Pneumococcal within-host diversity during colonization, transmission and treatment

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Understanding pathogen genetic diversity is crucial for disease surveillance and transmission chain reconstruction.
• Inter-strain competition in bacteria influences the prevalence of resistant and sensitive strains.
• Streptococcus pneumoniae colonization in infants is a significant public health concern.

Purpose of the Study:

• To characterize the genetic diversity of Streptococcus pneumoniae within infant and maternal populations.
• To evaluate the sensitivity of deep sequencing for detecting multiple colonizations and invasive serotypes.
• To investigate the impact of antimicrobial treatment on bacterial colonization and evolution within hosts.

Main Methods:

• Deep sequencing of whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples.
• Analysis of samples from 468 infants and 145 mothers.
• Correlation of genomic data with comprehensive antimicrobial treatment data.

Main Results:

• Deep sequencing significantly increased the detection rate of highly invasive serotype 1 bacteria compared to gold-standard methods.
• An elevated rate of mother-to-child transmission of S. pneumoniae was observed in the first year of life.
• Infants receiving antimicrobial treatment showed increased risk of acquiring and persistently colonizing multidrug-resistant bacteria.

Conclusions:

• Deep sequencing offers superior sensitivity for pathogen detection and characterization, enhancing genomic surveillance.
• Antimicrobial treatment can promote the persistence of multidrug-resistant bacteria, while susceptible strains generally dominate in untreated hosts.
• Understanding within-host evolution and transmission dynamics is vital for controlling bacterial pathogens like S. pneumoniae.