To investigate the genomic features and perform cluster analysis of Carbapenem-resistant Klebsiella pneumoniae (CRKP) to provide an experimental basis for guiding the prevention and treatment of CRKP infections.A retrospective case-cohort study was conducted on 19 non-redundant CRKP strains isolated from the Tenth Affiliated Hospital of Southern Medical University between January and June 2023. Whole genome sequencing (WGS) and multilocus sequence typing (MLST) were performed to compare genomic features and analyze the resistance genes and homology of the strains.The results showed that the 19 CRKP strains were isolated from 8 different clinical departments, mainly from respiratory specimens. The whole genome sequencing revealed that the genomic lengths of CRKP ranged from 4.90 to 5.85 Mbp, with contigs N50 values>20 kb for each genome. The median overall GC content was 57.0% (50.4%-57.1%). Comparative genomic analysis identified three regions with high genomic variability. WGS detected 32 resistance genes across 11 categories. All 19 strains carried carbapenem resistance genes (blaKPC-2 and blaOXA-48), blaTEM-1B extended-spectrum β-lactamase resistance genes, qnrS1 quinolone resistance gene, and fosA fosfomycin resistance gene, with each strain carrying only one carbapenemase gene. The detection rate of blaKPC-2 was 94.7% (18/19). MLST identified three sequence types: ST11, ST437 and ST147, with ST11 being predominant (89.5%, 17/19). Clustering analysis based on acquired resistance genes revealed three clonal transmission patterns among strains 72 and 90, and strains 88, 84, 66 and 79.In conclusion, CRKP strains carry multiple resistance genes, and clustering analysis indicating that nosocomial clonal transmission is closely related to acquired resistance genes. The ST11-blaKPC-2 type strain is the predominant clone. Strengthened surveillance and effective control strategies are necessary to reduce nosocomial transmission of CRKP.
探讨碳青霉烯类耐药肺炎克雷伯菌（CRKP）基因组特征并进行相关聚类分析，为防治CRKP引起的感染提供实验依据。采用回顾性病例-队列研究方法，对2023年1—6月南方医科大学第十附属医院临床非重复的19株CRKP进行全基因组测序（WGS）分析和多位点序列分型（MLST），比较菌株间基因组特征，对菌株携带的耐药基因及同源性进行相关聚类分析。结果显示，19株CRKP分离自8个不同临床科室，主要来源于呼吸道标本。全基因组测序结果显示CRKP基因组长度在4.90~5.85 Mbp之间，每个CRKP基因组的重叠群（contigs）N50均>20 kb；总体GC含量中位数M（Q1，Q3）为 57.0%（50.4%，57.1%）；比较基因组特征发现3个基因组变异度较高的区域。WGS检测到11类共32种耐药基因，19株CRKP均携带碳青霉烯类耐药基因（blaKPC-2和blaOXA-48）、blaTEM-1B超广谱β-内酰胺酶耐药基因、qnrS1喹诺酮类耐药基因和fosA磷霉素耐药基因，且每株菌仅携带一种碳青霉烯酶基因，blaKPC-2检出率高达94.7%（18/19）。MLST分型为ST11、ST437和ST147三种型别，ST11型占89.5%（17/19），属优势克隆型别，以获得性耐药基因为基础作聚类分析，发现菌株72和菌株90，菌株88、84、66和菌株79等耐药基因聚类分析较为接近，存在3个克隆传播模式。综上，CRKP菌株同时携带多种耐药基因，聚类分析显示院内克隆传播与获得性耐药基因密切相关，以ST11-blaKPC-2型菌株为优势菌株，应加强CRKP监控，并制定有效的防控策略，以减少院内传播。.