人体肠道耐药基因组的研究进展

段宇婧, 吴新颜, 陈则友, 陈颖, 李林云, 祝思源, 毛大庆, 罗义. 人体肠道耐药基因组的研究进展[J]. 生态毒理学报, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001
引用本文: 段宇婧, 吴新颜, 陈则友, 陈颖, 李林云, 祝思源, 毛大庆, 罗义. 人体肠道耐药基因组的研究进展[J]. 生态毒理学报, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001
Duan Yujing, Wu Xinyan, Chen Zeyou, Chen Ying, Li Linyun, Zhu Siyuan, Mao Daqing, Luo Yi. Advances in Human Gut Resistome[J]. Asian Journal of Ecotoxicology, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001
Citation: Duan Yujing, Wu Xinyan, Chen Zeyou, Chen Ying, Li Linyun, Zhu Siyuan, Mao Daqing, Luo Yi. Advances in Human Gut Resistome[J]. Asian Journal of Ecotoxicology, 2020, 15(4): 1-10. doi: 10.7524/AJE.1673-5897.20200325001

人体肠道耐药基因组的研究进展

    作者简介: 段宇婧(1990-),女,博士研究生,研究方向为微生物耐药基因,E-mail:cathydyj@126.com
    通讯作者: 罗义, E-mail: luoy@nankai.edu.cn
  • 基金项目:

    国家自然科学基金重点资助项目(41831287);国家杰出青年科学基金资助项目(41525013);国家自然科学基金资助项目(31670509,41977367,31870351,41807483);天津市自然科学基金资助项目(19JCZDJC40800)

  • 中图分类号: X171.5

Advances in Human Gut Resistome

    Corresponding author: Luo Yi, luoy@nankai.edu.cn
  • Fund Project:
  • 摘要: 人类肠道菌群是耐药基因(antibiotic resistance genes,ARGs)的"储存库",且与人体健康密切相关。目前,抗生素的滥用严重,进一步加剧了耐药基因的传播和扩散。细菌耐药问题严重影响人体健康、食品安全和生态安全,携带耐药基因的致病菌对临床治疗造成巨大威胁。本文结合国内外研究进展,在总结人体肠道耐药基因组研究方法的基础上,探讨了肠道耐药基因的组成、来源、传播和进化,并对未来研究进行了展望,旨在促进公众对肠道耐药基因的认知,并为抗生素的合理使用提供理论支持。
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  • Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing[J]. Nature, 2010, 464(7285):59-65
    郭慧玲, 邵玉宇, 孟和毕力格, 等. 肠道菌群与疾病关系的研究进展[J]. 微生物学通报, 2015, 42(2):400-410

    Guo H L, Shao Y Y, Menghe B, et al. Research on the relation between gastrointestinal microbiota and disease[J]. Microbiology China, 2015, 42(2):400-410(in Chinese)

    杨凤霞, 毛大庆, 罗义, 等. 环境中抗生素抗性基因的水平传播扩散[J]. 应用生态学报, 2013, 24(10):2993-3002

    Yang F X, Mao D Q, Luo Y, et al. Horizontal transfer of antibiotic resistance genes in the environment[J].Chinese Journal of Applied Ecology, 2013, 24(10):2993-3002(in Chinese)

    Allen H K, Donato J, Wang H H, et al. Call of the wild:Antibiotic resistance genes in natural environments[J]. Nature Reviews Microbiology, 2010, 8(4):251-259
    Martinez J. Natural antibiotic resistance and contamination by antibiotic resistance determinants:The two ages in the evolution of resistance to antimicrobials[J]. Frontiers in Microbiology, 2012, 3(1):1
    Cant ón R. Antibiotic resistance genes from the environment:A perspective through newly identified antibiotic resistance mechanisms in the clinical setting[J]. Clinical Microbiology and Infection, 2009, 15(s1):20-25
    Wright G D. The antibiotic resistome:The nexus of chemical and genetic diversity[J]. Nature Reviews Microbiology, 2007, 5(3):175-186
    李显志. 抗生素耐药基因古老起源与现代进化及其警示[J]. 中国抗生素杂志, 2013, 38(2):81-89

