1-Acquiredantibioticresistancegenes-anoverview

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基因研究在抗生素耐药中的应用

•研老进展•基因研究在抗生素耐药中的应用成荣赵德军I,朱龙2，(1清镇市第一人民医院，贵州清镇551400；2惠水县公安局，贵州惠水550600)摘要：随着抗生素的广泛使用，诸多病原菌产生了耐药性。

耐药问题已成为二十一世纪人类面临的最严峻的环境健康问题之一，受到了诸多研究者的关注。

目前，新型抗生素研发、现有抗生素改良以及阐明微生物的耐药机制等研究正在不断的开展。

基因组学的不断发展为病原菌耐药性研究带来了极大的便捷，高通量测序技术结合分子生物学技术构建了多种抗生素抗性基因数据库及分析工具，这极有利于研究者高效地发现各种新的耐药基因，了解耐药性产生的原因与发展过程。

本综述的目的在于从基因的视角认识病原菌耐药性，为科学研究及临床工作中更好的理解和应对耐药问题提供便利。

关键词：抗生素；耐药；基因；数据库；进化中图分类号：R978.1文献标志码：A文章编号：1001-8751(2021)02-0065-05Application of Genomics in Antibiotic ResistanceCheng Rong1,Zhao De-jun1,Zhu Long2(1Qingzhen First Peopled Hospital,Qingzhen Guizhou551400；2Huishui Public Security Bureau,Huishui Guizhou550600) Abstract:The discovery of antibiotics is a big revolution in human history,and its clinical application hassaved countless lives.However,with the widespread use of antibiotics,many pathogens have developed resistance. The problem of resistance has become one of the most severe environmental health problems faced by mankind in the21st century.At the same time,resistance has attracted the attention of many researchers.At present,researches on the development of new antibiotics,the improvement of antibiotics,and the elucidation of microbial resistance mechanisms are constantly being carried out.In the process of research on antibiotics resistance,the research progress of genomics provides a great convenience.High-throughput sequencing technology combined with molecular biology technology also constructed a variety of antibiotic resistance gene databases and analysis tools,which is extremely helpful for us to efficiently discover new drug resistance genes and understand the generation and development process of drug resistance.Our purpose of this review is to understand the drug resistance of pathogens from a genetic perspective,so as to facilitate our better understanding and response to drug resistance in scientific research and clinical work.Keywords:antibiotics；resistance；genetics；databases；evolution抗生素是人类历史上的一大重要发现，其拯救了无数感染患者的生命。

宏基因组学在微生物抗生素抗性基因检测中的应用

宏基因组学在微⽣物抗⽣素抗性基因检测中的应⽤抗⽣素的使⽤已经成为全球⼴泛关注的热点，抗⽣素的⼴泛使⽤以及滥⽤造成了抗⽣素耐药性在微⽣物中的发展和传播[1]，并且加速了全球多重耐药细菌和抗⽣素抗性基因(Antibiotic resistance genes，ARGs)的出现和传播[2]。

在医疗和农业中对抗⽣素的需求⽇益增加，这使得环境中细菌耐药性⽔平⽇益加剧，并且破坏了微⽣物和抗⽣素之间的⾃然平衡[3]。

ARGs作为⼀种新型的环境污染物[4]，⼴泛存在于⼈类、动物体内以及复杂的环境中。

ARGs起源早于⼈类使⽤抗⽣素，抗⽣素耐药性是⼀种存在于环境中的古⽼的、⾃然发⽣的现象，从晚更新世(Late pleistocene)永久冻⼟沉积物中回收的DNA序列，确定存在四环素类(tetM)、万古霉素(vanX)以及β-内酰胺酶类(bla)抗性基因[5]。

⼈和动物会将未代谢完的抗⽣素及ARGs通过粪便和肠道细菌排放到环境中，环境中的耐药细菌会在抗⽣素选择压⼒下获得富集[6]，或通过⽔平基因转移(Horizontal gene transfer，HGT)的⽅式将它们携带的ARGs传播到⽔原微⽣物中[7]，造成ARGs在不同菌之间的传播，这些原因共同促成了ARGs在畜禽养殖废⽔、医院废⽔和⽣活污⽔中的聚集。

然⽽⾷物链富集代表了⼀种特殊情况，在⾁类⽣产和⽔产养殖过程中，可能会造成抗⽣素在组织细胞的富集，产⽣含有短暂⽽⾼浓度抗⽣素的细菌[8]。

⾃1991年Pace⾸次提出环境基因组学(也称微⽣物环境基因组学、宏基因组学、⽣态组学)的概念，并在同年构建了第⼀个通过克隆环境样品中DNA的噬菌体⽂库以来[9-10]，发现ARGs在⼟壤[11]、废⽔[12-13]、河⽔[14]、饮⽤⽔[15]、海⽔[16]、沉积物[17]等环境中⼴泛存在，尤其是⽔⽣⽣态系统(例如城市和医院废⽔)，是获取和传播ARGs的理想环境，甚⾄在动物源性⾷品[18-19]以及⼈体(例如肠道[20-21])中也检测到丰富的ARGs。

Lecture2

Types of cells
GENE 3000: Increase Your Knowledge to Its Full Potential
GENE 3000: Increase Your Knowledge to Its Full Potential
GENE 3000: Increase Your Knowledge to Its Full Potential
3. An animal cell
GENE 3000: Increase Your Knowledge to Its Full Potential
Organelles of an eukaryotic cell
GENE 3000: Increase Your Knowledge to Its Full Potential
• Robert Hooke’s double lens microscope in 1665. He was 27 years old • A thin slice of cork, showing the honeycomb-like network of “cells”
GENE 3000: Increase Your Knowledge to Its Full Potential
GENE 3000: Increase Your Knowledge to Its Full Potential
Cell Replacement Therapy
GENE 3000: Increase Your Knowledge to Its Full Potential
A change in host-cell specificity
penicillin β-lactamase

细菌耐药性

1．耐药基因发生突变使耐药谱增大。 2．细菌间遗传物质相互交换使耐药基因在细菌间转移。
3．抗生素选择压力增加。
四、The biochemical mechanism of antibiotic resistance
1. Produce of inactivated enzyme or modified enzyme
2. Modify of the target
3. The increase of antibiotic exclusion
1. Produce of inactivated enzyme or modified enzyme
Familiar modified enzyme:
① β-lactamase
对付细菌耐药性的主要策略
1．合理使用抗菌药物。 2．消毒隔离防止耐药菌交叉感染。 3．研制新型抗生素及新的抗感染方法。
4．加强药政管理及相关法律制度的建设，
使合理用药走上法制化的轨道。
END
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抗生素（antibiotics）或化学合成的药物。
Some of Familiar Antibiotics Resistant Bacteria
M.tuberculolsis
E.coli
P.aeruginosa
S.dysenteriae
S.pneumoniae
H.influenzae
N.gonorrhoeae
② Aminoglycoside-modified enzyme: include
phosphotransferase,acetyl transferase, adenyl

关于人类耐药性的英语作文

关于人类耐药性的英语作文Antibiotic Resistance: A Global Health Crisis。

Antibiotics have been a lifesaving discovery in thefield of medicine. They have been used to treat bacterial infections for over 70 years and have saved countless lives. However, the overuse and misuse of antibiotics have led to the emergence of antibiotic-resistant bacteria, which has become a global health crisis.Antibiotic resistance occurs when bacteria mutate and become resistant to the antibiotics that are used to treat them. This is often caused by the overuse and misuse of antibiotics, which can lead to the development ofantibiotic-resistant bacteria. When antibiotics are usedtoo frequently or inappropriately, bacteria can develop resistance to them, making them less effective in treating infections.The overuse of antibiotics in agriculture is also amajor contributor to antibiotic resistance. Antibiotics are often used in livestock to promote growth and prevent disease, but this practice can lead to the development of antibiotic-resistant bacteria that can be transmitted to humans through the food chain.Antibiotic resistance is a serious threat to global health. It can lead to longer hospital stays, higher healthcare costs, and increased mortality rates. In addition, the development of new antibiotics is slow and expensive, which means that there are limited treatment options for antibiotic-resistant infections.To combat antibiotic resistance, it is important to use antibiotics only when necessary and to follow proper prescribing guidelines. This includes not using antibiotics for viral infections such as the common cold, and completing the full course of antibiotics as prescribed by a healthcare professional.In addition, reducing the use of antibiotics in agriculture and promoting better hygiene practices can alsohelp to prevent the spread of antibiotic-resistant bacteria. This includes proper handwashing and sanitation practices, as well as the development of new vaccines to prevent bacterial infections.In conclusion, antibiotic resistance is a global health crisis that requires immediate action. By reducing the overuse and misuse of antibiotics, promoting better hygiene practices, and developing new vaccines and treatments, we can help to prevent the spread of antibiotic-resistant bacteria and ensure that antibiotics remain an effectivetool in the fight against bacterial infections.。

