摘要
目的分析全球屎肠球菌耐药基因分布、序列分型(ST)及流行特点,以期为抗菌药物的合理使用和院内感染防控提供理论依据。方法从美国国家生物技术信息中心数据库(NCBI)下载了3256个屎肠球菌基因组序列,并通过Perl程序从GenBank文件中提取核酸序列,使用Prodigal软件进行注释。利用CheckM v1.1.3和Quest 5.0.2软件对基因组进行质量过滤,筛选出2235个高质量基因组。随后构建了一个结构化的耐药基因数据库,并使用blastn软件比对基因组中的基因,详细分析其耐药基因分布。同时,从pubMLST网站获取了7个屎肠球菌看家基因序列文件及其Profile文件,通过blastn比对得到ST。通过Perl程序从基因组的GenBank文件中提取关键菌株信息,包括分离时间、国家、宿主及样本来源,并进行深入分析。结果多位点ST分析显示,ST17(104,6.9%)是全球屎肠球菌中的主要序列类型。耐药基因检测显示,99.7%的菌株检测出氨基糖苷类耐药基因,而94.0%的菌株携带大环内酯类/链阳菌素耐药基因。结论全球屎肠球菌的ST以ST17型为主,中国的屎肠球菌分型以ST78为主。全球和中国最常见的耐药基因是抗氨基糖苷类的aac(6)-I基因。为规范抗菌药物使用,加强屎肠球菌的监测力度并有效防控院内感染,从而防止其大规模流行,需要加强对耐药基因携带情况的监测和研究。
Objective To analyze the global distribution,sequence types(ST),and epidemiological characteristics of antibiotic-resistant genes among global Enterococcus faecium,providing insights for antimicrobial agent usage and nosocomial infection control.Methods A total of 3256 genomic sequences of Enterococcus faecium were obtained from the national center of biotechnology information(NCBI)website.Nucleotide sequences were extracted from GenBank files using Perl,and annotation was conducted using Prodigal.Quality filtering of each genome was performed with CheckM v1.1.3 and Quest 5.0.2 software,resulting in 2235 high-quality genomes for further analysis.A structured antibiotic-resistant genes(ARGs)database was constructed,and genomic sequences were aligned against it using blastn for detailed ARGs distribution analysis.7 Enterococcus faecium housekeeping gene sequence and profile files were obtained from the pubMLST website and underwent blastn alignment to determine ST results.Strain information,including isolation time,country,host,and sample sourcewas extracted from GenBank files using Perl for comprehensive analysis.Results Multilocus sequence typing results revealed ST17 as the predominant global sequence type,with 104 strains detected(6.9%).ARGs detection indicated that 99.7%of strains harbored aminoglycoside-resistant genes,and 94.0%carried macrolide/lincosamide/streptogramin B-resistant genes.Conclusions Global Enterococcus faecium ST is predominantly characterized by ST17,while in China,ST78 is predominant.The most prevalent ARG globally and in China is aac(6)-I,conferring resistance to aminoglycosides.Strengthening monitoring and research on ARGs carriage is imperative to standardize antimicrobial usage,enhance surveillance and control of Enterococcus faecium infections in healthcare settings,and prevent widespread occurrence.
作者
严茹钰
沈瀚
曹小利
Yan Ruyu;Shen Han;Cao Xiaoli(Department of Laboratory Medicine,Nanjing Drum Tower Hospital,Clinical College of Nanjing University of Chinese Medicine,Nanjing Jiangsu 210008,China)
出处
《中华临床实验室管理电子杂志》
2025年第1期27-34,共8页
Chinese Journal of Clinical Laboratory Management(Electronic Edition)
基金
国家自然科学基金项目(81902124)。
关键词
屎肠球菌
耐药基因
序列分型
流行分布
Enterococcus faecium
antibiotic resistance genes
sequence types
epidemic distribution
