Table 1_Genomic surveillance of the pneumonia outbreak caused by Mycoplasma pneumoniae among patients in Russia from January 2024 to June 2025.xlsx

BackgroundMycoplasma 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.
MethodsMP, 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.
ResultsMP 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.
ConclusionThis 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.

背景：肺炎支原体（Mycoplasma pneumoniae, MP）是引发呼吸道感染（包括社区获得性肺炎（community-acquired pneumonia, CAP））的主要病原体之一。本研究旨在对2024年1月至2025年6月期间俄罗斯联邦多个地区发生的MP所致肺炎暴发开展分子流行病学监测。方法：采用实时荧光定量PCR（real-time PCR）法，对482份社区获得性肺炎患者的鼻咽拭子标本进行MP检测及病毒、细菌共感染筛查。为探究与大环内酯类（macrolides）和喹诺酮类（quinolones）耐药相关的突变，本研究开发并使用了针对完整mgpA、23S、parC、parE、gyrA、gyrB基因的引物组（primer panels），随后开展高通量测序（high-throughput sequencing）。为验证MP的PCR检测结果，我们对75份血清标本采用了酶联免疫吸附试验（ELISA）。结果：经实时荧光定量PCR检测，81.5%的标本确诊为MP感染；经ELISA检测，69.3%的标本呈MP阳性。27.8%的标本检出细菌共感染，其中以流感嗜血杆菌（H. influenzae）最为常见，检出率为19.7%，其次为肺炎链球菌（S. pneumoniae，13.1%）和肺炎衣原体（C. pneumoniae，0.8%）。最常见的病毒共感染类型为呼吸道合胞病毒（RSV，16.2%）、鼻病毒（RV，14.7%）及人副流感病毒（hPIVs，9.5%）。与大环内酯类耐药相关的A2063G突变在23%的标本中被检出；另有6份标本（占1.8%）检出A2064G及A2064C点突变。对完整parC、parE、gyrA、gyrB基因的测序结果显示，未发现与喹诺酮类耐药相关的显著性突变。系统发育分析（phylogenetic analysis）表明，mgpA基因序列可分为两个明确的进化枝：97.2%的序列归为P1型1，剩余2.8%归为P1型2。结论：本研究揭示了新冠后时代（post-COVID-19 era）MP流行病学的根本性转变，即从周期性暴发转变为全年持续性地方性流行。本研究记录了疾病严重程度的升高、病毒与细菌共感染的动态谱特征，以及大环内酯类耐药率的显著地域异质性：各地区耐药率介于0%至50%之间。总体大环内酯类耐药率为23%，低于此前的报道。此外，对完整P1黏附素基因（P1 adhesin gene）的基因分型结果显示序列存在分化：大部分序列聚类于P1型1，少数聚类于P1型2。