Genomic epidemiological analysis reveals new insights into the resurgence of Mycoplasma pneumoniae in China

Objectives After coronavirus disease 2019 pandemic restrictions, Mycoplasma pneumoniae ( M. pneumoniae ) re-surged widely across the world. This study aimed to determine the genomic epidemiological characteristics of resurging M. pneumoniae , which has dominated the respiratory infection outbreak in Beijing, China, since mid-September 2023. Methods M. pneumoniae samples were collected from patients with acute respiratory-tract infections in Beijing in 2018–2023. A total of 160 M. pneumoniae genomes were sequenced via probe-capture-based approach. The genetic features of M. pneumoniae were characterized by multilocus sequence typing and comparative genomic analysis. Results In total, 160 patients with M. pneumoniae infections were enrolled. ST3 (n = 93) and ST14 (n = 65) were the predominant sequence types. The macrolide-resistant mutation rate of ST3 was maintained at 100%, whereas that of ST14 increased rapidly. Comparative genomic analysis revealed 99% to > 99% similarity among the Beijing strains from 2023 when aligned to the reference M129 genome. The major variation occurs in the P1 gene. MAUVE indicated a lack of rearrangement, yet it included four subtype-specific insertions and non-conserved hsdS genes. The phylogenetic tree showed that strains from Asia and other world regions clustered into distinct clades, with significant evolutionary differences. Further genomic analyses identified some Asia-dominant genetic variations in genes associated with genome stability, pathogenesis, and drug resistance. Conclusions The 2023 outbreak of M. pneumoniae was not attributable to a novel variant but stemmed from the resurgence of the pre-existing strains. Our genomic epidemiological findings demonstrated that the endemic strains in different regions exhibit distinct genomic characteristics, associated with genomic stability.