浙江农业学报 ›› 2023, Vol. 35 ›› Issue (9): 2068-2078.DOI: 10.3969/j.issn.1004-1524.20221113
基于细菌全基因组的大口黑鲈源维氏气单胞菌AV040株致病性与耐药性解析
邹文腾(
), 刘振红, 杨靖璇, 陆阳阳, 彭开松()
- 安徽农业大学 动物科技学院,水产养殖健康与公共卫生实验室,安徽 合肥 230036
-
收稿日期:2022-07-28出版日期:2023-09-25发布日期:2023-10-09 -
作者简介:彭开松,E-mail:kaisongpeng@ahau.edu.cn
邹文腾(1996—),男,广东惠东人,硕士研究生,主要从事水产疾病微生物研究。E-mail:zouwenteng@163.com -
通讯作者:彭开松 -
基金资助:安徽省现代农业产业技术体系(皖农科〔2016〕84号)
Genome-wide analysis of pathogenicity and drug resistance of Micropterus salmoides-derived Aeromonas veronii strain AV040
ZOU Wenteng(), LIU Zhenhong, YANG Jingxuan, LU Yangyang, PENG Kaisong()
- Laboratory of Aquaculture Health and Public Health, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
-
Received:2022-07-28Online:2023-09-25Published:2023-10-09 -
Contact:PENG Kaisong
摘要：
2021年7月安徽某养殖场的大口黑鲈(Micropterus salmoides)苗在下塘期发生了爆发性死亡。在排除寄生虫和病毒感染后,从患鱼脾脏和肾脏分离到多株细菌,经鉴定,血平板单菌落β-溶血试验和回归感染筛选出一株致病力较强的维氏气单胞菌(Aeromonas veronii)AV040株。AV040全基因组测序(GenBank ID:CP095841)显示,253个编码序列为毒力基因,其中编码的黏附(adherence)分子156个、分泌系统(secretion system)85个、毒素(toxin)12个。腹腔注射AV040株对大口黑鲈(约10 g)和昆明白小鼠(约20 g)的半数致死浓度(median lethal dose, LD50)分别为6.53×106 CFU·g-1和2.97×107 CFU·g-1;受染大口黑鲈表现为胸鳍、腹鳍、肛门、肝胰腺、脾脏和幽门垂出血;受染小鼠表现为蜷缩、眯眼和颤抖,肝脏和肠道出血。AV040全基因组中有5个耐药基因,并采用K-B药敏试验进行表型验证。其中OXA-912和cphA3与碳青霉烯类(carbapenem)的耐药性有关,对碳青霉烯类(carbapenems)的亚胺培南耐药;rsmA和adeF与氨基糖苷类(aminoglycosides)、喹诺酮类(quinolones)和四环素类(tetracyclines)的耐药性有关,对氨基糖苷类的庆大霉素、卡那霉素、新霉素和丁胺卡那,喹诺酮类的诺氟沙星、恩诺沙星、环丙沙星和氧氟沙星,四环素类的多西环素和四环素敏感和中介;EF-Tu突变体与利福霉素类(rifamycin)的耐药性有关,对利福霉素类的利福平耐药。AV040株基因组中未检测出耐药基因,但表型为耐药的抗生素,包括林可酰胺类的克林霉素和林可霉素、硝基咪唑类的甲硝唑、甲氧苄啶类的甲氧苄啶、青霉素类的青霉素G和氨苄西林。本研究以全基因组测序为基础,解析了AV040株致病性和耐药性的表型与基因型间的复杂关系,加深了对大口黑鲈源维氏气单胞菌病原学的理解。
中图分类号:
引用本文
邹文腾, 刘振红, 杨靖璇, 陆阳阳, 彭开松. 基于细菌全基因组的大口黑鲈源维氏气单胞菌AV040株致病性与耐药性解析[J]. 浙江农业学报, 2023, 35(9): 2068-2078.
ZOU Wenteng, LIU Zhenhong, YANG Jingxuan, LU Yangyang, PENG Kaisong. Genome-wide analysis of pathogenicity and drug resistance of Micropterus salmoides-derived Aeromonas veronii strain AV040[J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2068-2078.
