大熊猫源致病大肠杆菌CCHTP全基因组测序及耐药和毒力基因分析

doi:10.16288/j.yczz.19-243

遗传 ›› 2019, Vol. 41 ›› Issue (12): 1138-1147.doi: 10.16288/j.yczz.19-243

大熊猫源致病大肠杆菌CCHTP全基因组测序及耐药和毒力基因分析

邓雯文¹, 李才武¹, 赵思越², 李仁贵¹, 何永果¹, 吴代福¹, 杨盛智², 黄炎¹, 张和民¹, 邹立扣²()

^1. 中国大熊猫保护研究中心,大熊猫国家公园珍稀动物保护生物学国家林业和草原局重点实验室,都江堰 611830
^2. 四川农业大学资源学院,成都 611130

收稿日期:2019-09-17 修回日期:2019-11-25 出版日期:2019-12-20 发布日期:2019-11-27
通讯作者: 邹立扣 E-mail:zoulikou@sicau.edu.cn
作者简介:邓雯文,硕士研究生,研究方向：大熊猫分子遗传学。E-mail: dwenwen130@163.com|李才武,硕士研究生,高级工程师,研究方向：大熊猫临床兽医。E-mail: 83330019@qq.com; 邓雯文和李才武并列第一作者。
基金资助:
中国大熊猫保护研究中心项目编号(CCRCGP181918);国家自然科学基金项目资助编号(31400066)

Whole genome sequencing reveals the distribution of resistance and virulence genes of pathogenic Escherichia coli CCHTP from giant panda

Wenwen Deng¹, Caiwu Li¹, Siyue Zhao², Rengui Li¹, Yongguo He¹, Daifu Wu¹, Shengzhi Yang², Yan Huang¹, Hemin Zhang¹, Likou Zou²()

^1. China Conservation and Research Centre of the Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, Dujiangyan 611830, China
^2. Faculty of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 611130, China

Received:2019-09-17 Revised:2019-11-25 Online:2019-12-20 Published:2019-11-27
Contact: Zou Likou E-mail:zoulikou@sicau.edu.cn
Supported by:
Supported by the Project of China Conservation and Research Center for the Giant Panda No(CCRCGP181918);the National Natural Science Foundation of China No(31400066)

摘要/Abstract

摘要：

致病性大肠杆菌是引起动物泌尿系统感染的重要病原菌,本研究对泌尿生殖道感染出现潜血的大熊猫尿液中分离的一株致病性大肠杆菌(Escherichia coli CCHTP)进行全基因组测序,检测其中耐药基因和毒力因子的情况,同时对基因岛上耐药和毒力基因及其基因环境进行研究。研究发现,大肠杆菌CCHTP中存在多种类型的耐药基因,其中外排泵系统基因数量最多,包括mdfA、emrE和mdtN等介导多重耐药外排泵的基因。此外,该菌还携带166种毒力因子及563个相关毒力基因,其中属于黏附与侵袭类的毒力因子及相关基因数量最多。对19个基因岛分析发现,基因岛GIs011和GIs017中各有一段包含耐药和毒力基因的序列,两侧与可移动遗传元件(转座酶和插入序列)相连,这些结构可能介导耐药及毒力基因水平转移。本研究通过全基因组测序分析了大熊猫源致病性大肠杆菌中存在的耐药及毒力基因情况,对大熊猫相关疾病的科学治疗、合理用药有重要意义。

关键词: 大熊猫, 大肠杆菌, 全基因组测序, 耐药基因, 毒力因子

Abstract:

Pathogenic Escherichia coli (E. coli) is the most common pathogen causing urinary tract infection in animals. We investigated the antibiotic resistance and virulence genes of pathogenic E. coli CCHTP derived from urine with occult blood of the giant panda by whole genome sequencing. The flanking sequencing of resistance and virulence genes in genomic islands were also analyzed. Our results demonstrate that E. coli CCHTP contains different families of antibiotic resistance genes, most of which are efflux pump related genes, including multiple drug resistance efflux pump genes mdfA, emrE, and mdtN. A total of 166 virulence factors and 563 virulence genes were identified, and the most virulence factors and related genes are involved in host cell attachment and invasion processes. Furthermore, sequence analysis of 19 genomic islands revealed that antibiotic and virulence genes are associated with mobile genetic elements (transposon and insertion sequence) in GIs011 and GIs017. These structures can mediate horizontal transfer of antibiotic and virulence genes. Our work described the distribution of antibiotic resistance genes and virulence genes in E. coli CCHTP, which may provide an important guidance for treatment and rational drug use of E. coli CCHTP infection in the giant panda.

Key words: giant panda, Escherichia coli, whole genome sequencing, resistance gene, virulence gene

邓雯文, 李才武, 赵思越, 李仁贵, 何永果, 吴代福, 杨盛智, 黄炎, 张和民, 邹立扣. 大熊猫源致病大肠杆菌CCHTP全基因组测序及耐药和毒力基因分析[J]. 遗传, 2019, 41(12): 1138-1147.

Wenwen Deng, Caiwu Li, Siyue Zhao, Rengui Li, Yongguo He, Daifu Wu, Shengzhi Yang, Yan Huang, Hemin Zhang, Likou Zou. Whole genome sequencing reveals the distribution of resistance and virulence genes of pathogenic Escherichia coli CCHTP from giant panda[J]. Hereditas(Beijing), 2019, 41(12): 1138-1147.

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耐抗生素大类	耐药基因	基因数量
外排泵	macB、adeL、patA、evgS、mdtF、 patB、sav1866和TaeA等	115
糖肽类	vanTG、vanTC、vanRI、vanRF、vanRE、 vanRB、vanHD、vanG、baeS和baeR	12
多肽类	pmrF、pmrE、pmrC、mcr-3、 basS、arnA和arlS	9
四环素类	tetT、tetB(60)、tetA(48)和tet34	7
喹诺酮类	gyrB、gyrA和mfd	4
抗结核药	ndh、katG和kasA	3
磺胺类	sul3和leuO	2
β-内酰胺类	mecC和bla_CMY-63	2
多磷类	glpT和murA	2
大环内酯类	chrB	1
环脂肽类	cls	1
肽类抗生素	bacA	1
林可酰胺类	clbB	1
利福霉素类	rphB	1

类别	抗生素	敏感(S)	耐药(R)
四环素类	四环素		R
β内酰胺抑制剂	阿莫西林/克拉维酸	S
单环内酰胺类	氨曲南	S
氨基糖苷类	卡那霉素		R
氨基糖苷类	庆大霉素		R
大环内酯类	红霉素		R
大环内酯类	阿奇霉素		R
喹诺酮类	诺氟沙星		R
	氧氟沙星		R
	恩诺沙星		R
β-内酰胺类	阿莫西林		R
	氨苄西林		R
	头孢克洛		R
	头孢噻肟		R
	头孢曲松		R

大熊猫源致病大肠杆菌CCHTP全基因组测序及耐药和毒力基因分析

Whole genome sequencing reveals the distribution of resistance and virulence genes of pathogenic Escherichia coli CCHTP from giant panda

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