Genetic factors driving the Mycoplasma pneumoniae outbreak among children post-COVID-19 in China: a whole genome analysis

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Background Mycoplasma pneumoniae (M. pneumoniae) is a leading cause of community-acquired pneumonia in children. Post-COVID-19, a significant resurgence of M. pneumoniae infections has been observed in China, but whole-genome analyses on the genetic mechanisms driving this resurgence remain limited. Methods We performed whole-genome sequencing on 169 M. pneumoniae isolates from Beijing and Baoding, collected before and after COVID-19. All M. pneumoniae genomes from GenBank were included for analysis. Genotypes were identified using multilocus variable-number tandem-repeat analysis (MLVA), multilocus sequence typing (MLST), phylogenetic analysis. Genomic conservation and transmission patterns were assessed via SNP distance. Findings We identified a post-COVID-19 resurgence of M. pneumoniae infections among children, with infection rates peaking at 60%–70% in late 2023, higher than during the pandemic (10%–20%) and pre-pandemic (∼30%). Genomic analysis revealed distinct genotypes, with T1-2 (4-5-7-2) dominating in Beijing, and both T1-2 and T2-2 (3-5-6-2) prevalent in Baoding. Minimal SNP distances and genomic conservation indicated rapid spread of M. pneumoniae . Genomic analysis uncovered key genetic factors driving the outbreak: near-100% macrolide resistance and increased prevalence of the 4-5-7-2 genotype (enriched in virulence and metabolism-related genes). Interpretation This study provides a comprehensive genomic analysis of genetic factors driving the outbreak. With near-100% macrolide resistance in China, urgent changes in treatment policies are needed. The rising prevalence of 4-5-7-2 and its functional advantages warrant close monitoring. Our findings offer insights into the outbreak causes and guide future prevention and control strategies. Funding National Key R&D Program of China; Training Plan for High level Public Health Technical Talents.

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