使用本文
图1 鱼体病症 A,体表溃烂;B,肝脏白点。
Fig.1 Fish illness A, Body surface ulceration; B, White spots on the liver.
图2 分离菌回归感染大口黑鲈病症图 A,胸、腹鳍和肛门出血(箭头); B,鳃出血、脾脏肿大(箭头); C,肝脏、幽门垂出血(箭头)。
Fig.2 Separated bacteria return to infect largemouth black bass disease diagram A, Bleeding from pectoral and ventral fins and anus (arrow); B, Bleeding from gills and enlarged spleen (arrow); C, Bleeding from enlarged liver and pyloric pendant (arrow).
图3 菌落形态 A,菌株形态;B,溶血圈;C,革兰氏染色。
Fig.3 Colony morphology A, MH isolation culture; B, Hemolytic ring; C, Microscopic observation of Gram staining.
| 测定项目 Test item | 标准株 Standard strain | AV040 | 测定项目 Test item | 标准株 Standard strain | AV040 |
|---|---|---|---|---|---|
| 吲哚Indole | + | + | 肌醇Inositol | - | - |
| 枸橼酸盐Citrates | + | + | 蔗糖Cane sugar | + | + |
| MR | + | + | 赖氨酸脱羧酶Lysine decarboxylase | + | + |
| VP | + | + | 阿拉伯糖Arabinose | - | - |
| 硫化氢Hydrogen sulfide | - | - | 葡萄糖Glucose | + | + |
| 明胶液化Gelatin liquefaction | + | + | 甘露糖Mannose | + | + |
| 氧化酶Oxidase | + | + | 精氨酸双水解酶Arginine bihydrolytic enzyme | +/- | + |
表1 病原菌的生化反应
Table 1 Biochemical reaction of pathogenic bacteria
| 测定项目 Test item | 标准株 Standard strain | AV040 | 测定项目 Test item | 标准株 Standard strain | AV040 |
|---|---|---|---|---|---|
| 吲哚Indole | + | + | 肌醇Inositol | - | - |
| 枸橼酸盐Citrates | + | + | 蔗糖Cane sugar | + | + |
| MR | + | + | 赖氨酸脱羧酶Lysine decarboxylase | + | + |
| VP | + | + | 阿拉伯糖Arabinose | - | - |
| 硫化氢Hydrogen sulfide | - | - | 葡萄糖Glucose | + | + |
| 明胶液化Gelatin liquefaction | + | + | 甘露糖Mannose | + | + |
| 氧化酶Oxidase | + | + | 精氨酸双水解酶Arginine bihydrolytic enzyme | +/- | + |
图4 AV040株系统发育树
Fig.4 Phylogenetic tree of the AV040 strain
图5 基因组圈图 从内到外依次为 GC skew、GC 含量、非编码 RNA(rRNA 红色,tRNA 蓝色, sRNA 绿色、滞后链 COG 注释、前导链 COG 注释)。
Fig.5 Genome circle map GC skew, GC content, non-coding RNA (rRNA red, tRNA blue, sRNA green, lagging strand COG annotation, leading strand COG annotation, in order from inside to outside).
图6 AV040 COG功能分类 1,RNA加工与修饰; 2,染色质结构和动态变化; 3,能量产生和转换; 4,细胞周期控制、细胞分裂、染色体分化; 5,氨基酸的转运和代谢; 6,核苷酸的运输和代谢; 7,碳水化合物的运输和代谢; 8,辅酶的运输和代谢; 9,脂质的运输和代谢; 10,翻译、核糖体结构和生物生成; 11,转录; 12,复制、重组和修复; 13,细胞壁、细胞膜、包膜的生物生成; 14,细胞运动; 15,翻译后修饰、蛋白质周转、伴侣蛋白; 16,无机离子运输和代谢; 17,次生代谢物的生物合成、运输和分解; 18,一般功能; 19,功能未知; 20,信号转导; 21,胞内分泌和囊泡运输; 22,防御机制。
Fig.6 AV040 COG functional classification 1, RNA processing and modification; 2, Chromatin structure and dynamics; 3, Energy production and conversion; 4, Cell cycle control, cell division, chromosome differentiation; 5, Amino acid transport and metabolism; 6, Nucleotide transport and metabolism; 7, Carbohydrate transport and metabolism; 8, Coenzyme transport and metabolism; 9, Lipid transport and metabolism; 10, Translation, ribosome structure and biogenesis; 11, Transcription; 12, Replication, recombination and repair; 13, Cell wall, membrane and envelope biogenesis; 14, Cell motility; 15, Post-translational modifications, protein turnover, chaperone proteins; 16, Inorganic ion transport and metabolism; 17, Secondary metabolite biosynthesis, transport and catabolism; 18, General function; 19, Function unknown; 20, Signal transduction; 21, Intracellular secretion and vesicular transport; 22, Defense mechanisms.
