Lower respiratory tract microbiome during the 2023–2024 pediatric Mycoplasma pneumoniae epidemic: age-specific microbial shifts, macrolide resistance, and co-infection profiles

Objective Recurrent outbreaks of macrolide-resistant Mycoplasma pneumoniae (MP) pneumonia pose substantial health risks to children. This study aimed to characterize the demographic–epidemiological features of pediatric MP pneumonia during 2023–2024 and to explore macrolide-resistance mutations, co-infecting pathogens, and age-specific disturbances in the lower-respiratory-tract microbiome. Methods A single-center retrospective study was conducted based on 255 bronchoalveolar lavage fluid metagenomic next-generation sequencing samples collected from hospitalized children diagnosed with pneumonia at Peking University First Hospital from June 1, 2023 to May 31, 2024. All enrolled cases were divided into MP-positive/-negative and age‐stratified subgroups to compare demographic features, pathogen distribution, and respiratory microbial diversity. Results In this cohort, MP was detected in 188 of 255 patients (73.7%), with the highest infection rate of 84.0% in those aged 6–11 years. Epidemiological seasonal analysis showed that MP prevalence peaked in autumn at 91.7%, followed by winter with a prevalence of 75.6%. Among all MP-positive specimens, 73.4% (138/188) harbored macrolide-resistant 23S rRNA A2063G mutation. The highest proportion was observed in the 6–11 age group (101/131, 77.1%). The predominant co-pathogens were Streptococcus pneumoniae , Haemophilus influenzae , human adenovirus, human bocavirus, and rhinovirus. Compared with the non-MP group, patients with MP infection presented markedly lower Shannon and Simpson indices ( p < 0.001) and decreased microbial species evenness. Microbiome analysis revealed alterations in the respiratory microbiome in MP-infected children. Age-stratified microbial analysis demonstrated that pulmonary microbial α-diversity increased progressively with age and total microbial burden was weakly positively correlated with age ( R = 0.17, p = 0.0055). Children aged under 3 years were predominantly colonized with Streptococcus species and multiple respiratory viruses, whereas adolescents aged 12–18 years harbored higher levels of commensal microbes including Cutibacterium acnes and Prevotella species. Conclusions The 2023–2024 MP epidemic predominantly affected school-aged children aged 6–11 years accompanied with a high prevalence of 23S rRNA A2063G macrolide resistance. MP-infected children exhibited reduced microbial diversity. The pediatric lower respiratory microbiome exhibited distinct age-dependent variations in diversity, microbial load, and community composition. The study provides age-specific evidence for diagnosis, anti-infective strategy formulation, and microbiome intervention of pediatric MP pneumonia.