Tian Chongmei, Zhao Yaping, Dong Su, You Zhixin, Chen Jingbai, Xu Hongfeng, Fang Yuejuan, Zhang Yapei
Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang, China.
Department of Clinical Laboratory, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, Zhejiang, China.
Front Cell Infect Microbiol. 2025 May 9;15:1564277. doi: 10.3389/fcimb.2025.1564277. eCollection 2025.
To characterize a rare ST852 strain co-producing NDM-1 and KPC-2 isolated from a clinical patient.
Minimum inhibitory concentrations (MICs) were measured using a VITEK 2 compact system and broth microdilution. Conjugation experiments were conducted using film matings. Whole genome sequencing (WGS) was performed using Illumina and Nanopore platforms. Antimicrobial resistance determinants were identified using the ABRicate program in the ResFinder database. Insertion sequences (ISs) were identified using ISFinder. Bacterial virulence factors were identified using a virulence factor database (VFDB). Genome function annotation and classification were further analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups (COG) databases. Capsular polysaccharides (KL) and lipooligosaccharides (OCL) were tested using Kleborate with the . Multilocus sequence typing (MLST) and replicon types were identified using the Center for Genomic Epidemiology website. Prophage region analysis was performed using PHASTEST software. Conjugation-related elements were predicted using finder. The plasmid structure was visualized using Circos and similar plasmids in the public database were tracked using BacWGSTdb. A global phylogeny for the ST852 isolates was further performed.
KPSY isolate was identified as ST852, with KL18 and O3/O3a. It has an extensive drug-resistant (XDR) profile. WGS analysis revealed that it contained one circular chromosome and three plasmids. The results of the COG and KEGG functional classifications showed that most of the functions were associated with metabolism. pKPSY-2 is a 239,226-bp IncU plasmid carrying the carbapenem resistance gene . pKPSY-3 is a smaller plasmid belonging to the IncN-type conjugative plasmid with . Importantly, sequence, the T4SS region, T4CP, and relaxase were identified. Tracking of the plasmids showed they were identified in different species in different countries, including , sp., sp., and . Global analysis data showed 13 ST852 strains were mainly isolated from China (84.62%, 11/13), and the remaining isolates were collected from Switzerland.
This is the first study to identify an ST852 NDM-1-KPC-2 coproducing clinical isolate. Surveillance is warranted, and early detection of this high-risk clone in the clinic is recommended to avoid its extensive spread.
对从一名临床患者分离出的同时产NDM-1和KPC-2的罕见ST852菌株进行特征分析。
使用VITEK 2 compact系统和肉汤微量稀释法测定最低抑菌浓度（MIC）。通过膜杂交进行接合试验。使用Illumina和Nanopore平台进行全基因组测序（WGS）。使用ResFinder数据库中的ABRicate程序鉴定抗菌药物耐药决定簇。使用ISFinder鉴定插入序列（IS）。使用毒力因子数据库（VFDB）鉴定细菌毒力因子。使用京都基因与基因组百科全书（KEGG）和直系同源簇（COG）数据库进一步分析基因组功能注释和分类。使用Kleborate测试荚膜多糖（KL）和脂寡糖（OCL）。使用基因组流行病学中心网站鉴定多位点序列分型（MLST）和复制子类型。使用PHASTEST软件进行前噬菌体区域分析。使用finder预测接合相关元件。使用Circos可视化质粒结构，并使用BacWGSTdb追踪公共数据库中的相似质粒。进一步对ST852分离株进行全球系统发育分析。
KPSY分离株被鉴定为ST852，具有KL18和O3/O3a。它具有广泛耐药（XDR）谱。WGS分析显示它包含一条环状染色体和三个质粒。COG和KEGG功能分类结果表明，大多数功能与代谢相关。pKPSY-2是一个239,226 bp的IncU质粒，携带碳青霉烯耐药基因 。pKPSY-3是一个较小的质粒，属于IncN型接合质粒，带有 。重要的是，鉴定出了 序列、IV型分泌系统（T4SS）区域、T4CP和松弛酶。对 质粒的追踪显示它们在不同国家的不同物种中被鉴定出来，包括 、 属、 属和 。全球分析数据显示，13株ST852菌株主要从中国分离得到（84.62%，11/13），其余分离株从瑞士收集。
这是首次鉴定出一株产NDM-1-KPC-2的ST852临床分离株的研究。有必要进行监测，建议在临床上尽早发现这种高风险克隆，以避免其广泛传播。
