Genomic‐Based Epidemiological Analysis of the Post‐Pandemic Mycoplasma pneumoniae Resurgence

TL;DR

This study tracks the resurgence of Mycoplasma pneumoniae in China after the pandemic, identifying new genetic lineages and a common mutation linked to resistance.

Contribution

The study introduces a new sequencing method and identifies three new Chinese clades of M. pneumoniae during the post-pandemic resurgence.

Findings

Three new main Chinese clades of M. pneumoniae emerged and co-circulated in China.

96.31% of isolates had the A2063G mutation, suggesting potential drug resistance.

Phylogenetic analysis revealed six distinct global lineages of M. pneumoniae.

Abstract

Mycoplasma pneumoniae infections resurged globally in 2023–2024 following a significant decline during the coronavirus disease 2019 (COVID‐19) pandemic. To understand the genomic epidemiology of this resurgence in China, a nationwide 1‐year genomic surveillance identified 9907 patients infected with M. pneumoniae, resulting in an overall positive rate of 10.05%. We developed a hybrid capture‐based targeted next‐generation sequencing (hc‐tNGS) assay, obtaining 271 high‐quality genomes directly from clinical samples. Phylogenetic analysis of a global collection of 562 M. pneumoniae genomes identified six distinct lineages, including three newly emerged main Chinese clades (MCCs) that co‐circulated across various regions of China. Among these MCCs, one clade, comprising P1‐1, ST17, and L4, was localized in Taiwan, while two others—P1‐1, ST3, and L6 clade, and P1‐2, ST14 and L2 clade—co‐circulated in different regions of China during the 2023–2024 epidemic season. Notably, 96.31% of the isolates identified in this study exhibited a point mutation, primarily A2063G (95.94%). This study offers a comprehensive genomic characterization of the post‐pandemic M. pneumoniae resurgence in China, highlighting the emergence and spread of resistant clades. These findings emphasize the importance of adopting a One Health approach to address the potential global public health threats posed by this resurgent pathogen.

Phylogenetic analysis of a global collection of 562 M. pneumoniae genomes revealed six distinct lineages, including three newly emerged main Chinese clades (MCCs) that co‐circulated in various regions of China. The recent emergence of these distinct clades and their differing geographical distributions may suggest ongoing divergent evolution within the species or indicate specific transmission patterns.

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