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Related Concept Videos

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Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonization using next-generation

Jada Hackman1,2,3, Martin L Hibberd4, Todd D Swarthout5,6

  • 1Faculty of Epidemiology and Population Health, Department of Infectious Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, United Kingdom.

Microbiology Spectrum
|November 5, 2024
PubMed
Summary
This summary is machine-generated.

Genomic serotyping accurately detects high-abundance pneumococcal serotypes in children. Increasing sequencing depth improves detection of low-abundance serotypes, aiding vaccine impact monitoring.

Keywords:
AfricaStreptococcus pneumoniaeco-carriagemicroarraypneumococcussequencingserotyping

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Area of Science:

  • Microbiology
  • Genomics
  • Vaccinology

Background:

  • Pneumococcal carriage is a precursor to invasive pneumococcal disease, a major cause of childhood pneumonia.
  • Multiple pneumococcal serotype carriage is common in high-burden populations, complicating vaccine impact assessment.
  • Accurate detection of co-carriage is crucial for monitoring the effectiveness of pneumococcal vaccines.

Purpose of the Study:

  • To evaluate the sensitivity of genomic serotyping methods for identifying co-carriage of pneumococcal serotypes.
  • To compare the performance of SeroCall and PneumoKITy against microarray serotyping.
  • To assess the utility of single-nucleotide polymorphism (SNP) density and sequencing depth for serotype detection.

Main Methods:

  • Collected 24 nasopharyngeal samples from healthy children in Blantyre, Malawi, for carriage surveillance.
  • Performed microarray serotyping and whole-genome sequencing (Illumina MiSeq) of pneumococcal DNA.
  • Analyzed genomic data using SeroCall and PneumoKITy, comparing results to microarray data and assessing SNP density.

Main Results:

  • Genomic serotyping showed high sensitivity (98%) for high-abundance pneumococcal serotypes (>10%) using SeroCall.
  • Sensitivity for low-abundance serotypes (<10%) was limited (20%) but improved with increased sequencing depth.
  • SNP frequency distribution correlated well with the relative abundance of high-abundance serotypes.

Conclusions:

  • Genomic serotyping is a sensitive method for detecting high-abundance pneumococcal serotypes in co-carriage samples.
  • Increased sequencing depth enhances the detection of low-abundance serotypes, crucial for comprehensive monitoring.
  • These findings support the use of genomic methods for evaluating pneumococcal vaccine impact in diverse populations.