    Li X Z. Ancient origin and modern evolution of antibiotic resistome and their implications[J]. Chinese Journal of Antibiotics, 2013, 38(2):81-89(in Chinese)

    Hu Y, Yang X, Qin J, et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota[J]. Nature Communications, 2013, 4:2151
    Salyers A A, Gupta A, Wang Y. Human intestinal bacteria as reservoirs for antibiotic resistance genes[J]. Trends in Microbiology, 2004, 12(9):412-416
    Baron S A, Diene S M, Rolain J M. Human microbiomes and antibiotic resistance[J]. Human Microbiome Journal, 2018, 10:43-52
    Lagier J C, Dubourg G, Million M, et al. Culturing the human microbiota and culturomics[J]. Nature Reviews Microbiology, 2018, 16:540-550
    Van Schaik W. The human gut resistome[J]. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 2015, 370(1670):doi.org/10.1098/rstb.2014.0087
    Mcarthur A G, Waglechner N, Nizam F, et al. The comprehensive antibiotic resistance database[J]. Antimicrobial Agents and Chemotherapy, 2013, 57(7):3348-3357
    Liu B, Pop M. ARDB-Antibiotic resistance genes database[J]. Nucleic Acids Research, 2008, 37(suppl_1):D443-D447
    Zhou C E, Smith J, Lam M, et al. MvirDB-A microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications[J]. Nucleic Acids Research, 2006, 35(suppl_1):D391-D394
    Scaria J, Chandramouli U, Verma S K. Antibiotic resistance genes online (ARGO):A database on vancomycin and beta-lactam resistance genes[J]. Bioinformation, 2005, 1(1):5-7
    Kleinheinz K A, Joensen K G, Larsen M V. Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences[J]. Bacteriophage, 2014, 4(2):e27943
    Gibson M K, Forsberg K J, Dantas G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology[J]. The ISME Journal, 2015, 9(1):207-216
    Gupta S K, Padmanabhan B R, Diene S M, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes[J]. Antimicrobial Agents and Chemotherapy, 2014, 58(1):212-220
    Li L G, Yin X, Zhang T. Tracking antibiotic resistance gene pollution from different sources using machine-learning classification[J]. Microbiome, 2018, 6(1):93
    Ufarté L, Potocki-Veronese G, Laville É. Discovery of new protein families and functions:New challenges in functional metagenomics for biotechnologies and microbial ecology[J]. Frontiers in Microbiology, 2015, 6:563
    Verastegui Y, Cheng J, Engel K, et al. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities[J]. mBio, 2014, 5(4):e01157-14
    王淑娴, 刁菁, 樊英, 等. MALDI-TOF MS技术用于细菌鉴定的研究进展[J]. 农业灾害研究, 2019, 9(5):20-23

    Wang S X, Diao J, Fan Y, et al. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacterial srain identification[J]. Journal of Agricultural Catastrophology, 2019, 9(5):20-23(in Chinese)