木糖葡萄球菌与金黄色葡萄球菌、表面葡萄球菌的基因组比较(阐述毒力、侵染性,样本是健康人的鼻腔)副本

LETTER TO THE EDITORGenome of Staphylococcus xylosus and Comparison with S.aureusand S.epidermidisStaphylococci are Gram-positive,AT-rich cocci,and often stick together in grape-like clusters.The genus can be classi-ﬁed into two groups based on their ability to produce coagu-lase,an enzyme that causes clotting of blood plasma (Otto,2004).Coagulase-positive Staphylococci include Staphylo-coccus aureus ,a common pathogen of community-acquired and nosocomial infections (Smith et al.,2009).Their inva-siveness is associated with the ability to adhere to host sur-faces (Vuong et al.,2003).Among coagulase-negative Staphylococci (CNS),S.epidermidis is the most frequently found pathogen in humans,and is also a common cause of nosocomial infections (Nostro et al.,2007;Wang et al.,2009).S.epidermidis is believed to account for most of the infections caused by CNS and is highly resistant to many antibiotics including penicillins and cephalosporins (Al-Shuneigat et al.,2005).S.xylosus is also a CNS.It is naturally present in raw meat and milk and is commonly used in starter culture for fermentation (Planchon et al.,2006,2007).This species is normally regarded as non-pathogenic,but a few strains are related to human opportunistic infections (Akhaddar et al.,2010).In addition,some S.xylosus strains have the ability to form bioﬁlm (Planchon et al.,2006).Bacterial virulence genes can be regulated by diffusible signal molecules termed autoinducers (AIs).Because the control of gene expression by AIs is cell-density dependent,this phenomenon has been called quorum sensing (Brelles-Marino and Bedmar,2001;Antunes et al.,2010).In Staphy-lococci,there are two quorum sensing systems,P2and P3.Their regulatory mechanism was described earlier by Liu et al.(2012).Other regulatory genes and virulence factors shared by S.epidermidis and S.aureus have also been reported (Frebourg et al.,2000;Gelosia et al.,2001).However,it is still not clear whether these virulence related genes are also present in non-pathogenic S.xylosus genome.In this study,we isolated S.xylosus NJ from a nasal sample of a healthy person at Jiangsu People’s Hospital in China and determined its genome sequence using whole-genome shotgun sequencing strategy with a Hiseq2000(Illumina,CA,USA)sequencer.The project generated a total of w 2739Mbsequences and w 927folds coverage of the genome.The draft genome data were assembled using the Velvet assembly pro-gram.The assembly generated 45contigs with a size of >200bp,22of which were longer than 500bp with the N 50length of 396,400bp.These 45contigs were deposited in GenBank and annotated using Rapid Annotation using Sub-system Technology (RAST)server.In addition,96tandem repeat sequences were found in these contigs.The draft genome contained a chromosome of 2,940,053bp with a 32.40%G þC content.The general features are listed in Table 1.There are 6predicted rRNA genes and 22tRNA genes,and 83.64%nucleotides are predicted to encode proteins.By a combination of coding potential prediction and homology search,2783coding DNA sequences (CDSs)with an average length of 884bp were identiﬁed on the draft genome (Table 1).The 2199CDSs annotated by speciﬁc Clusters of Orthologous Groups (COG)function groups can be classiﬁed into 21COG categories,and 2456CDSs can be annotated into 1221KEGG orthology by KAAS (Moriya et al.,2007).The organization of the genome of S.xylosus NJ was shown in a circular map in Fig.1A.In addition,phylogenetic dendrogram based on a comparison of 16S rRNA sequences for S.xylosus NJ with members of the Staphylococcus was shown in Fig.S1.There is another S.xylosus draft genome,S.xylosus DMB3-Bh1,in GenBank.Therefore,we compared S.xylosus NJ with S.xylosus DMB3-Bh1using BLAST (version 2.2.26).The result showed that there are 2319CDSs in S.xylosus DMB3-Bh1(89.30%)similar to S.xylosus NJ (Fig.S2).The metabolic network of S.xylosus NJ was constructed using the RAST server with the 411subsystems identiﬁed in the genome.There are many carbohydrate subsystem features,including genes involved in organic acids,fermentation,sugar alcohols,di-and oligo-saccharides,central carbohydrates,monosaccharides,and one-carbon metabolisms.Many protein metabolism features are also present,including protein biosynthesis machinery such as the small subunit (SSU)and large subunit (LSU)of the bacterial ribosome.Moreover,we prepared the comparative analysis of this genome with other staphylococcal genomes (S.aureus subsp.aureus N315(S.Available online at ScienceDirectJournal of Genetics and Genomics 41(2014)413e 416JGG1673-8527/$-see front matter Copyright Ó2014,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,and Genetics Society of China.Published by Elsevier Limited and Science Press.All rights reserved./10.1016/j.jgg.2014.03.007aureus N315)and S.epidermidis ATCC12228).The results showed that there are 404subsystems for S.aureus N315genome and 381subsystems for S.epidermidis ATCC12228genome.A comparative metabolic network analysis showed that D-galacturonate and D-glucuronate utilization subsystem is only present in S.xylosus NJ genome.However,serine-glyoxylate cycle subsystem is absent in S.aureus N315genome.A more detailed comparative analysis of this genome with these two staphylococcal genomes is summarized in Table S1.The genomic organization of S.xylosus NJ was compared with those of S.aureus N315and S.epidermidis ATCC12228(Table 1).There are 1502CDSs (55.20%)in S.xylosus NJ similar to those in S.aureus N315and 1446CDSs (53.14%)similar to those in S.epidermidis ATCC12228.The number of shared genes among S.xylosus NJ,S.aureus N315,and S.epidermidis ATCC12228was shown in Fig.1B.Over 92%of homologous genes were assigned to COG function groups (Fig.S3).In addition,the larger amount of unique proteins is present for S.xylosus NJ with 1145proteins.Meanwhile,unique genes of three strains were assigned to COG function group.The result showed that the numbers of genes related to energy production and conversion,carbohydrate transport and metabolism,and general function in S.xylosus NJ genome are considerably more than other strains (Fig.S4).Compared to S.aureus N315and S.epidermidis ATCC12228genomes,S.xylosus NJ genome possesses some signiﬁcant differences,such as virulence and defense ability,cell wall and capsule constitution,phages,prophages,trans-posable elements and plasmids,and cell regulation and signaling.In virulence and defense category,adhesins have previously been reported as virulence factors by promoting the accumu-lation phase of bioﬁlm (Corrigan et al.,2007;Kim et al.,2010).In consistent with the non-pathogenic property,no adhesin was detected in S.xylosus NJ.In contrast,six adhesins were present in S.epidermidi s ATCC12228and 22in S.aureus N315(Table S2).Another important gene family,staphylococcal enterotoxins (SEs)encodes powerfulsuperantigens that stimulate non-speciﬁc T-cell proliferation (Balaban and Rasooly,2000).However,there was no gene associated with SEs in S.xylosus NJ genome.S.aureus pro-duce a -hemolysin,g -hemolysin,and leukocidin toxins,which function as two component toxins in the disruption and lysis of erythrocytes and leukocytes (Gouaux et al.,1997).Compared with S.aureus N315,there was no gene in the subcategory of toxins and superantigens in S.xylosus NJ.However,S.xylosusTable 1Chromosome features of S.xylosus NJ,S.aureus N315,and S.epidermidis ATCC12228S.xylosus S.aureus S.epidermidisFig.1.The genomic organization of S.xylosus NJ and the comparison with other Staphylococcus .A:Circular representation of the S.xylosus NJ chromosome.GC-skew:sliding window size of 10kb and calculating (G ÀC)/(G þC)in 500bp steps.Circles from outside to inside:1,contigs were arrange in clockwise direction from large to small;2,CDS on forward strand;3,CDS on reverse strand;4,tRNA genes;5,rRNA genes;6,GC-skew (window size of 10kb);and 7,purple indicates C content and yellow indicates G content (step size 500bp).B:Venn diagram for the deduced proteins in S.xylosus NJ,S.aureus N315and S.epidermidis ATCC12228.The total number of all deduced proteins for these three species is 7781.The number of proteins per each chromosome is given.Values were identiﬁed by BLASTCLUST (version 2.2.26)using an identity of >60%,an alignment coverage of >70%and an e -value of 1e-6as cut-off.The number of clusters represents the non-redundant protein coding genes for intersection.The overlapping sections indicate shared numbers of proteins.414Letter to the Editor /Journal of Genetics and Genomics 41(2014)413e 416NJ carried fewer antibiotic-resistance genes.For instance, teicoplanin andﬂuoroquinolones resistance genes were pre-sent in S.xylosus NJ.Meanwhile,multidrug-resistance efﬂux pumps were also present in S.xylosus NJ,which supports a previous observation made by Piddock(2006)that multidrug-resistance efﬂux pumps have roles not only for resistance to antibiotics,but also in bacterial pathogenicity.However, methicillin resistance genes were not found in S.xylosus NJ.In cell wall and capsule category,sialic acid is a bioavail-able carbon and nitrogen source that is abundant on mucosal surfaces and in secretions in the commensal environment (Olson et al.,2013).It has been shown by Almagro-Moreno and Boyd(2009)that several pathogens,including S.aureus N315,could utilize sialic acid