图7 AV040 KEGG通路注释 1,消化系统;2,免疫系统;3,神经系统;4,循环系统;5,内分泌系统;6,环境适应;7,老化;8,发育和再生;9,排泄系统;10,核苷酸代谢;11,脂质代谢;12,其他氨基酸的代谢;13,糖类的生物合成和代谢;14,其他次级代谢物的生物合成;15,外来生物的生物降解和代谢;16,萜类和聚酮类的代谢;17,碳水化合物的代谢;18,氨基酸的代谢;19,辅因子和维生素的代谢;20,能量代谢;21,内分泌和新陈代谢疾病;22,心血管疾病;23,癌症:特定类型;24,耐药性:抗生素;25,感染性疾病:寄生虫病;26,传染性疾病:细菌性;27,免疫性疾病;28,传染性疾病:病毒性;29,癌症:概况;30,神经退行性疾病;31,耐药性:抗肿瘤;32,翻译;33,折叠、分类和降解;34,复制和修复;35,转录;36,膜运输;37,信号转导;38,细胞运动;39,细胞生长和死亡;40,细胞群落-原核生物;41,运输和分解代谢。
Fig.7 AV040 KEGG pathway annotation 1, Digestive system; 2, Immune system; 3, Nervous system; 4, Circulatory system; 5, Endocrine system; 6, Environmental adaptation; 7, Aging; 8, Development and regeneration; 9, Excretory system; 10, Nucleotide metabolism; 11, Lipid metabolism; 12, Metabolism of other amino acids; 13, Biosynthesis and metabolism of sugars; 14, Biosynthesis of other secondary metabolites; 15, Foreign biodegradation and metabolism of organisms; 16, Metabolism of terpenoids and polyketides; 17, Metabolism of carbohydrates; 18, Metabolism of amino acids; 19, Metabolism of cofactors and vitamins; 20, Energy metabolism; 21, Endocrine and metabolic diseases; 22, Cardiovascular diseases; 23, Cancer: specific types; 24, Drug resistance: antibiotics; 25, Infectious diseases: parasitic disease; 26, Infectious diseases: bacterial disease; 27, Immune diseases; 28, Infectious diseases: viral disease; 29, Cancer: profile; 30, Neurodegenerative diseases; 31, Drug resistance: antitumor; 32, Translation; 33, Folding, sorting and degradation; 34, Replication and repair; 35, Transcription; 36, Membrane transport; 37, Signal transduction; 38, Cell motility; 39, Cell growth and death; 40, Cell communities-prokaryotes; 41, Transport and catabolism.