    Yatsunenko T, Rey F E, Manary M J, et al. Human gut microbiome viewed across age and geography[J]. Nature, 2012, 486:222-227
    Lu N, Hu Y, Zhu L, et al. DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related[J]. Scientific Reports, 2014, 4(1):4302
    Ruppé E, Ghozlane A, Tap J, et al. Prediction of the intestinal resistome by a three-dimensional structure-based method[J]. Nature Microbiology, 2019, 4(1):112-123
    Feng J, Li B, Jiang X, et al. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses[J]. Environmental Microbiology, 2018, 20(1):355-368
    Duan Y, Chen Z, Tan L, et al. Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals[J]. The Science of the Total Environment, 2019, 705:135674
    Scott K P, Melville C M, Barbosa T M, et al. Occurrence of the new tetracycline resistance gene tet (W) in bacteria from the human gut[J]. Antimicrobial Agents and Chemotherapy, 2000, 44(3):775-777
    Moore A M, Ahmadi S, Patel S, et al. Gut resistome development in healthy twin pairs in the first year of life[J]. Microbiome, 2015, 3(1):27
    Bäckhed F, Roswall J, Peng Y, et al. Dynamics and stabilization of the human gut microbiome during the first year of life[J]. Cell Host & Microbe, 2015, 17(5):690-703
    Vangay P, Ward T, Gerber Jeffrey S, et al. Antibiotics, pediatric dysbiosis, and disease[J]. Cell Host & Microbe, 2015, 17(5):553-564
    Palleja A, Mikkelsen K H, Forslund S K, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure[J]. Nature Microbiology, 2018, 3(11):1255-1265
    Raymond F, Ouameur A A, Déraspe M, et al. The initial state of the human gut microbiome determines its reshaping by antibiotics[J]. The ISME Journal, 2015, 10:707-720
    Li J, Rettedal E A, van der Helm E, et al. Antibiotic treatment drives the diversification of the human gut resistome[J]. Genomics, Proteomics & Bioinformatics, 2019, 17(1):39-51
    Forslund K, Sunagawa S, Roat Kultima J, et al. Country-specific antibiotic use practices impact the human gut resistome[J]. Genome Research, 2013, 23(7):1163-1169
    Maier L, Pruteanu M, Kuhn M, et al. Extensive impact of non-antibiotic drugs on human gut bacteria[J]. Nature, 2018, 555(7698):623
    Wang Y, Lu J, Mao L, et al. Antiepileptic drug carbamazepine promotes horizontal transfer of plasmid-borne multi-antibiotic resistance genes within and across bacterial genera[J]. The ISME Journal, 2019, 13(2):509-522
    Lu J, Jin M, Nguyen S H, et al. Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation[J]. Environment International, 2018, 118:257-265
    Häsler R, Kautz C, Rehman A, et al. The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany[J]. Microbiome, 2018, 6(1):37
    Smits S A, Leach J, Sonnenburg E D, et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania[J]. Science, 2017, 357(6353):802-806
    Pehrsson E C, Tsukayama P, Patel S, et al. Interconnected microbiomes and resistomes in low-income human habitats[J]. Nature, 2016, 533(7602):212
    Pal C, Bengtsson-Palme J, Kristiansson E, et al. The structure and diversity of human, animal and environmental resistomes[J]. Microbiome, 2016, 4(1):54
    Xie J, Jin L, Luo X, et al. Seasonal disparities in airborne bacteria and associated antibiotic resistance genes in PM2.5 between urban and rural sites[J]. Environmental Science & Technology Letters, 2018, 5(2):74-79
    Liu Y Y, Wang Y, Walsh T R, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China:A microbiological and molecular biological study[J]. The Lancet Infectious Diseases, 2016, 16(2):161-168
    Ma L, Li B, Jiang X T, et al. Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey[J]. Microbiome, 2017, 5(1):154
    李林云, 谭璐, 崔玉晓, 等. 饮用水中细菌耐药及其健康风险研究进展[J]. 生态毒理学报, 2018, 13(2):2-12

    Li L Y, Tan L, Cui Y X, et al. Bacterial resistance and human health risk in drinking water[J]. Asian Journal of Ecotoxicology, 2018, 13(2):2-12(in Chinese)

    盛嫣然, 朱晓勇. 母-胎肠道内微生物群落以及母-胎微生物传输的研究进展[J]. 中华生殖与避孕杂志, 2017, 37(9):773-778

    Sheng Y R, Zhu X Y. Research progress on the maternal-fetal intestinal microbiome and maternal-fetal microbial transmission[J]. Chinese Journal of Reproduction and Contraception, 2017, 37(9):773-778(in Chinese)

