Distribution of van genes and sequence typing of Enterococcus faecium based on NCBI database
10.13602/j.cnki.jcls.2025.06.13
- VernacularTitle:基于NCBI数据库的粪肠球菌van基因的分布及序列分型分析
- Author:
Yayun CHEN
1
;
Huilin WAN
1
Author Information
1. 江苏卫生健康职业学院附属南京市高淳人民医院医学检验科,南京 211300
- Publication Type:Journal Article
- Keywords:
Enterococcus faecalis;
van gene;
sequence type;
vancomycin-resistant Enterococci
- From:
Chinese Journal of Clinical Laboratory Science
2025;43(6):457-460
- CountryChina
- Language:Chinese
-
Abstract:
Objective To analyze the global distribution characteristics,sequence typing(ST),and the distribution of van genes in Enterococcus faecium globally to provide reference for the prevention,control and clinical treatment of glycopeptide-resistant strains in-fection.Methods This study used Aspera software to download all Enterococcus faecium genome sequence data from NCBI in batches up to December 7,2023.The nucleotide sequences and strain metadata of all genomes were then extracted from the downloaded GBK files using a Perl script.The sequence data of van resistance genes were obtained from the NCBI Pathogen Antimicrobial Resistance Gene Database and analyzed using BLASTN software to determine their distribution across genomes.For the ST analysis,allele se-quence files for seven housekeeping genes of Enterococcus faecium were downloaded from pubMLST website,and all of the strains were sequence typed using a self-developed ST_tool.Results A total of 2 781 Enterococcus faecium genomes were obtained,with isolation dates ranging from 1920 to 2023,showing an increasing peak of isolation rates observed in 2019.In terms of geographic distribution,China,the United States,and New Zealand accounted for 15.61％(434 strains),12.87％(358 strains),and 5.57％(155 strains)of the isolates,respectively,and ranked in the top three.A total of 771 strains originated from human samples,primarily isolated from u-rine(168 strains),feces(154 strains),and rectal swabs(69 strains).In terms of ST,2 781 Enterococcus faecium strains were clas-sified into 359 STs,with ST16(188 strains,7.29％),ST6(178 strains,6.90％),and ST179(150 strains,5.82％)being the pre-dominant types.On the national level,the dominant STs in the United States,China,and New Zealand were ST6(10.71％),ST16(9.59％),and ST108(67.10％),respectively.Additionally,282 Enterococcus faecium strains carried glycopeptide resistance genes,mainly vanA(207 strains)and vanB(72 strains),with ST108(100 strains)and ST6(43 strains)being the predominant types asso-ciated with vanA and vanB,respectively.Conclusion There are significant regional differences in the distribution of Enterococcus fae-cium globally.The vanA and vanB glycopeptide resistance genes are prevalent among resistant strains and exhibit a trend toward multi-drug resistance evolution,highlighting the need for enhanced clinical monitoring and control measures.