as a carbon source,which in turn establish a competitive advantage in heavily sialylated environments such as the human gut.Our data indicate that S. xylosus NJ,but not S.epidermidis ATCC12228,contains genes associated with sialic acid metabolism(Table S3).Most Staphylococci produce types5and8microcapsules,which account for75%of human infections(Lowy,1998).Types5 and8cap genes were not found in S.xylosus NJ(Table S3).In category of phages,prophages,transposable elements and plasmids,Tn552is not detected in the genome of S.xylosus NJ. The staphylococcal pathogenicity islands(SaPIs)encoded one or more staphylococcal superantigens.We identiﬁed17path-ogenicity islands in S.aureus N315.However,no one was detected in S.xylosus NJ(Table S4).Interestingly,in contrast to S.aureus N315and S.epidermidis ATCC12228,ten copies related to phages and prophages were detected in S.xylosus NJ.In category of cell regulation and signaling,S.xylosus NJ showed signiﬁcant differences in bioﬁlm formation and staph-ylococcal accessory gene regulator systems compared to S. aureus N315and S.epidermidis ATCC12228.Besides adhesins absence in S.xylosus NJ,entire ica genes involved in bioﬁlm formation were not found.Although a few bioﬁlm-positive strains do not produce detectable polysaccharide intercellular adhesin(PIA),the mechanism was not due to the absence of the ica operon,but was a result of reduced transcription or trans-lation of ica genes(Zhang et al.,2003).In addition,S.epi-dermidis ATCC12228is non-bioﬁlm-forming strain due to lack of ica operon(Zhang et al.,2003).So,we speculated that S. xylosus NJ may not form bioﬁlm.However,staphylococcal accessory regulator A(SarA),biofunctional autolysin Atl,and RNA polymerase sigma factor SigB were present in S.xylosus NJ(Table S5).Therefore,we speculated that the function of these genes may be not for bioﬁlm formation,but for others such as virulence factor production.In staphylococcal acces-sory gene regulator system,there were13genes in S.aureus N315and8in S.epidermidis ATCC12228,but none in S. xylosus NJ(Table S5).This may explain the great difference among these strains in virulence.One of the important factors contributing to staphylococcal toxin is their peptide-based quorum sensing system,encoded by the accessory gene regu-lator(agr)locus(Balaban et al.,2004;Kiran et al.,2008; Antunes et al.,2010).The agr locus(agr ABCD)and related genes were not detected in S.xylosus NJ.The comparative genomic analysis suggests that S.xylosus NJ may be less virulent.In addition,we found that ElaA protein and prophage Clp protease-like protein were only present in S.xylosus NJ.In summary,the comparative genomic analysis of S.xylo-sus NJ with S.aureus N315and S.epidermidis ATCC12228 showed great difference on genome composition within this genus.Particularly,ica operon and agr operon were absent in S.xylosus NJ.Here,we described the genome analysis of S. xylosus NJ to provide a new genome for Staphylococcus genome database.In addition,we analyzed genes in S.xylosus NJ different from those in S.aureus N315and S.epidermidis ATCC12228.Their differences mainly exist in genes associ-ated with virulence and pathogenicity,such as adhesins, superantigens,resistance to antibiotics,capsular poly-saccharide synthesis enzymes,pathogenicity islands,quorum sensing and bioﬁlm formation.This study can help reveal how commensal S.xylosus strains evolved into invasive strains. ACKNOWLEDGMENTSThis work was supported by the grants from the National Natural Science Foundation of China(Nos.81301475, 31170131and31070312)and Jiangsu Qinglan Project,and the Shaoxing Major Scientiﬁc and Technological Projects(No. 2011A11013).SUPPLEMENTARY DATASupplementary data related to this article can be found at /10.1016/j.jgg.2014.03.007Xiaojuan Tan a,1,Lin Liu b,c,1,Shili Liu d,Dongting Yang a, Yikun Liu c,Shuang Yang c,Aiqun Jia a,*,Nan Qin b,* a School of Environmental and Biological Engineering,Nanjing University ofScience and Technology,Nanjing210094,Chinab State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Afﬁliated Hospital,Zhejiang University,Hangzhou310003,Chinac NGS Sequencing Department,Beijing Genomics Institute(BGI),Shenzhen518083,China d Institute of Pathogen Microbiology,School of Medicine,Shandong University,Jinan250012,China*Corresponding authors.Tel/fax:þ86057187236421. E-mail addresses:nqin@(N.Qin);jiaaiqun@(A.Jia)1These authors contributed equally to this work.Received24January2014Revised21March2014Accepted25March2014Available online12April2014 REFERENCESAkhaddar,A.,Elouennass,M.,Naama,O.,Boucetta,M.,2010.Staphylo-coccus xylosus isolated from an otogenic brain abscess in an adolescent.Surg.Infect.(Larchmt)11,559e561.Almagro-Moreno,S.,Boyd,E.F.,2009.Insights into the evolution of sialic acid catabolism among bacteria.BMC Evol.Biol.9,118.415Letter to the Editor/Journal of Genetics and Genomics41(2014)413e416Al-Shuneigat,J.,Cox,S.D.,Markham,J.L.,2005.Effects of a topical essential oil-containing formulation on bioﬁlm-forming coagulase-negative staph-ylococci.Lett.Appl.Microbiol.41,52e55.Antunes,L.C.,Ferreira,R.B.,Buckner,M.M.,Finlay,B.B.,2010.Quorum sensing in bacterial virulence.Microbiology156,2271e2282. Balaban,N.,Gov,Y.,Giacometti, A.,Cirioni,O.,Ghiselli,R., Mocchegiani,F.,Orlando,F.,D’Amato,G.,Saba,V.,Scalise,G.,Saba,V., Scalise,G.,Bernes,S.,Mor,A.,2004.A chimeric peptide composed of a dermaseptin derivative and an RNA III-inhibiting peptide prevents graft-associated infections by antibiotic-resistant staphylococci.Antimicrob.Agents Chemother.48,2544e2550.Balaban,N.,Rasooly,A.,2000.Staphylococcal enterotoxins.Int.J.Food Microbiol.61,1e10.Brelles-Marino,G.,Bedmar,E.J.,2001.Detection,puriﬁcation and charac-terisation of quorum-sensing signal molecules in plant-associated bacteria.J.Biotechnol.91,197e209.Corrigan,R.M.,Rigby, D.,Handley,P.,Foster,T.J.,2007.The role of Staphylococcus aureus surface protein SasG in adherence and bioﬁlm formation.Microbiology153,2435e2446.Frebourg,N.B.,Lefebvre,S.,Baert,S.,Lemeland,J.F.,2000.PCR-Based assay for discrimination between invasive and contaminating Staphylo-coccus epidermidis strains.J.Clin.Microbiol.38,877e880.Gelosia,A.,Baldassarri,L.,Deighton,M.,van Nguyen,T.,2001.Phenotypic and genotypic markers of Staphylococcus epidermidis virulence.Clin.Microbiol.Infect.7,193e199.Gouaux, E.,Hobaugh,M.,Song,L.,1997.alpha-hemolysin,gamma-hemolysin,and leukocidin from Staphylococcus aureus:distant in sequence but similar in structure.Protein Sci.6,2631e2635.Kim,H.K.,Cheng,A.G.,Kim,H.Y.,Missiakas,D.M.,Schneewind,O.,2010.Nontoxigenic protein A vaccine for methicillin-resistant Staphylococcus aureus infections in mice.J.Exp.Med.207,1863e1870.Kiran,M.D.,Adikesavan,N.V.,Cirioni,O.,Giacometti,A.,Silvestri,C., Scalise,G.,Ghiselli,R.,Saba,V.,Orlando,F.,Shoham,M.,Balaban,N., 2008.Discovery of a quorum-sensing inhibitor of drug-resistant staphy-lococcal infections by structure-based virtual screening.Mol.Pharmacol.73,1578e1586.Liu,L.,Tan,X.,Jia,A.,2012.Relationship between bacterial quorum sensing and bioﬁlm formation e a review.Acta Microbiologica Sinica52,271e278 (in Chinese with an English abstract).Lowy,F.D.,1998.Staphylococcus aureus infections.N.Engl.J.Med.339, 520e532.Moriya,Y.,Itoh,M.,Okuda,S.,Yoshizawa,A.C.,Kanehisa,M.,2007.KAAS: an automatic genome annotation and pathway reconstruction server.Nucleic Acids Res.35,182e185.Nostro, A.,Sudano,R.A.,Bisignano,G.,Marino, A.,Cannatelli,M.A., Pizzimenti,F.C.,Cioni,P.L.,Procopio,F.,Blanco,A.R.,2007.Effects of oregano,carvacrol and thymol on Staphylococcus aureus and Staphylo-coccus epidermidis bioﬁlms.J.Med.Microbiol.56,519e523.Olson,M.E.,King,J.M.,Yahr,T.L.,Horswill,A.R.,2013.Sialic acid catab-olism in Staphylococcus aureus.J.Bacteriol.195,1779e1788.Otto,M.,2004.Virulence factors of the coagulase-negative staphylococci.Front.Biosci.9,841e863.Piddock,L.J.,2006.Multidrug-resistance efﬂux pumps-not just for resis-tance.Nat.Rev.Microbiol.4,629e636.Planchon,S.,Gaillard-Martinie, B.,Dordet-Frisoni, E.,Bellon-Fontaine,M.N.,Leroy,S.,Labadie,J.,He´braud,M.,Talon,R.,2006.Formation of bioﬁlm by Staphylococcus xylosus.Int.J.Food Microbiol.109,88e96.Planchon,S.,Chambon,C.,Desvaux,M.,Chafsey,I.,Leroy,S.,Talon,R., He´braud,M.,2007.Proteomic analysis of cell envelope from Staphylo-coccus xylosus C2a,a coagulase-negative staphylococcus.J.Proteome Res.6,3566e3580.Smith,K.,Perez,A.,Ramage,G.,Gemmell,C.G.,Lang,S.,parison of bioﬁlm-associated cell survival following in vitro exposure of meticillin-resistant Staphylococcus aureus bioﬁlms to the antibiotics clindamycin, daptomycin,linezolid,tigecycline and vancomycin.Int.J.Antimicrob.Agents33,374e378.Vuong, C.,Gerke, C.,Somerville,G.A.,Fischer, E.R.,Otto,M.,2003.Quorum-sensing control of bioﬁlm factors in Staphylococcus epidermidis.J.Infect.Dis.188,706e718.Wang,X.,Yao,X.,Zhu,Z.,Tang,T.,Dai,K.,Sadovskaya,I.,Flahaut,S., Jabbouri,S.,2009.Effect of berberine on Staphylococcus epidermidis bioﬁlm formation.Int.J.Antimicrob.Agents34,60e66.Zhang,Y.Q.,Ren,S.X.,Li,H.L.,Wang,Y.X.,Fu,G.,Yang,J.,Qin,Z.Q., Miao,Y.G.,Wang,W.Y.,Chen,R.S.,Shen,Y.,Chen,Z.,Yuan,Z.H., Zhao,G.P.,Qu,D.,Danchin,A.,Wen,Y.M.,2003.Genome-based analysis of virulence genes in a non-bioﬁlm-forming Staphylococcus epidermidis strain(ATCC12228).Mol.Microbiol.49,1577e1593.416Letter to the Editor/Journal of Genetics and Genomics41(2014)413e416。

