马腺疫链球菌马亚种新疆株XJ 5012的全基因组解析及其耐药性分析  

Whole genome sequencing and antimicrobial resistance analysis of Streptococcus equi subsp.equi XJ 5012 strain isolated from Xinjiang

作　　者：张雨薇 汪丽 吕芬芬 苏艳[1] ZHANG Yuwei;WANG Li;LYU Fenfen;SU Yan(College of Veterinary Medicine,Xinjiang Agricultural University,Urumqi 830052,China)

机构地区：[1]新疆农业大学动物医学学院,新疆乌鲁木齐830052

出　　处：《中国兽医学报》2024年第6期1175-1183,1193,共10页Chinese Journal of Veterinary Science

基　　金：自治区“三农”骨干人才培养资助项目(2023SNGGGCC001);国家自然科学基金资助项目(U1803108)。

摘　　要：为了解新疆地区马腺疫链球菌(Streptococcus equi subsp.equi,S.equi)分离株XJ 5012的基因组特征,探究其毒力及进化、耐药表型及耐药基因型的相关性,为马腺疫的有效防控提供理论依据。本研究对S.equi XJ 5012进行了全基因组测序,对获得的测序序列进行16S rRNA进化、SeM基因分型、耐药基因及毒力基因的比较与分析,并对其进行了抗菌药物敏感性试验。药敏试验结果表明,该菌对阿莫西林、氨苄西林、头孢呋辛、头孢噻呋、头孢西丁、链霉素、红霉素、土霉素、左氧氟沙星、诺氟沙星、环丙沙星、利福平、克林霉素、磺胺嘧啶钠共14种抗菌药物敏感,对青霉素、庆大霉素、克拉霉素、多西环素、四环素、恩诺沙星共6种抗菌药物耐药。全基因组测序结果表明,S.equi XJ 5012基因组大小为2.21 Mb,GC含量为41.31%,含有2264个编码基因。耐药基因数据库注释分析的结果显示,该菌株携带有135个耐药相关基因,且耐药基因主要分为大环内脂类、喹诺酮类、氨基糖苷类、多肽类、四环素和β-内酰胺类抗生素耐药基因,耐药基因的携带情况与药敏试验验结果具有明显的一致性。毒力基因数据库注释显示该菌株携带197个毒力相关基因,主要包括黏附、抗吞噬、胞外酶、分泌、铁摄取等毒力基因。基于16S rRNA基因构建系统发育树显示菌株XJ 5012与S.equi 4047亲缘关系最近;基于SeM基因分型分析结果显示S.equi XJ 5012为SeM-217,该基因型与新疆地区分离株的SeM-209、SeM-215及国外分离株的SeM-195和SeM-196亲缘关系较近。本研究利用第3代测序技术对XJ 5012基因组进行深度测序分析,为更全面深入地认识该菌的基因组、分子流行特征及耐药性提供了参考,并为今后S.equi感染的防控及致病机制研究奠定试验基础。In order to explore the genomic characteristics,its virulence,evolution,the correlation between drug resistance phenotype and resistance genes of S.equi XJ 5012,to laid a theoretical basis for efficient prevention and control of strangles,whole genome sequencing was investigated.In this study,the antimicrobial suceptibility of S.equi XJ 5012 was tested by the paper disk method and its whole genome was sequenced,Then the 16S rRNA evolution,SeM genotyping,antibiotic resistance gene and virulence gene were compared and analyzed.Drug susceptibility results showed that S.equi XJ5012 was sensitive to 13 antibiotics,such as amoxicillin,ampicillin,cefuroxime,cefotiofur,cefoxitin,streptomycin,erythromycin,oxytetracycline,levofloxacin,norfloxacin,ciprofloxacin,rifampicin,clindamycin,sulfadiazine sodium,and resistant to 6 antibiotics,such as penicillin,gentamicin,clarithromycin,doxycycline,tetracycline and sulfonamide isoxazole.The whole genome sequencing results of showed that the genome size of S.equi XJ 5012 was 2.21 Mb,the GC content was 41.31%and this strain has 2264 code genes.Antibiotic resistance genes database(ARDB)indicated that the S.equi XJ 5012 carried 135 drug resistance gene,among which the resistance genes mainly were macrocyclic lipids,fluoroquinolones,aminoglycosides,peptides,tetracyclines andβ-lactam antibiotics,correlating well with the results of drug susceptibility test.Virulence Factors Database(VFDB)indicated that S.equi XJ 5012 carried 197 virulence genes include adhesion,antiphagocytosis,extracellular enzyme encoding,secrtion,and iron uptake.The phylogenetic tree based on16S rRNA gene confirmed that the strain XJ 5012 was closely related to S.equi 4047.The results of SeM genotyping revealed that S.equi XJ 5012 was SeM-217,which was closely related to Xinjiang isolates SeM-209 and SeM-215 and foreign isolates SeM-195 and SeM-196.In this study,the whole genome sequencing analysis of S.equi XJ 5012 based on the third generation sequencing technology is the first report on the genome of S.equi in Chin

关 键 词：马腺疫链球菌XJ 5012 全基因组测序 SeM基因分型 耐药特性分析 进化分析 

分 类 号：S852.61[农业科学—基础兽医学]