1株鸭疫里默氏杆菌的全基因组测序及耐药性与遗传进化分析

doi:10.16431/j.cnki.1671-7236.2023.03.028

中国畜牧兽医 ›› 2023, Vol. 50 ›› Issue (3): 1140-1149.doi: 10.16431/j.cnki.1671-7236.2023.03.028

1株鸭疫里默氏杆菌的全基因组测序及耐药性与遗传进化分析

祝希辉¹, 李艳兰¹, 王志伟¹, 庞喆羽¹, 李玉保¹, 刘成¹, 司振书¹, 路建彪¹, 曹胜亮¹, 薛希娟²

1. 聊城大学农学与农业工程学院, 聊城 252059,;
2. 山东信得科技股份有限公司, 青岛 266000

收稿日期:2022-07-18 出版日期:2023-03-05 发布日期:2023-03-02
通讯作者: 李玉保 E-mail:liyubao@lcu.edu.cn
作者简介:祝希辉,E-mail:1059900375@qq.com。
基金资助:
山东省重点研发计划项目(2022CXGC010606、2019QYTPY011);聊城大学畜牧学学科开放课题(319312101-04);山东省自然科学基金(ZR2020MC175、ZR202112010377);科技部科技伙伴计划(KY202204002)

Whole Genome Sequencing of a Resistant Riemerella anatipestifer Strain and Analysis of Antibiotic Resistance and Genetic Evolution

ZHU Xihui¹, LI Yanlan¹, WANG Zhiwei¹, PANG Zheyu¹, LI Yubao¹, LIU Cheng¹, SI Zhenshu¹, LU Jianbiao¹, CAO Shengliang¹, XUE Xijuan²

1. College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252059, China;
2. Shandong Xinde Technology Co., Ltd., Qingdao 266000, China

Received:2022-07-18 Online:2023-03-05 Published:2023-03-02

摘要/Abstract

摘要： 【目的】了解鸭疫里默氏杆菌的耐药性、基因组结构与遗传变异程度,为鸭疫里默氏杆菌耐药性与基因组研究提供参考。【方法】本研究对1株从病死鸭脑组织分离的鸭疫里默氏杆菌疑似菌株进行了PCR鉴定、耐药性检测及全基因组框架图测序,并基于16S rDNA与管家基因对其进行了遗传进化分析。【结果】测序数据经过质控与过滤后成功组装为1个包含38个contigs的基因组框架,使用Abricate软件、CARD在线数据库共检测出6种不同的耐药基因,其中4种与耐药表型符合;将基因序列提交至MLST数据库,发现了一种新ST型,定为ST93。构建的16S rDNA和管家基因进化树结果表明,分离菌株与2株鸭疫里默氏杆菌具有较近的亲缘关系。【结论】分离鉴定得到1株鸭疫里默氏杆菌,该菌株为多药耐药菌株,其基因组中携带多个耐药基因;鸭疫里默氏杆菌的基因变异程度较大,且存在跨区域流行传播风险。在临床用药时应注意合理用药,及时监控抗性基因的水平转移,防止鸭疫里默氏杆菌跨区域流行。

关键词: 鸭疫里默氏杆菌; 耐药性; 耐药基因; 基因组; 生物信息学

Abstract: 【Objective】 This study was aimed to understand the antibiotic resistance,genome structure and degree of genetic variation of Riemerella anatipestifer,so as to provide a reference for studying of antibiotic resistance and genome of Riemerella anatipestifer.【Method】 PCR identification,antibiotic resistance detection and draft whole genome sequencing of a suspected strain of Riemerella anatipestifer were performed,this suspected strain was isolated from brain tissue of died ducks,and its genetic evolutionary analysis was performed based on 16S rDNA and housekeeping genes.【Result】 After quality control and filtering,the sequencing data was successfully assembled into a draft genome containing 38 contigs.Six different antibiotic resistance genes were detected using Abricate software and CARD online database,four of which were consistent with the antibiotic resistance phenotype.The gene sequence was submitted to MLST database,and a new ST type (ST93) was found.The results of 16S rDNA and housekeeping gene phylogenetic trees showed that the isolates were closely related to two Riemerella anatipestifer strains.【Conclusion】 A strain of Riemerella anatipestifer was isolated and identified,which was a multiantibiotic resistant strain and carries multiple antibiotic resistance genes in its genome.The gene variation of Riemerella anatipestifer was large,and there was a risk of cross regional epidemic transmission.In clinical medication,we should pay attention to rational medication,timely monitor the horizontal transfer of resistance genes,and conduct regular epidemiological investigation to prevent the cross regional epidemic of Riemerella anatipestifer.

Key words: Riemerella anatipestifer; antibiotic resistance; antibiotic resistance gene; genome; bioinformatics

中图分类号:

Q939.48

祝希辉, 李艳兰, 王志伟, 庞喆羽, 李玉保, 刘成, 司振书, 路建彪, 曹胜亮, 薛希娟. 1株鸭疫里默氏杆菌的全基因组测序及耐药性与遗传进化分析[J]. 中国畜牧兽医, 2023, 50(3): 1140-1149.

ZHU Xihui, LI Yanlan, WANG Zhiwei, PANG Zheyu, LI Yubao, LIU Cheng, SI Zhenshu, LU Jianbiao, CAO Shengliang, XUE Xijuan. Whole Genome Sequencing of a Resistant Riemerella anatipestifer Strain and Analysis of Antibiotic Resistance and Genetic Evolution[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1140-1149.

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1株鸭疫里默氏杆菌的全基因组测序及耐药性与遗传进化分析

Whole Genome Sequencing of a Resistant Riemerella anatipestifer Strain and Analysis of Antibiotic Resistance and Genetic Evolution

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