细菌的多样抗性

infectious disease is curable by antibiotic therapy. Antibiotics are manufactured at an estimated scale of about 100,000 tons annually worldwide, and their use had profound impact on the life of bacteria on
人造化合物是几乎不可能被以下所描述的酶机制所灭活的，如氟喹诺酮类.
However, bacteria can still become resistant through mutations that make the target protein less susceptible to the agent.Fluoroquinolone
Mutational Alterationof the Target Protein
靶蛋白的突变改建 Man-made compounds, such as fluoroquinolones,are unlikely to become inactivated by the enzymatic mechanisms described below.

Hence, there are almost no agents that could be used against these strains, in which an outer membrane barrier of low permeability and an array of efficient multidrug efflux pumps are combined with multitudes of specific resistance mechanisms. 因此，几乎没有代理可用于抵制这些菌株，其中低渗透性的外膜屏障和高效率的阵列多药外排泵结合了许许多多具体的耐药机制。

_13_Mobile_Genetic_Elements

General structure of bacterial transposons, such as Tn9 of E. coli.
❖ Transposons are very valuable tools for the bacterial geneticist. They can be introduced into cells on plasmids or viral genomes. Once transferred into a cell, transposons can act as mutagens that affect only a single cellular gene. Although transposition is a rare event, mutagenized cells are readily isolated because of their newly acquired antibiotic resistance gene.
accompanied by an increase in the number of copies of the
transposon. Replicative transposition involves two types of
enzymatic activity: a transposase that acts on the ends of the original transposon; and a resolvase that acts on the
❖ This process results in duplication of the target-site sequence on each side of the inserted IS element. Note that the length of the target site and IS10 are not to scale.

