Abdirassilova Aigul A, Yessimseit Duman T, Kassenova Altynai K, Abdeliyev Beck Z, Zhumadilova Zauresh B, Tokmurziyeva Gulnara Zh, Kovaleva Galina G, Abdel Ziyat Zh, Meka-Mechenko Tatiyana V, Umarova Saule K, Begimbayeva Elmira Zh, Agzam Sanzhar D, Motin Vladimir L, Reva Oleg N, Rysbekova Altyn K
National Scientific Center of Especially Dangerous Infections named after Masgut Aikimbayev, Laboratory of Molecular-Genetic Studies, Almaty, Kazakhstan.
National Scientific Center of Especially Dangerous Infections named after Masgut Aikimbayev, Almaty, Kazakhstan.
PLoS Negl Trop Dis. 2025 Sep 12;19(9):e0013533. doi: 10.1371/journal.pntd.0013533. eCollection 2025 Sep.
The genetic diversity and biovar classification of Yersinia isolates from Central Asia were investigated using whole-genome sequencing. In total, 98 isolates from natural plague foci were sequenced using the MiSeq platform. Computational pipelines were developed for accurate assembly of Y. pestis replicons, including small cryptic plasmids, and for identifying genetic polymorphisms. A panel of 99 diagnostic polymorphisms was established, enabling the distinction of dominant Medievalis isolates derived from desert and upland regions. Evidence of convergent evolution was observed in polymorphic allele distributions across genetically distinct Y. pestis biovars, Y. pseudotuberculosis, and other Y. pestis strains, likely driven by adaptation to similar environmental conditions. Genetic polymorphisms in the napA, araC, ssuA, and rhaS genes, along with transposon and CRISPR-Cas insertion patterns, were confirmed as suitable tools for identifying Y. pestis biovars, although their homoplasy suggests limited utility for phylogenetic inference. Notably, a novel cryptic plasmid, pCKF, previously associated with the strain of the population 2.MED0 from the Central-Caucasus high-altitude autonomous plague focus, was detected in a genetically distinct isolate of 2.MED1 population from the Ural-Embi region, indicating potential plasmid transfer across the 2.MED lineage. These findings emphasize the need for ongoing genomic surveillance to monitor the spread of virulence-associated genetic elements and to improve our understanding of Y. pestis evolution and ecology.
利用全基因组测序技术对从中亚分离出的耶尔森氏菌的遗传多样性和生物变种分类进行了研究。总共使用MiSeq平台对来自自然鼠疫疫源地的98株分离菌进行了测序。开发了计算流程，用于准确组装鼠疫耶尔森氏菌的复制子，包括小型隐蔽质粒，并用于识别遗传多态性。建立了一组99个诊断性多态性位点，能够区分源自沙漠和高地地区的主要中世纪型分离菌。在遗传上不同的鼠疫耶尔森氏菌生物变种、假结核耶尔森氏菌和其他鼠疫耶尔森氏菌菌株的多态等位基因分布中观察到趋同进化的证据，这可能是由对相似环境条件的适应所驱动的。napA、araC、ssuA和rhaS基因中的遗传多态性，以及转座子和CRISPR-Cas插入模式，被确认为识别鼠疫耶尔森氏菌生物变种的合适工具，尽管它们的同塑性表明其在系统发育推断中的效用有限。值得注意的是，在来自乌拉尔-恩比地区的2.MED1种群的一个遗传上不同的分离菌中检测到了一种新型隐蔽质粒pCKF，该质粒先前与来自中高加索高海拔自主鼠疫疫源地的2.MED0种群的菌株有关，这表明在2.MED谱系中可能存在质粒转移。这些发现强调了持续进行基因组监测的必要性，以监测与毒力相关的遗传元件的传播，并增进我们对鼠疫耶尔森氏菌进化和生态学的理解。
