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Published on: January 17, 2014
Evidence of virulence and antimicrobial resistance in Streptococcus pneumoniae serotype 16F lineages
Introduction:
Due to the emergence of non-vaccine serotypes in vaccinated populations, Streptococcus pneumoniae remains a major global health challenge despite advances in vaccine development. Serotype 16F is among the predominant non-vaccine serotypes identified among vaccinated infants in South Africa (SA).
Aim:
To characterise lineages and antimicrobial resistance in 16F isolates obtained from South Africa and placed the local findings in a global context.
Methodology:
We analysed 10923 S. pneumoniae carriage isolates obtained from infants recruited as part of a broader SA birth cohort. We inferred serotype, resistance profile for penicillin, chloramphenicol, cotrimoxazole, erythromycin and tetracycline, and Global Pneumococcal Sequence Clusters (GPSCs) from genomic data. To ensure global representation, we also included S. pneumoniae carriage and disease isolates from the Global Pneumococcal Sequencing (GPS) project database (n=19,607, collected from 49 countries across five continents, years covered (1995 - 2018), accessed on 17 th March 2022).
Results:
Nine percent (934/10923) of isolates obtained from infants in the Drakenstein community in SA and 2% (419/19607) of genomes in the GPS dataset were serotype 16F. Serotype 16F isolates were from 28 different lineages of S. pneumoniae, with GPSC33 and GPSC46 having the highest proportion of serotype 16F isolates at 26% (346/1353) and 53% (716/1353), respectively. Serotype 16F isolates were identified globally, however, most isolates were collected from Africa. GPSC33 was associated with carriage [OR (95% CI) 0.24 (0.09 - 0.66); p=0.003], while GPSC46 was associated with disease [OR (95% CI) 19.9 (2.56 - 906.50); p=0.0004]. 10% (37/346) and 15% (53/346) of isolates within GPSC33 had genes associated with resistance to penicillin and co-trimoxazole, respectively, and 18% (128/716) of isolates within GPSC46 had genes associated with resistance to co-trimoxazole. Resistant isolates formed genetic clusters which may suggest emerging resistant lineages.
Discussion:
Serotype 16F lineages are common in Southern Africa. Some of these lineages are associated with disease, and resistance to penicillin and cotrimoxazole. We recommend continuous genomic surveillance to determine long term impact of serotype 16F lineages on vaccine efficacy and antimicrobial therapy globally. Investing in vaccine strategies that offer protection over a wide range of serotypes/lineages remains essential.
Data Summary:
The sequencing reads for the genomes analysed have been deposited in the European Nucleotide Archive and the accession numbers for each isolate are listed in Supplementary Table1 . Phylogenetic tree of serotype 16F pneumococcal genomes and associated metadata are available for download and visualisation on the Microreact website: Phylogenies of seotype 16F, GPSC33 and GPSC46 are available on the Microreact serotype-16F , GPSC33 and GPSC46 , respectively.
Impact Statement:
This study shows that serotype 16F lineages are predominant in Southern Africa and are associated with disease and antimicrobial resistance. Although serotype 16F has been included in the newer formulation of the upcoming vaccine formulations of PCV21 and IVT-25, continuous surveillance to determine long term impact of serotype 16F lineages on vaccines and antimicrobial therapy remains essential.
Insights
Streptococcus pneumoniae serotype 16F is prevalent in Southern Africa, with some lineages linked to disease and antibiotic resistance. Continuous genomic surveillance is crucial for monitoring vaccine impact and guiding antimicrobial therapy globally.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Streptococcus pneumoniae remains a global health concern due to non-vaccine serotypes emerging in vaccinated populations.
- Serotype 16F is a predominant non-vaccine serotype in vaccinated infants in South Africa.
Approach:
- Genomic analysis of 10,923 S. pneumoniae isolates from South African infants.
- Inclusion of 19,607 global isolates from the Global Pneumococcal Sequencing project (1995-2018).
- Inferred serotype, antimicrobial resistance profiles, and Global Pneumococcal Sequence Clusters (GPSCs).
Key Points:
- Serotype 16F isolates were found globally, predominantly in Africa, with GPSC33 and GPSC46 being the most common lineages.
- GPSC33 was associated with carriage, while GPSC46 was associated with disease.
- Significant proportions of GPSC33 and GPSC46 isolates exhibited resistance to penicillin and co-trimoxazole, forming genetic clusters.
Conclusions:
- Serotype 16F lineages are widespread in Southern Africa and linked to disease and antimicrobial resistance.
- Continuous genomic surveillance is essential to assess the long-term impact of 16F on vaccine efficacy and antimicrobial treatment.
- Vaccine strategies offering broad serotype/lineage protection are vital.