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REVIEW ARTICLE published:28September2011 doi:10.3389/fmicb.2011.00203 Acquired antibiotic resistance genes:an overviewAngela H.A.M.van Hoek1,Dik Mevius2,3,Beatriz Guerra4,Peter Mullany5,Adam Paul Roberts5andHenk J.M.Aarts1*1Laboratory for Zoonoses and Environmental Microbiology,Centre for Infectious Disease Control,National Institute of Public Health and the Environment,Utrecht, Netherlands2Central Veterinary Institute of Wageningen UR,Lelystad,Netherlands3Department of Infectious Diseases and Immunology,Utrecht University,Utrecht,Netherlands4National Salmonella Reference Laboratory,Federal Institute for Risk Assessment,Berlin,Germany5Department of Microbial Diseases,University College London Eastman Dental Institute,University College London,London,UKEdited by:Timothy Rutland Walsh,Cardiff University,UKReviewed by:M.Pilar Francino,Center for Public Health Research,SpainJun Liu,Mount Sinai School of Medicine,USA*Correspondence:Henk J.M.Aarts,National Institute of Public Health and the Environment, Antonie van Leeuwenhoekla9,3721 MA Bilthoven,Utrecht,Netherlands. e-mail:henk.aarts@rivm.nl In this review an overview is given on antibiotic resistance(AR)mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the dis-covery and mode of action of the different classes of antibiotics.As this review is only dealing with acquired resistance,attention is also paid to mobile genetic elements such as plasmids,transposons,and integrons,which are associated with AR genes,and involved in the dispersal of antimicrobial determinants between different bacteria.Keywords:antimicrobial resistance mechanisms,acquired,antibiotics,mobile genetic elementsINTRODUCTIONThe discovery and production of(synthetic)antibiotics in theﬁrst half of the previous century has been one of medicine’s greatest achievements.The use of antimicrobial agents has reduced mor-bidity and mortality of humans and contributed substantially to human’s increased life span.Antibiotics are,either as therapeutic or as prophylactic agents,also widely used in agricultural practices.Theﬁrst discovered antimicrobial compound was penicillin (Flemming,1929)aβ-lactam antibiotic.Soon after this very important discovery,antibiotics were used to treat human infec-tions starting with sulfonamide and followed by the aminoglyco-side streptomycin and streptothricin(Domagk,1935;Schatz and Waksman,1944).Nowadays numerous different classes of antimi-crobial agents are known and they are classiﬁed based on their mechanisms of action(Neu,1992).Antibiotics can for instance inhibit protein synthesis,like aminoglycoside,chloramphenicol, macrolide,streptothricin,and tetracycline or interact with the syn-thesis of DNA and RNA,such as quinolone and rifampin.Other groups inhibit the synthesis of,or damage the bacterial cell wall asβ-lactam and glycopeptide do or modify,like sulfonamide and trimethoprim,the energy metabolism of a microbial cell.Upon the introduction of antibiotics it was assumed that the evolution of antibiotic resistance(AR)was unlikely.This was based on the assumption that the frequency of mutations generating resistant bacteria was negligible(Davies,1994).Unfortunately, time has proven the opposite.Nobody initially anticipated that microbes would react to this assault of various chemical poi-sons by adapting themselves to the changed environment by developing resistance to antibiotics using such a wide variety of mechanisms.Moreover,their ability of interchanging genes, which is now well known as horizontal gene transfer(HGT)emergence of resistance actually began before theﬁrst antibiotic, penicillin,was characterized.Theﬁrstβ-lactamase was identi-ﬁed in Escherichia coli prior to the release of penicillin for use in medical practice(Abraham and Chain,1940).Besidesβ-lactams, the aminoglycoside–aminocyclitol family was also one of theﬁrst groups of antibiotics to encounter the challenges of resistance (Wright,1999;Bradford,2001).Over the years it has been shown by numerous ecological studies that(increased)antibiotic con-sumption contributes to the emergence of AR in various bacterial genera(MARAN,2005,2007;NethMap,2008).Some examples of the link between antibiotic dosage and resistance development are the rise of methicillin-resistant Staphylococcus aureus(MRSA) and vancomycin-resistant enterococci(VRE).The initial appear-ance of MRSA was in1960(Jevons et al.,1963),whereas VRE were ﬁrst isolated about20years ago(Uttley et al.,1988).Over the last decades they have remained a reason for concern,but additional public health threats in relation to resistant microorganisms have also arisen(see for example Cantón et al.,2008;Goossens,2009; Allen et al.,2010).Bacteria have become resistant to antimicrobials through a number of mechanisms(Spratt,1994;McDermott et al.,2003; Magnet and Blanchard,2005;Wright,2005):I.Permeability changes in the bacterial cell wall which restrictsantimicrobial access to target sites,II.Active efﬂux of the antibiotic from the microbial cell,III.Enzymatic modiﬁcation of the antibiotic,IV.Degradation of the antimicrobial agent,V.Acquisition of alternative metabolic pathways to those inhib-ited by the drug,VI.Modiﬁcation of antibiotic targets,These AR phenotypes can be achieved in microorganisms by chro-mosomal DNA mutations,which alter existing bacterial proteins, through transformation which can create mosaic proteins and/or as a result of transfer and acquisition of new genetic material between bacteria of the same or different species or genera(Spratt, 1994;Maiden,1998;Ochman et al.,2000).There are numerous examples of mutation based resistance. For example,macrolide resistance can be due to nucleotide(s)base substitutions in the23S rRNA gene.However,a similar resistance phenotype may also result from mutations within the riboso-mal proteins L4and L22(Vester and Douthwaite,2001).Single nucleotide polymorphisms(SNPs)can be the cause for resis-tance against the synthetic drugs quinolones,sulfonamides,and trimethoprim(Huovinen et al.,1995;Hooper,2000;Ruiz,2003) and mutations within the rpsL gene,which encodes the riboso-mal protein S12,can result in a high-level streptomycin resistance (Nair et al.,1993).A frame shift mutation in the chromosomal ddl gene,encoding a cytoplasm enzyme d-Ala–d-Ala ligase,can account for glycopeptides resistance(Casadewall and Courvalin, 1999).ACQUIRED RESISTANCEThis review deals with the description of acquired resistance against several classes of antibiotics.For each class the develop-ment of resistance is summarized along with the mechanisms of action.Furthermore an extensive summary is given of the resistance mechanisms and resistance genes involved. AMINOGLYCOSIDEHistory and action mechanismThe aminoglycoside antibiotics initially known as aminoglyco-sidic aminocyclitols are over60years old(Siegenthaler et al.,1986; Begg and Barclay,1995).In the early1940s theﬁrst amino-glycoside discovered was streptomycin in Streptomyces griseus (Schatz and Waksman,1944).Several years later,additional amino-glycosides were characterized from other Streptomyces species; neomycin and kanamycin in1949and1957,respectively.Further-more,in the1960s gentamicin was recovered from the actino-mycete Micromonospora purpurea.Because most aminoglycosides have been isolated from either Streptomyces or