What question did this study set out to answer?

The aim is to conduct molecular genetic surveillance of Mycoplasma pneumoniae pneumonia outbreaks in Russia.

March 29, 2026Open Access

Genomic surveillance of the pneumonia outbreak caused by Mycoplasma pneumoniae among patients in Russia from January 2024 to June 2025

Key Points

The aim is to conduct molecular genetic surveillance of Mycoplasma pneumoniae pneumonia outbreaks in Russia.
Collected 482 nasopharyngeal swabs from patients with community-acquired pneumonia (CAP).
Used real-time PCR to detect Mycoplasma pneumoniae and co-infections.
Developed primer panels for genes associated with resistance and employed high-throughput sequencing.
Applied ELISA on 75 serum samples to confirm PCR results.
Confirmed Mycoplasma pneumoniae in 81.5% of samples via PCR and 69.3% via ELISA.
Identified bacterial co-infections in 27.8% of samples, most commonly H. influenzae (19.7%).
Detected macrolide resistance mutation A2063G in 23% of samples.
Phylogenetic analysis revealed two distinct clades of the mgpA gene.

Abstract

Background Mycoplasma pneumoniae (MP) is one of the major pathogens that causes respiratory tract infections, including community-acquired pneumonia (CAP). The aim of the current study was to conduct molecular genetic surveillance of an outbreak of pneumonia caused by MP in various regions of the Russian Federation between January 2024 and June 2025. Methods MP, viral and bacterial co-infections were detected in 482 nasopharyngeal swabs from patients with CAP using real-time PCR method. To investigate the mutations associated with resistance to macrolides and quinolones we describe the development and usage of primer panels for the complete mgpA , 23S, parC , parE , gyrA , gyrB genes followed by high-throughput sequencing. To support the results of PCR for MP we applied the ELISA for 75 serum samples. Results MP was confirmed in 81.5% samples by real-time PCR and in 69.3% samples by ELISA. Bacterial co-infections were identified in 27.8% samples. H. influenzae was the most prevalent, detected in 19.7% samples, followed by S. pneumoniae (13.1%) and C. pneumoniae (0.8%). The most prevalent viral co-infections were RSV (16.2%), RV (14.7%), and hPIVs (9.5%). The A2063G mutation associated with macrolide resistance was found in 23% samples. Point mutations, A2064G and A2064C, were detected in 6 samples (1,8%). No significant mutations associated with resistance to quinolones were identified according to the sequencing of complete parC , parE , gyrA , gyrB genes. The phylogenetic analysis revealed that the mgpA gene sequences formed two distinct clades, 97.2% were classified as P1 type 1, while the remaining 2.8% were classified as P1 type 2. Conclusion This study demonstrates a fundamental shift in the epidemiology of MP in the post-COVID-19 era, characterized by a transition from cyclical epidemics to year-round endemic circulation. We document increased disease severity, a dynamic profile of viral and bacterial co-infections, and significant geographic heterogeneity in macrolide resistance rates, which ranged from 0% to 50% across regions. The overall macrolide resistance rate was 23%, which is lower than previously reported. Furthermore, genotyping of the complete P1 adhesin gene revealed divergence, with a majority of sequences clustering within P1 type 1 and a minority within P1 type 2.

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