图8 AV040菌株感染小鼠解剖图
Fig.8 Anatomical diagram of AV040 strain infected mice
图9 AV040感染大口黑鲈累计死亡量
Fig.9 Accumulated deaths of AV040 infected largemouth bass
| 抗生素分类 Classification of antibiotics | 耐药基因 Drug resistance genes | 耐药机制 Mechanism of drug resistance | 抗生素名称 Antibiotic | 每片含药量 Dosage per tablet/μg | 抑菌圈直径 Inhibition zone diameter/mm | 中介度 Degree of intermediation/mm |
|---|---|---|---|---|---|---|
| 肽类抗生素 | — | — | 万古霉素Vancomycin | 30 | 11 (I) | 10~11 |
| Peptide antibiotics | 替考拉宁Teicoplanin | 30 | 12 | — | ||
| 多黏菌素B Polymyxin B | 300 IU | 12 (S) | 8~11 | |||
| 大环内酯类 | — | — | 阿奇霉素Azithromycin | 15 | 19 (S) | 14~17 |
| Macrolides | 克拉霉素Clarithromycin | 15 | 19 (S) | 14~17 | ||
| 红霉素Erythromycin | 15 | 16 (I) | 14~22 | |||
| 林可酰胺类 | — | — | 克林霉素Clindamycin | 2 | 6 (R) | — |
| Lincoamides | 林可霉素Lincomycin | 2 | 6 (R) | — | ||
| 碳青霉烯 Carbapenem | cphA3 OXA-912 | 抗生素灭活 Antibiotic inactivation | 亚胺培南 Imipenem | 10 | 12 (R) | 14~15 |
| 美罗培南Meropenem | 10 | 12 | — | |||
| 磷霉素Fosfomycin | — | — | 磷霉素Fosfomycin | 200 | 34 (S) | 13~15 |
| 硝基咪唑类 Nitroimidazoles | — | — | 甲硝唑 Metronidazole | 5 | 6 (R) | — |
| 四环素类 Tetracyclines | adeF | 抗生素外排 Antibiotics efflux | 多西环素 Doxycycline | 30 | 16 (S) | 13~15 |
| 四环素tetracycline | 30 | 15 (I) | 15~18 | |||
| 头孢菌素类 | — | — | 头孢氨苄Cefproxin | 30 | 21 (S) | 15~17 |
| Cephalosporins | 头孢噻肟Cefotaxime | 30 | 40 (S) | 15~22 | ||
| 甲氧苄啶类 | — | — | 甲氧苄啶Trimethoprim | 5 | 6 (R) | 11~15 |
| Trimethoprim | ||||||
| 青霉素类 | — | — | 青霉素G Penicillin G | 10 | 6 (R) | 14~15 |
| Penicillins | ||||||
| — | — | 氨苄西林 Ampicillin | 10 | 6 (R) | 14~16 | |
| 氨基糖苷类 Aminoglycosides | rsmA | 抗生素外排 Antibiotics efflux | 庆大霉素 Gentamicin | 10 | 18 (S) | 13~14 |
| rsmA — | 抗生素外排 Antibiotics efflux | 卡那霉素 Kanamycin | 30 | 18 (S) | 14~17 | |
| 氨基香豆素类 | rsmA | 抗生素外排 | 新霉素N eomycin | 30 | 17 (S) | 13~16 |
| Aminocoumarins | rsmA | Antibiotics efflux | 丁胺卡那Butamikana | 30 | 20 (S) | 15~16 |
| — | — | 新生霉素Novobiocin | 30 | 11 (R) | 13~16 | |
| 利福霉素类 Rifamycin | EF-Tu mutants | 抗生素靶位改变 Antibiotic target change | 利福平 Rifampicin | 5 | 7 (R) | 17~19 |
| 喹诺酮类 Quinolones | rsmA adeF | 抗生素外排 Antibiotics efflux | 诺氟沙星 Norfloxacin | 10 | 30 (S) | 13~16 |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 恩诺沙星 Enrofloxacin | 10 | 32 (S) | 16~20 | |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 环丙沙星 Ciprofloxacin | 5 | 32 (S) | 16~20 | |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 氧氟沙星 Ofloxacin | 5 | 30 (S) | 13~15 | |
| 复方磺胺类 Compound sulfonamides | — | — | 复方新诺明 Compound neonolemin | 23.75/1.25 | 22 (S) | 13~16 |
| 氯霉素类/酰胺醇 Chloramphenicols/ amide alcohols | — | — | 氯霉素 Chloramphenicol | 30 | 30 (S) | 13~17 |
| — | — | 氟苯尼考Florfenicol | 30 | 32 (S) | 13~17 |
