Shelenkov Andrey, Slavokhotova Anna, Mikhaylova Yulia, Akimkin Vasiliy
Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, Moscow, 111123, Russia.
BMC Microbiol. 2025 Jan 6;25(1):3. doi: 10.1186/s12866-024-03720-8.
The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the 'global clones of high risk'. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is more and more often used for these purposes, including the epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations.
In this database, we provide the results of a thorough genomic analysis of 61,857 genomes of a highly dangerous bacterial pathogen Klebsiella pneumoniae. Important isolate typing information including multilocus sequence typing (MLST) types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, the presence of CRISPR-Cas systems, and cgMLST profiles are given, and the information regarding the presence of AMR, virulence genes and plasmid replicons within the genomes is provided.
This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.11069018 . The database will facilitate selection of the proper reference isolate sets for any types of genome-based investigations. It will be helpful for investigations in the field of K. pneumoniae genomic epidemiology, as well as antimicrobial resistance analysis and the development of prevention measures against this important pathogen.
细菌感染在临床和社区环境中都是全球公共卫生保健面临的重大问题。近十年来，由于各种细菌物种获得并传播的抗菌药物耐药性（AMR）不断增加，尤其是那些引起医疗保健相关感染的细菌，使得细菌感染的治疗选择受到限制，这已成为世界卫生组织关注的一个危险问题。大量报告表明，AMR的传播通常由几种特定物种的谱系驱动，这些谱系通常被称为“高风险全球克隆”。因此，追踪属于此类克隆的分离株并研究其致病性和AMR获得机制至关重要。目前，基于全基因组的分析越来越多地用于这些目的，包括流行病学监测和对参与耐药性转移的移动元件的分析。然而，尽管可用细菌基因组呈指数增长，但其代表性通常缺乏统一性和支持元数据的可用性，这为此类研究造成了瓶颈。
在这个数据库中，我们提供了对61857个高度危险的细菌病原体肺炎克雷伯菌基因组进行全面基因组分析的结果。给出了重要的分离株分型信息，包括多位点序列分型（MLST）类型（STs）、将分离株分配到已知的全球克隆、荚膜（KL）和脂寡糖（O）类型、CRISPR-Cas系统的存在以及cgMLST图谱，并提供了有关基因组中AMR、毒力基因和质粒复制子存在情况的信息。
该数据库可在https://doi.org/10.5281/zenodo.11069018 以CC BY-NC-SA许可免费获取。该数据库将有助于为任何类型的基于基因组的研究选择合适的参考分离株集。它将有助于肺炎克雷伯菌基因组流行病学领域的研究，以及抗菌药物耐药性分析和针对这种重要病原体的预防措施的制定。
