Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong, China.
Department of Paediatrics, Weifang People's Hospital, Weifang, Shandong, China.
Microb Pathog. 2024 Dec;197:107070. doi: 10.1016/j.micpath.2024.107070. Epub 2024 Oct 22.
This study aimed to analyze the prevalence, phenotypes, and carriage of resistance genes of carbapenem-resistant Klebsiella michiganensis strains isolated in our hospital.
ology: Four K. michiganensis strains were collected from January 2015 to December 2023. Antimicrobial susceptibility was tested using 21 antibiotics with the BD Phoenix™ M50 System. Whole-genome sequencing of the four strains was performed on an Illumina NovaSeq 6000 platform. Species identification was performed using Kleborate software, sequence type (ST) was performed using MLST, and prediction of antibiotic resistance genes and virulence genes were performed using ABRicate. PlasmidFinder was used to search for plasmids. Whole genome data from 211 strains of carbapenem-resistant K. michiganensis were downloaded from the NCBI database; together with the strains in this study, these data were used to construct an phylogenetic tree using genome single nucleotide polymorphisms (SNP).
Antimicrobial susceptibility showed that K. michiganensis was highly resistant to β-lactams. For the three carbapenems, strain WF0046 was only resistant to ertapenem, while WF0047, WF0052, and WF0053 were resistant to all three carbapenems tested. The four strains of K. michiganensis only showed complete sensitivity to polymyxin E and tigecycline. The four K. michiganensis strains were found to have 43 resistance genes, and all carried carbapenem resistance genes; WF0046 carried the carbapenem resistance gene bla, while the other three strains carried bla. Among the other resistance genes, β-lactam resistance genes were predicted most (11 types), followed by eight types of aminoglycoside resistance genes. Of the strains characterized in this study, WF0046 belonged to ST158, WF0047 belonged to ST40, WF0052 belonged to ST533, and WF0053 belonged to ST13. These four strains, along with 211 carbapenem-resistant K. michiganensis strains downloaded from NCBI, were divided into five clades; WF0052 belonged to clade A, WF0046 belonged to clade C, and WF0047 and WF0053 both belonged to clade D. The four strains had relatively distant genetic relationships; WF0046, WF0047, and WF0053 were closely related to strains of human origin from other regions of China, while WF0052 was genetically close with a strain of K. michiganensis isolated in the United States.
The strains of K. michiganensis from our hospital were resistant to multiple antibiotics, and all strains carried carbapenem resistance genes along with multiple other antibiotic resistance genes. The phylogenetic results showed that these four strains had distant genetic relationships and different ST types, indicating that they came from different sources and the possibility of polyclonal transmission.
本研究旨在分析我院分离的耐碳青霉烯类肺炎克雷伯菌的流行率、表型和耐药基因携带情况。
从 2015 年 1 月至 2023 年 12 月收集了 4 株 K. michiganensis 菌株。采用 BD Phoenix™ M50 系统对 21 种抗生素进行药敏试验。对 4 株菌进行全基因组测序，在 Illumina NovaSeq 6000 平台上进行。采用 Kleborate 软件进行种属鉴定，采用 MLST 进行序列型（ST）鉴定，采用 ABRicate 预测抗生素耐药基因和毒力基因。使用 PlasmidFinder 搜索质粒。从 NCBI 数据库下载了 211 株耐碳青霉烯类肺炎克雷伯菌的全基因组数据；将这些数据与本研究中的菌株一起，使用基因组单核苷酸多态性（SNP）构建系统发育树。
药敏结果显示，K. michiganensis 对β-内酰胺类抗生素高度耐药。对于三种碳青霉烯类药物，菌株 WF0046 仅对厄他培南耐药，而 WF0047、WF0052 和 WF0053 对三种测试的碳青霉烯类药物均耐药。这 4 株 K. michiganensis 对多粘菌素 E 和替加环素完全敏感。这 4 株 K. michiganensis 共携带 43 个耐药基因，均携带碳青霉烯类耐药基因；WF0046 携带碳青霉烯类耐药基因 bla，而其他三株菌携带 bla。在预测的耐药基因中，β-内酰胺类耐药基因最多（11 种），其次是氨基糖苷类耐药基因 8 种。本研究中鉴定的菌株 WF0046 属于 ST158，WF0047 属于 ST40，WF0052 属于 ST533，WF0053 属于 ST13。这 4 株菌和从 NCBI 下载的 211 株耐碳青霉烯类肺炎克雷伯菌分为 5 个分支；WF0052 属于分支 A，WF0046 属于分支 C，WF0047 和 WF0053 都属于分支 D。这 4 株菌的遗传关系较远；WF0046、WF0047 和 WF0053 与来自中国其他地区的人类来源菌株密切相关，而 WF0052 与美国分离的一株 K. michiganensis 遗传关系密切。
我院分离的 K. michiganensis 菌株对多种抗生素耐药，且均携带碳青霉烯类耐药基因及多种其他抗生素耐药基因。系统发育结果显示，这 4 株菌遗传关系较远，ST 型不同，提示它们来自不同来源，存在多克隆传播的可能性。
