Population structure reveals clade- and region-specific dissemination of macrolide-resistant Mycoplasma pneumoniae

Macrolide-resistant Mycoplasma pneumoniae (MRMP) has become highly prevalent in East Asia since the early 2000s, whereas its prevalence remains relatively low in many other regions. This striking geographic disparity has often been attributed to the expansion of a limited number of resistant lineages. However, the population-structural basis of this regional pattern remains incompletely understood. To address this, we analyzed whole-genome sequences of 613 M. pneumoniae strains, including 86 strains isolated in Japan and 527 publicly available genomes, to investigate the relationships among phylogenetic structure, geographic distribution, and macrolide resistance.

Macrolide resistance was identified in 61.5% (377/613) of strains, and 94.2% of resistant strains carried the A2063G mutation in the 23S rRNA gene. Resistant strains were strongly concentrated in East Asia (70.5% vs 13.4% in non-East Asian regions), with resistance rates varying across countries, ranging from 30.4% in Japan to 99.0% in China. This pattern cannot be fully explained by the expansion of the well-characterized resistant clade T1-3R alone, but is more likely attributable to the emergence of resistance in multiple genetic backgrounds. Notably, in T1-2 and T2-2, resistance rates among East Asian strains were 66.0% and 45.4%, respectively, whereas no resistant strains were identified in non-East Asian populations, highlighting regional disparities within the same clonal backgrounds. Phylogenetic network analysis of these clades further suggested that resistant variants did not arise sporadically but appeared to reflect mutation acquisition followed by regional clonal expansion. In contrast to the geographically restricted expansion of resistant clones, macrolide-susceptible strains from different regions occasionally showed close genetic relatedness within 10 SNPs, suggesting that cross-regional dissemination of M. pneumoniae strains can occur.

These findings suggest that the high prevalence of MRMP in East Asia cannot be explained solely by the expansion of a single resistant lineage. Instead, multiple resistant clones appear to have emerged and expanded within several clades that are prevalent in East Asia. This population-structured view of MRMP dissemination provides a framework for understanding regional differences in resistance dynamics and underscores the importance of continued genome-based surveillance to monitor the emergence and regional spread of resistant clones.