Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data

Area of Science:

• Microbiology
• Epidemiology
• Genomics

Background:

• Streptococcus pneumoniae (pneumococcus) is a major global cause of infectious disease morbidity and mortality.
• Invasive pneumococcal disease (IPD) rates remain stable in Israel despite vaccination efforts.
• Understanding pathogen geographical spread is key for effective control measures.

Purpose of the Study:

• To investigate the geographical dissemination patterns of Streptococcus pneumoniae in Israel.
• To analyze the spatial mixing of pneumococcal isolates using whole-genome sequencing data.

Main Methods:

• Analysis of 1174 pneumococcal genomes from patients with IPD across various Israeli regions.
• Inference of evolutionary distance between isolate pairs using whole-genome data.
• Application of a relative risk (RR) ratio framework to assess geographical structure.

Main Results:

• No significant geographical structure was detected at the overall pneumococcal lineage level.
• Whole-genome sequencing data revealed that invasive pneumococcal isolates require approximately 5 years for complete geographical mixing within Israel.

Conclusions:

• Genomic granularity is essential for understanding pathogen spread dynamics.
• Invasive pneumococcal isolates exhibit a relatively slow mixing rate across Israel, taking around 5 years to disperse nationwide.
• Findings inform public health strategies for controlling pneumococcal disease transmission.