Genomic study substantiates the intensive care unit as a reservoir for carbapenem-resistant Klebsiella pneumoniae in a teaching hospital in China.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
Shuo Jiang, Zheng Ma, Huiluo Cao, Li Mo, Jinlan Jin, Bohai Yu, Kankan Chu, Jihua Hu
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Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has recently emerged as a notable public health concern, while the underlying drivers of CRKP transmission among patients across different healthcare facilities have not been fully elucidated. To explore the transmission dynamics of CRKP, 45 isolates were collected from both the intensive care unit (ICU) and non-ICU facilities in a teaching hospital in Guangdong, China, from March 2020 to August 2023. The collection of clinical data and antimicrobial resistance phenotypes was conducted, followed by genomic data analysis for these isolates. The mean age of the patients was 75.2 years, with 18 patients (40.0%) admitted to the ICU. The predominant strain in hospital-acquired CRKP was sequence type 11 (ST11), with k-locus type 64 and serotype O1/O2v1 (KL64:O1/O2v1), accounting for 95.6% (43/45) of the cases. The CRKP ST11 isolates from the ICU exhibited a low single nucleotide polymorphism (SNP) distance when compared to isolates from other departments. Genome-wide association studies identified 17 genes strongly associated with SNPs that distinguish CRKP ST11 isolates from those in the ICU and other departments. Temporal transmission analysis revealed that all CRKP isolates from other departments were genetically very close to those from the ICU, with fewer than 16 SNP differences. To further elucidate the transmission routes among departments within the hospital, we reconstructed detailed patient-to-patient transmission pathways using hybrid methods that combine TransPhylo with an SNP-based algorithm. A clear transmission route, along with mutations in potential key genes, was deduced from genomic data coupled with clinical information in this study, providing insights into CRKP transmission dynamics in healthcare settings.

基因组研究证实中国一家教学医院的重症监护室是耐碳青霉烯类肺炎克雷伯菌的 "蓄水池"。
耐碳青霉烯类肺炎克雷伯氏菌(CRKP)近来已成为一个值得关注的公共卫生问题,而CRKP在不同医疗机构的患者间传播的根本原因尚未完全阐明。为了探索CRKP的传播动态,研究人员于2020年3月至2023年8月期间从中国广东一家教学医院的重症监护室(ICU)和非ICU设施中收集了45株分离株。收集了这些分离物的临床数据和抗菌药耐药性表型,并对其进行了基因组数据分析。患者的平均年龄为 75.2 岁,其中 18 名患者(40.0%)住进了重症监护室。医院获得性 CRKP 的主要菌株是序列 11 型(ST11),k-locus 64 型和血清型 O1/O2v1 (KL64:O1/O2v1)占 95.6%(43/45)。与来自其他科室的分离株相比,来自重症监护室的CRKP ST11分离株表现出较低的单核苷酸多态性(SNP)距离。全基因组关联研究发现了17个与SNP密切相关的基因,这些基因将CRKP ST11分离株与重症监护室和其他科室的分离株区分开来。时间传播分析表明,来自其他科室的所有CRKP分离株与来自重症监护室的分离株在基因上非常接近,SNP差异少于16个。为了进一步阐明医院内各科室之间的传播途径,我们采用 TransPhylo 与基于 SNP 的算法相结合的混合方法重建了详细的患者间传播途径。在这项研究中,我们从基因组数据和临床信息中推断出了一条清晰的传播途径以及潜在的关键基因突变,为我们深入了解 CRKP 在医疗机构中的传播动态提供了依据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Microbial Genomics
Microbial Genomics Medicine-Epidemiology
CiteScore
6.60
自引率
2.60%
发文量
153
审稿时长
12 weeks
期刊介绍: Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.
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