Related Experiment Video

Updated: Feb 25, 2026

Experimental Human Pneumococcal Carriage
07:47

Experimental Human Pneumococcal Carriage

Published on: February 15, 2013

16.3K

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

John A Lees1, Nicholas J Croucher2, David Goldblatt3

  • 1Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.

Elife
|July 26, 2017
PubMed

Insights

Genomic variation in Streptococcus pneumoniae explains most carriage duration differences, not host factors. Prophage sequences significantly reduce carriage time, impacting bacterial competition and antibiotic resistance dynamics.

Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Streptococcus pneumoniae causes invasive infant disease, particularly in low-income regions.
  • Nasopharyngeal carriage is essential for disease but its duration varies.
  • Current understanding of carriage duration variability is limited, primarily at the serotype level.

Purpose of the Study:

  • To develop a model for calculating pneumococcal carriage episode duration.
  • To investigate the contribution of genomic variation to carriage duration.
  • To identify specific genomic factors influencing pneumococcal carriage duration.

Main Methods:

  • Developed a model to estimate carriage duration from longitudinal swab data.
  • Integrated carriage duration data with whole genome sequencing data.
  • Performed a pan-genome-wide association study (GWAS) to identify genetic associations.

Main Results:

  • Pneumococcal genomic variation accounted for 63% of carriage duration variation; host traits explained <5%.
  • Serotype (17%), drug resistance (9%), and other loci contributed significantly to duration variation.
  • Prophage sequences were associated with decreased carriage duration, independent of serotype.

Conclusions:

  • Genomic factors, particularly prophages, are major drivers of pneumococcal carriage duration.
  • Findings support models of pneumococcal competition and the evolution of antibiotic resistance.
  • Understanding genomic influences on carriage duration can inform public health strategies.

Keywords:
GWASS. pneumoniaecarriage durationepidemiologyevolutionary biologygenomicsheritabilityinfectious diseasemicrobiology

More Related Videos

Characterization of Inflammatory Responses During Intranasal Colonization with Streptococcus pneumoniae09:12

Characterization of Inflammatory Responses During Intranasal Colonization with Streptococcus pneumoniae

Published on: January 17, 2014

13.2K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.8K

Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
774
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
15.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
18.8K