Genetic Diversity of Streptococcus pneumoniae Isolated from Thirteen Arab Countries and over 22 Years: A Retrospective Bioinformatics Analysis

Streptococcus pneumoniae (S. pneumoniae) is responsible for a wide range of infections. The aim of this study was to investigate the clonal diversity of S. pneumoniae in thirteen Arab countries. Multi-Locus Sequence Typing (MLST) data were extracted from PubMLST database. Genetic analysis was performed using DnaSP software version 6.0. A Minimum Spanning Tree (MST) analysis was conducted to evaluate the population structure of S. pneumoniae strains. Genetic data from 1008 Arab S. pneumoniae strains, collected over 22 years (1996–2018), were analyzed. MLST analysis identified a highly diverse population comprising 600 sequence types grouped into 87 clonal complexes and 295 singletons. Both internationally disseminated clones (e.g., ST156) and country-specific lineages (e.g., ST2307, Saudi Arabia) were observed, indicating substantial geographic structuring. Significant associations were detected between sequence types and geographical origin, decade of isolation, patient age, disease type, and serotype (p < 0.05). Although recombination events were presented, the population retained a predominantly clonal structure over time (ISA = 0.0715, p < 0.001). Overall, these findings demonstrated extensive genetic heterogeneity and spatiotemporal structuring of S. pneumoniae in the Arab region, providing valuable insights for regional surveillance and vaccine-related strategies.