表2 耐药基因和药敏抑菌圈
Table 2 Resistance genes and susceptibility inhibition zone
| 抗生素分类 Classification of antibiotics | 耐药基因 Drug resistance genes | 耐药机制 Mechanism of drug resistance | 抗生素名称 Antibiotic | 每片含药量 Dosage per tablet/μg | 抑菌圈直径 Inhibition zone diameter/mm | 中介度 Degree of intermediation/mm |
|---|---|---|---|---|---|---|
| 肽类抗生素 | — | — | 万古霉素Vancomycin | 30 | 11 (I) | 10~11 |
| Peptide antibiotics | 替考拉宁Teicoplanin | 30 | 12 | — | ||
| 多黏菌素B Polymyxin B | 300 IU | 12 (S) | 8~11 | |||
| 大环内酯类 | — | — | 阿奇霉素Azithromycin | 15 | 19 (S) | 14~17 |
| Macrolides | 克拉霉素Clarithromycin | 15 | 19 (S) | 14~17 | ||
| 红霉素Erythromycin | 15 | 16 (I) | 14~22 | |||
| 林可酰胺类 | — | — | 克林霉素Clindamycin | 2 | 6 (R) | — |
| Lincoamides | 林可霉素Lincomycin | 2 | 6 (R) | — | ||
| 碳青霉烯 Carbapenem | cphA3 OXA-912 | 抗生素灭活 Antibiotic inactivation | 亚胺培南 Imipenem | 10 | 12 (R) | 14~15 |
| 美罗培南Meropenem | 10 | 12 | — | |||
| 磷霉素Fosfomycin | — | — | 磷霉素Fosfomycin | 200 | 34 (S) | 13~15 |
| 硝基咪唑类 Nitroimidazoles | — | — | 甲硝唑 Metronidazole | 5 | 6 (R) | — |
| 四环素类 Tetracyclines | adeF | 抗生素外排 Antibiotics efflux | 多西环素 Doxycycline | 30 | 16 (S) | 13~15 |
| 四环素tetracycline | 30 | 15 (I) | 15~18 | |||
| 头孢菌素类 | — | — | 头孢氨苄Cefproxin | 30 | 21 (S) | 15~17 |
| Cephalosporins | 头孢噻肟Cefotaxime | 30 | 40 (S) | 15~22 | ||
| 甲氧苄啶类 | — | — | 甲氧苄啶Trimethoprim | 5 | 6 (R) | 11~15 |
| Trimethoprim | ||||||
| 青霉素类 | — | — | 青霉素G Penicillin G | 10 | 6 (R) | 14~15 |
| Penicillins | ||||||
| — | — | 氨苄西林 Ampicillin | 10 | 6 (R) | 14~16 | |
| 氨基糖苷类 Aminoglycosides | rsmA | 抗生素外排 Antibiotics efflux | 庆大霉素 Gentamicin | 10 | 18 (S) | 13~14 |
| rsmA — | 抗生素外排 Antibiotics efflux | 卡那霉素 Kanamycin | 30 | 18 (S) | 14~17 | |
| 氨基香豆素类 | rsmA | 抗生素外排 | 新霉素N eomycin | 30 | 17 (S) | 13~16 |
| Aminocoumarins | rsmA | Antibiotics efflux | 丁胺卡那Butamikana | 30 | 20 (S) | 15~16 |
| — | — | 新生霉素Novobiocin | 30 | 11 (R) | 13~16 | |
| 利福霉素类 Rifamycin | EF-Tu mutants | 抗生素靶位改变 Antibiotic target change | 利福平 Rifampicin | 5 | 7 (R) | 17~19 |
| 喹诺酮类 Quinolones | rsmA adeF | 抗生素外排 Antibiotics efflux | 诺氟沙星 Norfloxacin | 10 | 30 (S) | 13~16 |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 恩诺沙星 Enrofloxacin | 10 | 32 (S) | 16~20 | |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 环丙沙星 Ciprofloxacin | 5 | 32 (S) | 16~20 | |
| rsmA adeF | 抗生素外排 Antibiotics efflux | 氧氟沙星 Ofloxacin | 5 | 30 (S) | 13~15 | |
| 复方磺胺类 Compound sulfonamides | — | — | 复方新诺明 Compound neonolemin | 23.75/1.25 | 22 (S) | 13~16 |
| 氯霉素类/酰胺醇 Chloramphenicols/ amide alcohols | — | — | 氯霉素 Chloramphenicol | 30 | 30 (S) | 13~17 |
| — | — | 氟苯尼考Florfenicol | 30 | 32 (S) | 13~17 |
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