Micromonospora a nomenclature system has been set up based on their source. Aminoglycosides that are derived from bacteria of the Streptomyces genus are named with the sufﬁx“-mycin,”while those which are derived from Micromonospora are named with the sufﬁx“-micin.”Theﬁrst semi-synthetic derivatives were isolated in the1970s. For example netilmicin is a derivative of sisomicin whereas amikacin is derived from kanamycin(Begg and Barclay,1995; Davies and Wright,1997).Aminoglycosides are antimicrobials since they inhibit protein synthesis and/or alter the integrity of bacterial cell membranes (Vakulenko and Mobashery,2003).They have a broad antimicro-bial spectrum.Furthermore,they often act in synergy with other antibiotics as such it makes them valuable as anti-infectants. Resistance mechanismsSeveral aminoglycoside resistance mechanisms have been recog-Decreased permeability(Hancock,1981;Taber et al.,1987),(III) Ribosome alteration(Poehlsgaard and Douthwaite,2005),(IV) Inactivation of the drugs by aminoglycoside-modifying enzymes (Shaw et al.,1993).Intrinsic mechanisms,i.e.,efﬂux pumps and 16S rRNA methylases but also chromosomal mutations can cause theﬁrst three resistance properties.In recent years acquired16S rRNA methylases appear to have increased in importance(Gali-mand et al.,2005;Doi and Arakawa,2007;Table1).Theﬁrst gene identiﬁed of a plasmid-mediated type of aminoglycoside resistance was armA(Galimand et al.,2003).To dateﬁve additional methy-lases have been reported,i.e.,npmA,rmt A,rmtB,rmtC,and rmtD (Courvalin,2008;Doi et al.,2008).Data regarding the16S rRNA methylase genes are accumulated and provided at the website: www.nih.go.jp/niid/16s_database/index.html.The major encountered aminoglycoside resistance mechanism is the modiﬁcation of enzymes.These proteins are classiﬁed into three major classes according to the type of modiﬁcation:AAC (acetyltransferases),ANT(nucleotidyltransferases or adenyltrans-ferases),APH(phosphotransferases;Shaw et al.,1993;Wright and Thompson,1999;Magnet and Blanchard,2005;Wright,2005; Ramirez and Tolmansky,2010).Within these classes,an additional subdivision can be made based on the enzymes different region speciﬁcities for aminoglycoside modiﬁcations:i.e.,there are four acetyltransferases:AAC(1),AAC(2 ),AAC(3),and AAC(6 );ﬁve nucleotidyltransferases:ANT(2 ),ANT(3 ),ANT(4 ),ANT(6), and ANT(9)and seven phosphotransferases:APH(2 ),APH(3 ), APH(3 ),APH(4),APH(6),APH(7 ),and APH(9).Furthermore, there also exists a bifunctional enzyme,AAC(6 )–APH(2 ),that can acetylate and phosphorylate its substrates sequentially(Shaw et al.,1993;Kotra et al.,2000).Table1displays the currently known aminoglycoside resistance genes.The action mechanisms of the determinants,the variety in gene lengths,accession numbers,and the distribution are all indicated.As can be deduced from the sec-ond column of Table1,inconsistencies arose in the nomenclature of genes for aminoglycoside-modifying enzymes(Vakulenko and Mobashery,2003).In some cases,genes were named according to the site of modiﬁcation,followed by a number to distinguish between ing a different nomenclature,for example,the genes for AAC(6 )-Ia and AAC(3)-Ia are referred to as aacA1and aacC1,respectively.The nomenclature proposed by Shaw et al. (1993),who utilize the identical names for the enzymes and the corresponding genes,but the names of genes are in lowercase letters and italicized will be used in this review(see Table1). According to this more convenient nomenclature,the genes for the AAC(6 )-Ia and AAC(3)-Ia enzymes are termed aac(6 )-Ia and aac(3)-Ia,respectively.β-LACTAMHistory and action mechanismAs already mentioned before,theﬁrst antibiotic discovered was aβ-lactam,i.e.,penicillin.The Scottish scientist Alexander Flemming accidentally noticed the production of a substance with antimi-crobial properties by the mold Penicillium notatum(Flemming, 1929).Over the last30years,many newβ-lactam antibiotics have been developed.By deﬁnition,allβ-lactam antibiotics have aβ-lactam nucleus in their molecular structure.Theβ-lactam antibi-T able1|Acquired Aminoglycoside resistance genes.Gene name Mechanism Length(nt)Accession numberor referenceCoding region Generaaac(2 )-Ia ACT537L06156264..800Providenciaaac(2 )-Ib ACT588U41471265..852Mycobacteriumaac(2 )-Ic ACT546U72714373..918Mycobacteriumaac(2 )-Id ACT633U72743386..1018Mycobacteriumaac(2 )-Ie ACT549NC_0118963039059..3039607Mycobacteriumaac(3)-I ACT465AJ8772255293..5757Pseudomonasaac(3)-Ia ACT534X158521250..1783Acinetobacter,Escherichia,Klebsiella,Salmonella,Serra-tia,Streptomycesaac(3)-Ib ACT531L06157555..1085Pseudomonasaac(3)-Ib-aac(6 )-Ib ACT1,005AF3551891435..2439Pseudomonasaac(3)-Ic ACT471AJ5112681295..1765Pseudomonasaac(3)-Id ACT477AB114632104..580Proteus,Pseudomonas,Salmonella,Vibrioaac(3)-Ie ACT477AY4637978583..9059Proteus,Pseudomonas,Salmonella,Vibrioaac(3)-If ACT465AY88405161..525Serratia,Pseudomonasaac(3)-Ig ACT477CP0002822333620..2334096Saccharophagusaac(3)-Ih ACT459CP000490509912..510370Paracoccusaac(3)-Ii ACT459CP000356638262..638720Sphingopyxisaac(3)-Ij ACT CP000155Hahellaaac(3)-Ik ACT444BX571856765853..766296Staphylococcusaac(3)-IIa ACT861X5153491..951Acinetobacter,Enterobacter,Escherichia,Klebsiella,Pseudomonas,Salmonelaaac(3)-IIb ACT810M97172656..1465Serratiaaac(3)-IIc ACT861X54723819..1679Escherichiaaac(3)-IId ACT861EU0223141..861Escherichiaaac(3)-IIe ACT861EU0223151..861Escherichiaaac(3)-IIIa ACT816X556521124..1939Pseudomonasaac(3)-IIIb ACT738L06160984..1721Pseudomonasaac(3)-IIIc ACT840L06161106..945Pseudomonasaac(3)-IVa ACT786X01385244..1029Escherichiaaac(3)-Vaaac(3)-Vbaac(3)-VIa ACT900M88012193..1092Enterobacter,Escherichia,Salmonellaaac(3)-VIIa ACT867M22999493..1359Streptomycesaac(3)-VIIIa ACT861M55426466..1326Streptomycesaac(3)-IXa ACT846M55427274..1119Micromonosporaaac(3)-Xa ACT855AB028*******..3565Streptomycesaac(6 )ACT441AY5533331392..1832Pseudomonasaac ACT555AJ6289831985..2539Pseudomonasaac(6 )ACT402DQ30272381..482Pseudomonasaac(6 )ACT555EU9125372092..2646Pseudomonasaac(6 )-Ia ACT558M18967757..1314Citrobacter,Escherichia,Klebsiella,Shigellaaac(6 )-Ib ACT606M21682380..985Klebsiella,Proteus,Pseudomonasaac(6 )-Ib-cr ACT519EF6364611124..1642Enterobacter,Escherichia,Klebsiella,Pseudomonas,Sal-monellaaac(6 )-Ic ACT441M940661554..1994Serratiaaac(6 )-Id ACT450X12618905..1354Klebsiellaaac(6 )-Ieaac(6 )-If ACT435X55353279..713Enterobacteraac(6 )-Ig ACT438L09246544..981Acinetobacteraac(6 )-Ih ACT441L29044352..792Acinetobacteraac(6 )-Ii ACT549L12710169..717EnterococcusGene name Mechanism Length(nt)Accession numberor referenceCoding region Generaaac(6 )-Ij ACT441L29045260..700Acinetobacteraac(6 )-Ik ACT438L29510369..806Acinetobacteraac(6 )-Il ACT522Z54241530..1051Acinetobacter,Citrobacteraac(6 )-Im ACT537AF3379471215..1751Escherichiaaac(6 )-In ACT573Wu et al.