    Jiménez E, Marín M L, Martín R, et al. Is meconium from healthy newborns actually sterile?[J]. Research in Microbiology, 2008, 159(3):187-193
    Aagaard K, Ma J, Antony K M, et al. The placenta harbors a unique microbiome[J]. Science Translational Medicine, 2014, 6(237):237ra65
    Gosalbes M J, Vallès Y, Jiménez-Hernández N, et al. High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples[J]. Journal of Developmental Origins of Health and Disease, 2015, 7(1):35-44
    关怀, 齐宸, 武晓旭, 等. 胎儿肠道菌群定植的研究进展[J]. 人民军医, 2019, 62(8):764-767
    Kelsall B. Recent progress in understanding the phenotype and function of intestinal dendritic cells and macrophages[J]. Mucosal Immunology, 2008, 1(6):460-469
    Pärnänen K, Karkman A, Hultman J, et al. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements[J]. Nature Communications, 2018, 9(1):3891
    Dominguez-Bello M G, Costello E K, Contreras M, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns[J]. Proceedings of the National Academy of Sciences, 2010, 107(26):11971-11975
    Martín R, Langa S, Reviriego C, et al. Human milk is a source of lactic acid bacteria for the infant gut[J]. The Journal of Pediatrics, 2003, 143(6):754-758
    Rizzo L, Manaia C, Merlin C, et al. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment:A review[J]. Science of the Total Environment, 2013, 447:345-360
    Karkman A, Pärnänen K, Larsson D G J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments[J]. Nature Communications, 2019, 10(1):80
    马筱玲, 鲁怀伟, 张艳. 认识细菌的天然耐药和获得性耐药[J]. 中华检验医学杂志, 2012, 35(8):762-763
    Cox G, Wright G D. Intrinsic antibiotic resistance:Mechanisms, origins, challenges and solutions[J]. International Journal of Medical Microbiology, 2013, 303(6-7):287-292
    Dodd M C. Potential impacts of disinfection processes on elimination and deactivation of antibiotic resistance genes during water and wastewater treatment[J]. Journal of Environmental Monitoring, 2012, 14(7):1754-1771
    Nordgård L, Brusetti L, Raddadi N, et al. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats[J]. BMC Research Notes, 2012, 5(1):170
    Stinear T P, Olden D C, Johnson P D R, et al. Enterococcal van B resistance locus in anaerobic bacteria in human faeces[J]. The Lancet, 2001, 357(9259):855-856
    Graham M, Ballard S A, Grabsch E A, et al. High rates of fecal carriage of nonenterococcal van B in both children and adults[J]. Antimicrobial Agents and Chemotherapy, 2008, 52(3):1195-1197
    Waters J L, Salyers A A. Regulation of CTnDOT conjugative transfer is a complex and highly coordinated series of events[J]. mBio, 2013, 4(6):e00569-13
    Manrique P, Dills M, Young J M. The human gut phage community and its implications for health and disease[J]. Viruses, 2017, 9(6):141
    Quirós P, Colomer-Lluch M, Martínez-Castillo A, et al. Antibiotic resistance genes in the bacteriophage DNA fraction of human fecal samples[J]. Antimicrobial Agents and Chemotherapy, 2014, 58(1):606-609
    Modi S R, Lee H H, Spina C S, et al. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome[J]. Nature, 2013, 499(7457):219-222
    D'costa V M, King C E, Kalan L, et al. Antibiotic resistance is ancient[J]. Nature, 2011, 477(7365):457-461
    Bhullar K, Waglechner N, Pawlowski A, et al. Antibiotic resistance is prevalent in an isolated cave microbiome[J]. PLoS One, 2012, 7(4):e34953
    Santiago-Rodriguez T M, Fornaciari G, Luciani S, et al. Gut microbiome of an 11th century A.D. pre-Columbian Andean mummy[J]. PLoS One, 2015, 10(9):e0138135
    Miteva V I, Sheridan P P, Brenchley J E. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core[J]. Applied and Environmental Microbiology, 2004, 70(1):202-213
    Davies J, Davies D. Origins and evolution of antibiotic resistance[J]. Microbiology and Molecular Biology Reviews, 2010, 74(3):417-433
    Zhang G, Leclercq S O, Tian J, et al. A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3'')-Ⅱ, is horizontally transferred among Acinetobacter spp. by homologous recombination[J]. PLoS Genetics, 2017, 13(2):e1006602
    Datta N P, Kontomichalou. Penicillinase synthesis controlled by infectious R factors in Enterobacteriaceae[J]. Nature, 1965, 208:239-241
    厉文辉, 史亚利, 高立红, 等. 加速溶剂萃取-高效液相色谱-串联质谱法同时检测鱼肉中喹诺酮、磺胺与大环内酯类抗生素[J]. 分析测试学报, 2010, 29(10):987-992

