从中国一条城市河流中分离出的产NDM-5肠杆菌科细菌的全基因组分析
Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China.
作者信息
Li Ying, Tang Min, Dai Xiaoyi, Zhou Yingshun, Zhang Zhikun, Qiu Yichuan, Li Chengwen, Zhang Luhua
机构信息
Department of Immunology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.
Immunological Technology Platform, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.
出版信息
Infect Drug Resist. 2021 Oct 27;14:4427-4440. doi: 10.2147/IDR.S330787. eCollection 2021.
PURPOSE
Three NDM-5-producing Enterobacteriaceae (, and , one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis.
METHODS
In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of -harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the -harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome.
RESULTS
Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, was carried by an IncX3 plasmid in , and on an IncR/IncX1 plasmid in . Conjugation experiments showed that these -haboring plasmids were successfully transferred to J53. Phylogenetic analysis revealed that SCLZR49 was present in a cluster with isolates of different origin, SCLZR50 was mainly clustered with clinical isolates, and SCLZR53 had closely genetic relationship with environmental isolates.
CONCLUSION
This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene , raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the "One-Health" perspective.
目的
在中国城市河流中产碳青霉烯酶肠杆菌科细菌（CPE）菌株的筛查研究中，分离出三株产NDM-5的肠杆菌科细菌（分别为 、 和 ，各一株）。本研究的目的是通过全基因组分析对这些产NDM-5的分离株进行特征描述。
方法
采用肉汤微量稀释法进行体外药敏试验。进行接合试验以研究携带 的质粒的可转移性。使用Illumina HiSeq结合PacBio RSII系统进行全基因组测序。分析携带 的质粒的遗传特征。从基因组序列中鉴定抗菌抗性基因和毒力基因。基于核心基因组进行系统发育分析。
结果
药敏试验表明，所有三株分离株均对碳青霉烯类、头孢菌素类、喹诺酮类和氨基糖苷类耐药，对黏菌素敏感。全基因组测序表明，每株分离株都携带多个介导多重耐药的抗生素抗性基因，并含有大量毒力基因，其中一些位于质粒上。在这些分离株中， 在 中由IncX3质粒携带，在 中由IncR/IncX1质粒携带。接合实验表明，这些携带 的质粒成功转移至J53。系统发育分析显示，SCLZR49与不同来源的分离株聚类在一起，SCLZR50主要与临床分离株聚类，SCLZR53与环境分离株有密切的遗传关系。
结论
本研究揭示了具有临床意义的碳青霉烯酶基因 在城市河流生态系统中的污染，增加了质粒从人类传播到环境中的可能性，并强调了在“同一健康”视角下对环境中CPE进行持续监测的必要性。
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