(1997)Citrobacteraac(6 )-Iq ACT552AF047556127..678Klebsiella,Salmonellaaac(6 )-Ir ACT441AF0313261..441Acinetobacteraac(6 )-Is ACT441AF0313271..441Acinetobacteraac(6 )-It ACT441AF0313281..441Acinetobacteraac(6 )-Iu ACT441AF0313291..441Acinetobacteraac(6 )-Iv ACT441AF0313301..441Acinetobacteraac(6 )-Iw ACT441AF0313311..441Acinetobacteraac(6 )-Ix ACT441AF0313321..441Acinetobacteraac(6 )-Iy ACT438AF1448803452..3979Salmonellaaac(6 )-Iz ACT462AF140221390..851Stenotrophomonasaac(6 )-Iaa ACT438NC_0031971707358..1707795Salmonellaaac(6 )-Iad ACT435AB1191051..435Acinetobacteraac(6 )-Iae ACT552AB1048521935..2486Pseudomonas,Salmonellaaac(6 )-Iaf ACT552AB4629031200..1751Pseudomonasaac(6 )-Iai ACT567EU886977544..1110Pseudomonasaac(6 )-I30ACT555AY2896081524..2078Salmonellaaac(6 )-31ACT519AJ6401972474..2992Acinetobacteraac(6 )-32ACT555EF6142352247..2801Pseudomonasaac(6 )-33ACT555GQ3370641203..1757Pseudomonasaac(6 )-IIa ACT555M29695707..1261Aeromonas,Klebsiella,Pseudomonas,Salmonellaaac(6 )-IIb ACT543L06163532..1074Pseudomonasaac(6 )-IIc ACT582AF16277162..643Enterobacter,Klebsiella,Pseudomonasaac(6 )-IIdaac(6 )-IIIaac(6 )-IV ACT435X55353279..713Enterobacteraac(6 )-aph(2 )NUT1,440M13771304..1743Enterococcus,Lactobacillus,Staphylococcus,Streptococ-cusaacA29ACT381AY139599768..1148UnknownaacA43ACT564HQ247816639..1202KlebsiellaaadA1NUT972X02340223..1194Acinetobacter,Aeromonas,Enterobacter,Escherichia,Klebsiella,Proteus,Pseudomonas,Salmonella,Shigella,VibrioaadA1b NUT792M952873320..4111Pseudomonas,SerratiaaadA2NUT780X68227166..945Acinetobacter,Aeromonas,Citrobacter,Enterobacter,Escherichia,Klebsiella,Proteus,Pseudomonas,Salmo-nella,Shigella,Staphylococcus,Vibrio,Y ersiniaaadA3NUT792AF0474791296..2087EscherichiaaadA4NUT789Z508021306..2094Acinetobacter,Aeromonas,Escherichia,Pseudomonas, aadA5NUT789AF13736164..852Acinetobacter,Aeromonas,Escherichia,Pseudomonas,Salmonella,Shigella,Staphylococcus,VibrioaadA6NUT846AF14062961..906PseudomonasaadA7NUT798AF22473332..829Escherichia,Salmonella,VibrioaadA8NUT792AF3262101..792Klebsiella,VibrioaadA8b NUT792AM0407081174..1965EscherichiaaadA9NUT837AJ42007226773..27609CorynebacteriumaadA10NUT834U371052807..3640PseudomonasGene name Mechanism Length(nt)Accession numberor referenceCoding region GeneraaadA11NUT846AY1445901..846Pseudomonas,RiemerellaaadA12NUT792AY6657711..792Escherichia,Salmonella,Y ersiniaaadA13NUT798AY7135041..798Escherichia,Pseudomonas,Y ersiniaaadA14NUT786AJ884726540..1325PasteurellaaadA15NUT792DQ3937831800..2591PseudomonasaadA16NUT846EU6756863197..4042Escherichia,Klebsiella,VibrioaadA17NUT792F J460181774..1565AeromonasaadA21NUT792AY17124447..838SalmonellaaadA22NUT792AM26183774..865Escherichia,SalmonellaaadA23NUT780AJ809407119..898SalmonellaaadA24NUT780AM7111291264..2043Escherichia,SalmonellaaadC NUT477V01282225..701StaphylococcusaadD NUT771AF1819503176..3946Staphylococcusant(2 )-Ia NUT543X045551296..1829Acinetobacter,Enterobacter,Escherichia,Klebsiella,Pro-teus,Pseudomonas,Salmonella,Serratia,Shigella,Vibrio ant(3 )-Ih-aac(6 )-IId NUT-ACT1,392AF4539983555..4946Serratiaant(4 )-Ib NUT771AJ506108209..979Bacillusant(4 )-IIa NUT759M98270145..903Pseudomonasant(4 )-IIb NUT756AY1141421061..1816Pseudomonasant(6)-Ia NUT909AF33069922..930Enterococcus,Staphylococcusant(6)-Ib NUT858FN59494927482..28339Campylobacterant(9)-Ia NUT783X02588331..1113Enterococcus,Staphylococcusant(9)-Ib NUT768M69221271..1038Enterococcus,Staphylococcusaph(2 )-Iaaph(2 )-Ib PHT900AF337947272..1171Enterococcus,Escherichiaaph(2 )-Ic PHT921U51479196..1116Enterococcusaph(2 )-Id PHT906AF016483131..1036Enterococcusaph(2 )-Ie PHT906AY743255131..1036Enterococcusaph(3 )-Ia PHT816J018391162..1977Escherichia,Klebsiella,Pseudomonas,Salmonellaaph(3 )-Ib PHT816M20305779..1594Escherichiaaph(3 )-Ic PHT816X625115410..1225Acinetobacter,Citrobacter,Escherichia,Klebsiella,Salmo-nella,Serratia,Y ersiniaaph(3 )-Id PHT816Z48231820..1635Escherichiaaph(3 )-IIa PHT795X577091..795Escherichia,Pseudomonas,Salmonellaaph(3 )-IIb PHT807X90856388..1194Pseudomonasaph(3 )-IIc PHT813AM7431692377498..2378310Stenotrophomonasaph(3 )-III PHT795M26832604..1398Bacillus,Campylobacter,Enterococcus,Staphylococcus,Streptococcusaph(3 )-IV PHT789X03364277..1065Bacillusaph(3 )-Va PHT807K00432307..1113Streptomycesaph(3 )-Vb PHT792M22126373..1164Streptomycesaph(3 )-Vc PHT795S81599282..1076Micromonosporaaph(3 )-Va PHT780X07753103..882Acinetobacter,Pseudomonasaph(3 )-VIb PHT780AJ6276434934..5713Alcaligenesaph(3 )-VIIa PHT753M29953131..1036Campylobacteraph(3 )-VIII PHT804AF1828451..804Streptomycesaph(3 )-XV PHT795Y180504758..5552Achromobacter,Citrobacter,Pseudomonasaph(3 )-Ia PHT819M16482501..1319Streptomycesaph(3 )-Ib PHT801AB36644111310..12110Enterobacter,Escherichia,Klebsiella,Pasteurella,Pseudomonas,Salmonella,Shigella,Y ersinia,Vibrioaph(4)-Ia PHT1,026V01499231..1256EscherichiaGene name Mechanism Length(nt)Accession numberor referenceCoding region Generaaph(4)-Ib PHT999X03615232..1230Streptomycesaph(6)-Ia PHT924AY9718011..924Streptomycesaph(6)-Ib PHT924X05648382..1305Streptomycesaph(6)-Ic PHT801X01702485..1285Escherichia,Pseudomonas,Salmonellaaph(6)-Id PHT837M28829866..1702Enterobacter,Escherichia,Klebsiella,Pasteurella,Pseudomonas,Salmonella,Shigella,Y ersinia,Vibrioaph(7 )-Ia PHT999X03615232..1230Streptomycesaph(9)-Ia PHT996U94857151..1146Legionellaaph(9)-Ib PHT993U703767526..8518StreptomycesapmA ACT822FN8067892858..3682StaphylococcusarmA MET774AY2205581978..2751Acinetobacter,Citrobacter,Enterobacter,Escherichia,Klebsiella,Salmonella,SerratianpmA MET660AB2610163069..3728EscherichiarmtA MET756AB1203216677..7432PseudomonasrmtB MET756AB1035061410..2165Enterobacter,Escherichia,Klebsiella,Pseudomonas,Ser-ratiarmtC MET846AB1947796903..7748Proteus,SalmonellarmtD MET744DQ9149608889..9632Klebsiella,PseudomonasrmtD2MET744HQ40156514139..14882Citrobacter,EnterobacterrmtE MET822GU20194755..876Escherichiaspc MET783X02588331..1113Enterococcus,Staphylococcussph NUT801X643356557..7354Escherichia,Pseudomonas,Salmonellastr NUT849X9294618060..18908Enterococcus,Staphylococcus,Lactococcussat2A ACT525X51546518..1042Acinetobacter,Enterobacter,Escherichia,Klebsiella,Pro-teus,Pseudomonas,Salmonella,Shigella,Vibriosat3A ACT543Z48231221..763Escherichiasat4A ACT543X9294538870..39412Campylobacter,Enterococcus,Staphylococcus,Strepto-coccusThis table was adapted from:Elbourne and Hall(2006),Magnet and Blanchard(2005),Partridge et al.(2009),Ramirez and Tolmansky(2010),Shaw et al.(1993), Vakulenko and Mobashery(2003),and data provided by B.Guerra,B.Aranda,D.Avsaroglu,B.Ruiz del Castillo,and R.Helmuth,on behalf of the Med-Vet Net(EU Network of Excellence)WP29Project Group.The data were collected within the subproject“AME’s,”with following participants representing their Institutions:Agnes Perry Guyomard(ANSES),Dik Mevius(CVI),Yvonne Agerso(DTU),Katie Hopkins(HPA),Silvia Herrera(ISCIII),Alessandra Carattoli(ISS),Antonio Battisti(IZS-Rome), Stefano Lollai(IZS-Sardegna),Lotte Jacobsen(SSI),Béla Nagy(VMRI),M.Rosario Rodicio and M.C.Mendoza(University of Oviedo,UO),Luis Martínez-Martínez (University Hospital of Valdecilla,HUV),and Bruno Gonzalez-Zorn(UCM).ACT,Acetyltransferase;MET,Methyltransferase;NUT,Nucleotidyltransferase;PHT,Phosphotransferase.A Although the sat genes are not aminoglycoside resistance determinants,they encode streptothricin acetyltransferases,for convenience they are included in this table.carbapenems,monobactams,andβ-lactam inhibitors(Williams, 1987;Bush,1989;Petri,2006;Queenan and Bush,2007).The core compound of penicillin,6-aminopenicillanic acid (6-APA)is used as the main starting point for the prepa-ration of numerous semi-synthetic derivatives.Although the cephalosporins are often thought of as new and improved deriv-atives of penicillin,they were actually discovered as naturally occurring substances(Petri,2006).They can be grouped inﬁrst, second,third,and forth generation cephalosporins according to their spectrum