    Li W H, Shi Y L, Gao L H, et al. Simultaneous determination of quinolones, sulfonamides and macrolides in fish samples using accelerated solvent extraction followed by high performance liquid chromatography-electrospray ionization tandem mass spectrometry[J]. Journal of Instrumental Analysis, 2010, 29(10):987-992(in Chinese)

    Bush K. Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae[J]. Current Opinion in Microbiology, 2010, 13(5):558-564
    Bradford P A. Extended-spectrum β-lactamases in the 21st Century:Characterization, epidemiology, and detection of this important resistance threat[J]. Clinical Microbiology Reviews, 2001, 14(4):933-951
    Bronzwaer S L A M, Cars O, Buchholz U, et al. The relationship between antimicrobial use and antimicrobial resistance in Europe[J]. Emerging Infectious Diseases, 2002, 8(3):278-282
    Tadesse D A, Zhao S, Tong E, et al. Antimicrobial drug resistance in Escherichia coli from humans and food animals, United States, 1950-2002[J]. Emerging Infectious Diseases, 2012, 18(5):741-749
    Kahn L H. Perspective:The one-health way[J]. Nature, 2017, 543(7647):S47
    李鹏媛, 原丽红, 陆家海. 应对新发传染病, One Health策略势在必行[J]. 传染病信息, 2018, 31(1):11-14

    , 54 Li P Y, Yuan L H, Lu J H. Imperative One Health strategy for the emerging infectious diseases[J]. Infectious Disease Information, 2018, 31(1):11-14, 54(in Chinese)

    刘羽. 国家自然科学基金环境地球科学学科布局优化战略研究[J]. 科学通报, 2020, doi:10.1360/TB-2020

    -0424 Liu Y. Research on the strategy of optimizing the discipline layout of environmental geosciences under the National Natural Science Foundation of China[J]. Chinese Science Bulletin, 2020, doi:10.1360/TB-2020-0424(in Chinese)

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  • 收稿日期:  2020-03-25

人体肠道耐药基因组的研究进展

    通讯作者: 罗义, E-mail: luoy@nankai.edu.cn
    作者简介: 段宇婧(1990-),女,博士研究生,研究方向为微生物耐药基因,E-mail:cathydyj@126.com
  • 1. 南开大学环境科学与工程学院, 环境污染过程与基准教育部重点实验室, 天津 300350;
  • 2. 南京大学环境学院, 污染控制与资源化国家重点实验室, 南京 210093;
  • 3. 南开大学医学院, 天津 300071;
  • 4. 辽宁大学环境学院, 沈阳 110036
基金项目:

国家自然科学基金重点资助项目(41831287);国家杰出青年科学基金资助项目(41525013);国家自然科学基金资助项目(31670509,41977367,31870351,41807483);天津市自然科学基金资助项目(19JCZDJC40800)

摘要: 人类肠道菌群是耐药基因(antibiotic resistance genes,ARGs)的"储存库",且与人体健康密切相关。目前,抗生素的滥用严重,进一步加剧了耐药基因的传播和扩散。细菌耐药问题严重影响人体健康、食品安全和生态安全,携带耐药基因的致病菌对临床治疗造成巨大威胁。本文结合国内外研究进展,在总结人体肠道耐药基因组研究方法的基础上,探讨了肠道耐药基因的组成、来源、传播和进化,并对未来研究进行了展望,旨在促进公众对肠道耐药基因的认知,并为抗生素的合理使用提供理论支持。

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