Genomic epidemiology and antimicrobial susceptibility of clinical Mycoplasma pneumoniae isolates in Shanghai, 2023-2024.

INTRODUCTION

Mycoplasma pneumoniae (M. pneumoniae) is a leading cause of respiratory infection in school-age children. A global resurgence occurred in 2023-2024, yet whole-genome molecular epidemiology and antimicrobial susceptibility data remains limited.

METHODS

In this study, we isolated M. pneumoniae strains from children with respiratory infections in Shanghai, collected clinical record data, and profiled antibiotic susceptibility using the broth microdilution method. Whole-genome sequencing was performed on all isolates and globally available M. pneumoniae genomes from GenBank were incorporated for comparative analysis.

RESULTS

A total of 148 M. pneumoniae strains were isolated, among which 79.7% (118/148) were from patients diagnosed with severe M. pneumoniae pneumonia (SMPP). All isolates were highly resistant to macrolides but remained susceptible to tetracyclines and fluoroquinolones. Of note, P1-2-type strains showed lower resistance levels to azithromycin and 16-membered macrolides compared with P1-1. Although the predominant genotypes were still P1-1 (92.6%), ST3 (88.5%), and M4-5-7-2 (79.7%), several previously uncommon MLVA types-M3-5-7-2, M4-3-7-2, and M4-4-7-2-have increased in frequency since the COVID-19 pandemic and were associated with milder inflammatory responses. Genomic analysis revealed high conservation across strains. Notably, a higher number of hsdS gene homologs, which serve as epigenetic modulators, correlated with reduced SMPP incidence and lower CD3+/CD4+ T-cell counts.

DISCUSSION: In this study we provided the first comprehensive WGS analysis and updated MIC profiles of clinically isolated M. pneumoniae in Shanghai. Our findings highlight the persistent macrolide resistance and the emergence of genomic variations that warrant ongoing surveillance. High virulence carriage and high macrolides resistance may be among the factors contributing to elevated SMPP levels.