黄牛源产气荚膜梭菌分离株基因组的生物信息学分析

doi:10.11843/j.issn.0366-6964.2024.04.032

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (4): 1707-1715.doi: 10.11843/j.issn.0366-6964.2024.04.032

黄牛源产气荚膜梭菌分离株基因组的生物信息学分析

田睿^1,2,3, 徐思翔^1,2,3, 谢烽^1,2,3, 刘广锦^1,2,3, 王刚⁴, 李庆霞⁴, 代蕾⁴, 谢国信⁴, 张琼文⁵, 陆亚警⁵, 王光文⁵, 王金秀^4*, 张炜^1,2,3*

1. 南京农业大学三亚研究院, 三亚 572025;
2. 南京农业大学动物医学院, 南京 210095;
3. 南京农业大学WOAH猪链球菌参考实验室, 南京 210095;
4. 海南省动物疫病预防控制中心, 海口 571100;
5. 昌江黎族自治县畜牧兽医技术服务中心, 昌江 572799

收稿日期:2023-07-10 出版日期:2024-04-23 发布日期:2024-04-26
通讯作者: 王金秀,主要从事动物疫病防控研究,E-mail:cauvetwjx681@163.com;张炜,主要从事微生物与免疫学研究,E-mail:vszw@njau.edu.cn
作者简介:田睿(1996-)，男，山西大同人，博士，主要从事微生物与免疫学研究，E-mail：740795088@qq.com
基金资助:
三亚崖州湾科技城“崖州湾”菁英人才科技专项(SCKJ-JYRC-2022-80)；三亚崖州湾科技城博士研究生科研创新基金项目(HSPHDSRF-2023-09-005)；海南省重点研发项目(现代农业)(ZDYF2022XDNY236)；南京农业大学三亚研究院2021年度引导资金项目(NAUSY-MS12)

Bioinformatics Analysis of the Genome of Clostridium perfringens Isolated from Cattle

TIAN Rui^1,2,3, XU Sixiang^1,2,3, XIE Feng^1,2,3, LIU Guangjin^1,2,3, WANG Gang⁴, LI Qingxia⁴, DAI Lei⁴, XIE Guoxin⁴, ZHANG Qiongwen⁵, LU Yajing⁵, WANG Guangwen⁵, WANG Jinxiu^4*, ZHANG Wei^1,2,3*

1. The Sanya Institute of Nanjing Agricultural University, Sanya 572025, China;
2. College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
3. WOAH Streptococcus suis Reference Laboratory, Nanjing Agricultural University, Nanjing 210095, China;
4. Hainan Center for Animal Disease Control and Prevention, Haikou 571100, China;
5. Animal Husbandry and Veterinary Technical Service Center of Changjiang Li Autonomous County, Changjiang 572799, China

Received:2023-07-10 Online:2024-04-23 Published:2024-04-26

摘要/Abstract

摘要： 本研究自猝死海南黄牛的组织器官中分离到2株A型产气荚膜梭菌，命名为ZWCP209和ZWCP210。基因组拼接结果显示其基因组大小处于3.4~3.5 Mb之间，tRNA和CDS数量稳定。多位点序列分析(MLST)显示，测序菌株属于同种新ST型。从NCBI数据库中获取27株牛源产气荚膜梭菌的基因组，与测序分离株共同进行生物信息学分析：共检测到13种耐药基因，其中四环素类耐药基因tetA(P)和tetB(P)的携带率最高(79.4%)，值得关注的是，本研究中2株海南黄牛分离株均携带了7种以上的耐药基因，其中包括非兽用抗生素唑烷酮的耐药基因optrA。泛基因组分析结果显示以上菌株的基因组中共含有7 345个基因，核心基因数量占比22.94%；在核心基因组和plc基因的系统进化分析中，两海南黄牛分离株处于同一分支，并具有相同的毒力因子，具有极高的同源性。本研究为国内首次对海南黄牛产气荚膜梭菌进行全基因组序列测定与生物信息学分析，对牛产气荚膜梭菌病的防治与基因组研究具有参考价值。

关键词: 海南黄牛, 产气荚膜梭菌, 分离鉴定, 全基因组测序, 生物信息学分析

Abstract: In this study, two strains of Clostridium perfringens type A, named ZWCP209 and ZWCP210, were isolated from the tissues and organs of sudden death Hainan cattle. Genome assembly results showed that the genome size was between 3.4-3.5 Mb, and the number of tRNA and CDS was stable. Multilocus sequence analysis (MLST) showed that the sequenced strains belonged to the same new ST type. The genomes of 27 bovine C. perfringens strains were obtained from the NCBI database and analyzed by bioinformatics together with sequenced isolates: A total of 13 resistance genes were detected, among which the tetracycline resistance genes tetA(P) and tetB(P) had the highest carrying rate (79.4%). It is noteworthy that the two Hainan cattle isolates in this study carried more than 7 resistance genes, including optrA, which is resistant to oxazolidinone for non-veterinary use. Pan-genome analysis showed that the genomes of these strains contained a total of 7 345 genes, and the number of core genes accounted for 22.94%. In the phylogenetic analysis of the core genome and plc gene, the two Hainan cattle isolates were in the same branch and had the same virulence factors, with high homology. This study is the first complete genome sequencing and bioinformatics analysis of C. perfringens isolated from cattle in Hainan Province in China, which has a reference value for the prevention and treatment of C. perfringens disease in cattle and the study of genome.

Key words: Hainan cattle, Clostridium perfringens, isolation and identification, Whole genome sequencing, bioinformatics analysis

中图分类号:

S852.616.3

田睿, 徐思翔, 谢烽, 刘广锦, 王刚, 李庆霞, 代蕾, 谢国信, 张琼文, 陆亚警, 王光文, 王金秀, 张炜. 黄牛源产气荚膜梭菌分离株基因组的生物信息学分析[J]. 畜牧兽医学报, 2024, 55(4): 1707-1715.

TIAN Rui, XU Sixiang, XIE Feng, LIU Guangjin, WANG Gang, LI Qingxia, DAI Lei, XIE Guoxin, ZHANG Qiongwen, LU Yajing, WANG Guangwen, WANG Jinxiu, ZHANG Wei. Bioinformatics Analysis of the Genome of Clostridium perfringens Isolated from Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1707-1715.

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黄牛源产气荚膜梭菌分离株基因组的生物信息学分析

Bioinformatics Analysis of the Genome of Clostridium perfringens Isolated from Cattle

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