of activity and timing of the agent’s intro-duction.In general,ﬁrst generation agents have good Gram-positive activity and relatively modest coverage for Gram-negative organisms;second generation cephalosporins have increased Gram-negative and somewhat less Gram-positive activity;third generation antimicrobials have improved Gram-negative and vari-able Gram-positive activity;forth generationβ-lactams have good true broad spectrum activity against both Gram-negatives and Gram-positives(Williams,1987;Marshall et al.,2006).The sec-ond generation cephamycins are sometimes also grouped among the cephalosporins.Because carbapenems diffuse easily in bacteria they are considered as broad spectrumβ-lactam antibiotic.Imipenem and meropenem are well known representative.Even though monobactams do not contain a nucleus with a fused ring attached, they still belong to theβ-lactam antibiotics.Theβ-lactamase inhibitors,like clavulanic acid,do contain theβ-lactam ring, but they exhibit negligible antimicrobial activity and are used in combination withβ-lactam antibiotics to overcome resistance inbacteria that secreteβ-lactamase,which otherwise inactivates most penicillins.Theβ-lactam antibiotics work by inhibiting the cell wall syn-thesis by binding to so-called penicillin-binding proteins(PBPs) in bacteria and interfering with the structural cross linking of pep-tidoglycans and as such preventing terminal transpeptidation in the bacterial cell wall.As a consequence it weakens the cell wall of the bacterium andﬁnally results in cytolysis or death due to osmotic pressure(Kotra and Mobashery,1998;Andes and Craig, 2005).Theβ-lactamase inhibitors can be classiﬁed as either reversible or irreversible and the latter are considered more effective in that they eventually result in the destruction of enzymatic activ-ity.Not surprisingly the inhibitors in clinical use,i.e.,clavulanic acid,sulbactam,and tazobactam are all examples of irreversible β-lactamase inhibitors(Bush,1988;Drawz and Bonomo,2010). Resistance mechanismsTheﬁrst bacterial enzyme reported to destroy penicillin was an AmpCβ-lactamase of E.coli(Abraham and Chain,1940).Nowa-days,bacterial resistance againstβ-lactam antibiotics is increas-ing at a signiﬁcant rate and has become a common problem. There are several mechanisms of antimicrobial resistance toβ-lactam antibiotics.The most common and important mechanism through which bacteria can become resistant againstβ-lactams is by expressingβ-lactamases,for example extended-spectrum β-lactamases(ESBLs),plasmid-mediated AmpC enzymes,and carbapenem-hydrolyzingβ-lactamases(carbapenemases;Brad-ford,2001;Jacoby and Munoz-Price,2005;Paterson and Bonomo, 2005;Poirel et al.,2007;Queenan and Bush,2007;Jacoby,2009).Theβ-lactamase family has been subdivided either based on functionality or molecular characteristics.Initially,before genes were routinely sequenced various biochemical parameters were determined of the differentβ-lactamases which allowed classiﬁca-tion of this AR determinants family into four groups(Bush et al., 1995;Wright,2005).Groups1,2,and4are serine-β-lactamases, while members of group3are metallo-β-lactamases.Classiﬁcation based on molecular characteristics,i.e.,amino acid homology has also resulted in four major groups,the so-called Ambler classes A–D,which correlate well with the functional scheme but lack details concerning the enzymatic activity.Ambler classes A,C, and D include theβ-lactamases with serine at their active site, whereas Ambler class Bβ-lactamases are all metallo-enzymes who require zinc as a metal cofactor for their catalytic activi-ties(Ambler,1980;Bradford,2001;Paterson and Bonomo,2005; Wright,2005;Poirel et al.,2007,2010;Bush and Jacoby,2010; Drawz and Bonomo,2010).In this review the Ambler classiﬁcation will be used(Table2).In addition to the production ofβ-lactamases resistance can also be due to possession of altered PBPs.Sinceβ-lactams cannot bind as effectively to these altered PBPs,the antibiotic is less effec-tive at disrupting cell wall synthesis.The PBPs are thought to be the ancestors of the naturally occurring chromosomally mediated β-lactamase in many bacterial genera(Bradford,2001).Although plasmid-encoded penicillinase arose much earlier in Gram-positives in Staphylococcus aureus,due to the use of peni-β-lactamase,TEM-1,was described in the early1960s in Gram-negatives(Datta and Kontomichalou,1965).Currently over1,150 chromosomal,plasmid,and transposon locatedβ-lactamases are currently known(Bush and Jacoby,2010;Drawz and Bonomo, 2010;Table2).Based on their activity to hydrolyze a small number or a vari-ety ofβ-lactams the enzymes can be subdivided into narrow-, moderate-,broad-,and ESBLs.A commonly used deﬁnition spec-iﬁes that broad spectrumβ-lactamases are capable to provide resistance to the penicillins and cephalosporins and are not inhib-ited by inhibitors such as clavulanic acid and tazobactam.The ESBLs confer resistance to the penicillins,ﬁrst-,second-,and third-generation cephalosporins and aztreonam,but not to car-bapenems and are inhibited byβ-lactamase inhibitors.In recent years acquired AR genes encoding ESBLs have become a major concern(Bradford,2001).In time the parent enzymes bla TEM-1, bla TEM-2,and bla SHV-1have undergone amino acid substitutions (point mutations)evolving to the ESBLs,starting with bla TEM-3 and bla SHV-2(Bradford,2001).Additional mutations at critical amino acids important for catalysis resulted in over140cur-rently known SHV and TEM ESBL variants.In addition,plasmid-encoded class Cβ-lactamases or AmpC determinants,like bla CMY have also caught people’s awareness(Jacoby,2009).Furthermore, in the past decade CTX-M enzymes have become very prevalent ESBLs,both in nosocomial and in community settings(Cantón and Coque,2006).Table2illustrates the size and diversity of the group ofβ-lactamases and ESBLs.The vast and still increasing number of (broad spectrum)β-lactamases and ESBLs has become a problem for the nomenclature for novel s have been assigned according to individual preference rather than according to sys-tematic procedures(Bush,1989).Fortunately,an authoritative website has been constructed on the nomenclature of ESBLs hosted by Jacoby and Bush1.CHLORAMPHENICOLHistory and action mechanismIn1947,theﬁrst chloramphenicol,originally referred to as chloromycetin,was isolated from Streptomyces venezuelae(Ehrlich et al.,1947).Probably because chloramphenicol is a molecule with a rather simple structure only a small number of syn-thetic derivates have been synthesized without adverse effects on antimicrobial activity(Schwarz et al.,2004).In azidamfenicol two chlorine atoms(−Cl2)are replaced by an azide group.Substi-tution of the nitro group(−NO2),by a methyl–sulfonyl residue (−SO2CH3)resulted in the synthesis of thiamphenicol,whereas in theﬂuorinated thiamphenicol derivativeﬂorfenicol the hydroxyl group(−OH)is replaced withﬂuorine(−F).Chloramphenicol is a highly speciﬁc and potent inhibitor of protein synthesis through its afﬁnity for the peptidyltrans-ferase of the50S ribosomal subunit of70S ribosomes(Schwarz et al.,2004).Due to its binding to this enzyme the antibiotic prevents peptide chain elongation.The substrate spectrum of chloramphenicol includes Gram-positive and Gram-negative,aer-obic and anaerobic bacteria.Chloramphenicol analogs including。