but recently macrolide resistance is becoming an increasingly important problem. The 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the National Immunization Program of Peru in 2015. This study aimed to evaluate the temporal evolution of macrolide resistance in S. pneumoniae isolates collected in five cross-sectional studies conducted before and after this vaccine introduction, from 2006 to 2019 in Lima, Peru. A total of 521 and 242 S. pneumoniae isolates recovered from nasopharyngeal swabs from healthy carrier children < 2 years old (2 carriage studies) and samples from normally sterile body areas from pediatric patients with invasive pneumococcal disease (IPD) (3 IPD studies), respectively, were included in this study. Phenotypic macrolide resistance was detected using the Kirby-Bauer method and/or MIC test. We found a significant increase in macrolide resistance over time, from 33.5% to 50.0% in carriage studies, and from 24.8% to 37.5% and 70.8% in IPD studies. Macrolide resistance genes [erm(B) and mef(A/E)] were screened using PCR. In carriage studies, we detected a significant decrease in the frequency of mef(A/E) genes among macrolide-resistant S. pneumoniae strains (from 66.7% to 50.0%) after introduction of PCV13. The most common mechanism of macrolide-resistant among IPD strains was the presence of erm(B) (96.0%, 95.2% and 85.1% in the 3 IPD studies respectively). Macrolide resistance was more common in serotype 19A strains (80% and 90% among carriage and IPD strains, respectively) vs. non-serotype 19A (35.5% and 34.4% among carriage and IPD strains, respectively). In conclusion, S. pneumoniae macrolide resistance rates are very high among Peruvian children. Future studies are needed in order to evaluate macrolide resistance trends among pneumococcal strains, especially now after the COVID-19 pandemic, since azithromycin was vastly used as empiric treatment of COVID-19 in Peru.