Karpenko Anna, Shelenkov Andrey, Petrova Lyudmila, Gusarov Vitaly, Zamyatin Mikhail, Mikhaylova Yulia, Akimkin Vasiliy
Central Research Institute of Epidemiology, Novogireevskaya str., 3a, 111123, Moscow, Russia.
National Medical and Surgical Center named after N.I. Pirogov, Nizhnyaya Pervomayskaya str., 70, 105203, Moscow, Russia.
Heliyon. 2024 Nov 29;10(23):e40821. doi: 10.1016/j.heliyon.2024.e40821. eCollection 2024 Dec 15.
bacteria is a component of normal intestinal microflora of humans and animals, but can also be found in hospital settings causing urinary tract infections and sepsis. The problem of treating such infections is complicated by multidrug-resistant isolates producing extended spectrum beta-lactamases (ESBL), and the number of ESBL-carrying strains has significantly increased recently. This study presents a detailed analysis of 12 multidrug-resistant isolates obtained from the wounds of different patients in one surgical department of a multidisciplinary hospital in Moscow, Russia, using the short- and long-read whole genome sequencing. The isolates under investigation divided into two clusters (clones) C1 and C2 based on their genomic profiles and carried antimicrobial resistance (AMR) genes corresponding well with phenotypic profiles, which was the first case of reporting two different clones obtained simultaneously from the same specimens at one hospital, to the best of our knowledge. Some genes, including ESBL encoding ones, were specific for either C1 or C2 ( and , , correspondingly). Additionally, the genomic islands 1 were found that differed in composition of multiple antibiotic resistance regions between C1 and C2 groups. CRISPR-Cas system type I-E was revealed only in C2 isolates, while the same set of virulence factors was determined for both clones. Diversity of all genetic factors found in case of simultaneous existence of two clones collected from the same source at one department indicates high pathogenic potential of and poses a requirement of proper spreading monitoring. The data obtained will facilitate the understanding of AMR transfer and dynamics within clinical isolates and contribute to epidemiological surveillance of this pathogen.
细菌是人类和动物正常肠道微生物群的组成部分，但在医院环境中也可发现，会导致尿路感染和败血症。治疗此类感染的问题因产生超广谱β-内酰胺酶（ESBL）的多重耐药菌株而变得复杂，且携带ESBL的菌株数量最近显著增加。本研究使用短读长和长读长全基因组测序，对从俄罗斯莫斯科一家多学科医院一个外科不同患者伤口分离得到的12株多重耐药菌株进行了详细分析。根据基因组图谱，所研究的菌株分为两个簇（克隆）C1和C2，其携带的抗菌耐药（AMR）基因与表型特征非常吻合，据我们所知，这是首次在一家医院从同一标本中同时获得两个不同克隆的报道。一些基因，包括编码ESBL的基因，分别对C1或C2具有特异性（相应地为 和 ， ， ）。此外，还发现基因组岛1在C1和C2组之间的多个抗生素耐药区域组成上存在差异。仅在C2分离株中发现了I-E型CRISPR-Cas系统，而两个克隆的毒力因子组相同。在一个科室从同一来源同时存在两个克隆的情况下发现的所有遗传因素的多样性表明 具有高致病潜力，并对适当的传播监测提出了要求。所获得的数据将有助于理解临床分离株中AMR的转移和动态，并有助于对该病原体进行流行病学监测。
