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Macrolide-resistant Mycoplasma pneumoniae resurgence in Chinese children in 2023: a longitudinal, cross-sectional, genomic epidemiology study
Chao Yan,Shanwei Tong, Yarong Wu, Yujie Chen,Xinyu Jia,Yan Guo,Mengnan Cui,Guangqian Pei, Zuming Zhang, Hao Zhou, BAdmin , Kai Mu,Xue Ren,Bing Du, Hanqing Zhao,Yanling Feng,Jinghua Cui,Yuyan Xia, MBBS , Zhen Wang, Yu Sun,Prof Linqing Zhao, Prof Chuangli Hao, Zhijie Zhu, Shengqiang Luo, Han Zhang, Yongjun Wang , Prof Lili Zhong, DehuiChen , Prof Yong Yin , Longji Hu, Prof Yuehua Ke, Prof Guanhua Xue, Prof Ling Cao, , Prof Xavier Didelot, Prof Jing Yuan, Prof Yujun Cui,
Background: After a prolonged period of low detection rates, Mycoplasma pneumoniae resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen.
Methods: We sequenced 685 M pneumoniae isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013–22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen’s evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China.
Findings: Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China’s large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China.
Interpretation: Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen.