Inhibiting conjugation as a tool in the fight against antibiotic resistance

Antibiotic resistance, especially in gram-negative bacteria, is spreading globally and rapidly. Development of new antibiotics lags behind; therefore, novel approaches to the problem of antibiotic resistance are sorely needed and this commentary highlights one relatively unexplored target for drug development: conjugation. Conjugation is a common mechanism of horizontal gene transfer in bacteria that is instrumental in the spread of antibiotic resistance among bacteria. Most resistance genes are found on mobile genetic elements and primarily spread by conjugation. Furthermore, conjugative elements can act as a reservoir to maintain antibiotic resistance in the bacterial population even in the absence of antibiotic selection. Thus, conjugation can spread antibiotic resistance quickly between bacteria of the microbiome and pathogens when selective pressure (antibiotics) is introduced. Potential drug targets include the plasmid-encoded conjugation system and the host-encoded proteins important for conjugation. Ideally, a conjugation inhibitor will be used alongside antibiotics to prevent the spread of resistance to or within pathogens while not acting as a growth inhibitor itself. Inhibiting conjugation will be an important addition to our arsenal of strategies to combat the antibiotic resistance crisis, allowing us to extend the usefulness of antibiotics.     

新型细菌耐药元件——整合子系统

已有证据表明整合子系统是微生物中主要的耐药机制,由其介导的细菌耐药是细菌发生水平基因转移和产生耐药机制的主要的途径。目前知道的整合子可分为两类:传统的整合子和超级整合子;前者的基因盒可编码一种或多种耐抗生素和消毒剂,存在于转座子、质粒和细菌染色体;而后者的基因盒编码了很多不同的功能,它们只在细菌的染色体上存在,有的可以同时携带一百多个基因盒;目前只在特定菌株中发现超级整合子。研究表明,整合子上的基因盒可能最初都来之于超级整合子。本文就整合子的结构、分布、起源及它对基因进化产生的影响等几个方面的研究进展进行讨论。     

Antibiotic resistance in gram-negative bacteria: the role of gene cassettes and integrons.

Resistance of gram-negative organisms to antibiotics such as beta-lactams, aminoglycosides, trimethoprim and chloramphenicol is caused by many different acquired genes, and a substantial proportion of these are part of small mobile elements known as gene cassettes. A gene cassette consists of the gene and a downstream sequence, known as a 59-base element (59-be), that acts as a specific recombination site. Gene cassettes can move into or out of a specific receptor site (attl site) in a companion element called an integron, and integration or excision of the cassettes is catalysed by a site-specific recombinase (Intl) that is encoded by the integron. At present count there are 40 different cassette-associated resistance genes and three distinct classes of integron, each encoding a distinct Intl integrase. The same cassettes are found in all three classes of integron, indicating that cassettes can move freely between different integrons. Integrons belonging to class I often contain a further antibiotic resistance gene, sull, conferring resistance to sulphonamides. The sull gene is found in a conserved region (3'-CS) that is not present in all members of this class. Class I integrons of the sull type are most prevalent in clinical isolates and have been found in many different organisms. Even though most of them are defective transposon derivatives, having lost at least one of the transposition genes, they are none the less translocatable and consequently found in many different locations. The transposon Tn7 is the best known representative of class 2 integrons, and Tn7 and relatives are also found in many different species.     

新型耐药基因传播元件：ISCR

随着抗生素的广泛使用和滥用,细菌的耐药问题日益严重。转座子和整合子可以解释大多数耐药基因在DNA分子间的移动,但它们不能解释耐药基因移动的实质和耐药基因亚种的增长。本文介绍一类传播耐药基因元件——ISCR,并阐明抗生素耐药基因广泛传播的实质。通过借鉴近几年来国内外研究的成果,概括论述ISCR因子与各类抗生素耐药基因的关系,这对耐药基因传播研究具有一定的指导意义。     

一株特殊耐药表型肺炎克雷伯菌的耐药机制研究

目的 研究对氨基糖苷类抗生素产生特殊耐药现象（双抑菌圈）的肺炎克雷伯菌的耐药表型和耐药机制.方法 用K-B法、E-test法、三维试验等方法对其耐药表型进行研究.采用聚合酶链反应（PCR）技术对7种氨基糖苷类钝化酶基因、2种核糖体甲基化基因和Ⅰ类整合子进行检测,并对PCR产物测序.结果 细菌的这种特殊耐药表型是稳定的;PCR结果表明：这株菌含有Aac（3）-Ⅱ钝化酶基因、armA核糖体甲基化耐药基因和1000bp左右的Ⅰ类整合子.结论 这株菌对氨基糖苷类抗生素的耐药是多种耐药机制相互作用的结果.但是这尚不能满意地解释这种特殊的耐药现象,其机理有待进一步研究.     

饥饿应激对整合子捕获耐药性基因盒频率影响的研究

目的 通过测定在不同培养时间下大肠杆菌BL21 (DE3)中整合子的整合频率,研究饥饿应激对整合子捕获耐药性基因盒频率的影响.方法 将整合子和氨基糖苷腺苷转移酶(aadA2)基因盒克隆到同一质粒pACYC184的不同位点,该重组质粒和高表达整合酶的重组质粒同时转化大肠杆菌BL21 (DE3),对10株此菌株培养12 h和24h后用实时荧光定量聚合酶链反应(PCR)测定发生整合作用的整合子的拷贝数和总的整合子的拷贝数,前者除以后者即为整合频率.结果 大肠杆菌BL21 (DE3)中整合子在12 h整合频率的均值为5.51×10-5,在24 h整合频率的均值为1.82×10-4.比较10株此菌株2个时点的整合频率,差异有统计学意义(P＜0.01).结论 饥饿应激对整合子捕获耐药性基因盒频率有明显的提高作用.     

Bacteroides mobilizable and conjugative genetic elements: antibiotic resistance among clinical isolates

The conjugation is one of the most important mechanisms of horizontal gene transfer in prokaryotes, leading to genetic variation within a species and the acquisition of new traits, such as antibiotic resistance. Bacteroides is an obligate anaerobe of the colon and a significant opportunistic pathogen. Antibiotic resistance among Bacteroides spp. is rapidly increasing, largely due to the dissemination of DNA transfer factors (plasmids and transposons) harbored by members of this genus. Transfer factors can be divided into two classes, conjugative and mobilizable. Species of the intestinal Bacteroides have yielded different resistance plasmids, all of which have been intensely studied, the plasmids encode high-level MLS resistance conferred by a conserved erm gene. It has been reported an interesting observation associated with the transfer of several of these types of elements, all of which conferred Tcr and displayed greatly increased transfer efficiency following exposure to tetracycline. Many of the conjugative transposons (CTns) in Bacteroides are related to various genetic elements (such as CTnDOT, CTnERL, NBU and others). CTnDOT carries a tetracycline resistance gene, tetQ, and an erythromycin resistance gene, ermF. Resistance to drugs used to treat Bacteroides infections, such as clindamycin, has also been increasing. These conjugal elements have been found in Bacteroides clinical isolates. Thus, horizontal gene transfer could conceivably have played a role in the rising incidence of resistance in this bacterial group.     

Antimicrobials: modes of action and mechanisms of resistance

After six decades of widespread antibiotic use, bacterial pathogens of human and animal origin are becoming increasingly resistant to many antimicrobial agents. Antimicrobial resistance develops through a limited number of mechanisms: (a). permeability changes in the bacterial cell wall/membrane, which restrict antimicrobial access to target sites; (b). active efflux of the antimicrobial from the cell; (c). mutation in the target site; (d). enzymatic modification or degradation of the antimicrobial; and (e). acquisition of alternative metabolic pathways to those inhibited by the drug. Numerous bacterial antimicrobial resistance phenotypes result from the acquisition of external genes that may provide resistance to an entire class of antimicrobials. These genes are frequently associated with large transferable extrachromosomal DNA elements called plasmids, on which may be other mobile DNA elements such as transposons and integrons. An array of different resistance genes may accumulate on a single mobile element, presenting a situation in which multiple antibiotic resistance can be acquired via a single genetic event. The versatility of bacterial populations in adapting to toxic environments, along with their facility in exchanging DNA, signifies that antibiotic resistance is an inevitable biological phenomenon that will likely continue to be a chronic medical problem. Successful management of current antimicrobials, and the continued development of new ones, is vital to protecting human and animal health against bacterial pathogens.     

Molecular epidemiology of clinically significant antibiotic resistance genes

Antimicrobials were first introduced into medical practice a little over 60 years ago and since that time resistant strains of bacteria have arisen in response to the selective pressure of their use. This review uses the paradigm of the evolution and spread of beta-lactamases and in particular beta-lactamases active against antimicrobials used to treat Gram-negative infections. The emergence and evolution particularly of CTX-M extended-spectrum beta-lactamases (ESBLs) is described together with the molecular mechanisms responsible for both primary mutation and horizontal gene transfer. Reference is also made to other significant antibiotic resistance genes, resistance mechanisms in Gram-negative bacteria, such as carbepenamases, and plasmid-mediated fluoroquinolone resistance. The pathogen Staphylococcus aureus is reviewed in detail as an example of a highly successful Gram-positive bacterial pathogen that has acquired and developed resistance to a wide range of antimicrobials. The role of selective pressures in the environment as well as the medical use of antimicrobials together with the interplay of various genetic mechanisms for horizontal gene transfer are considered in the concluding part of this review.     

人类肠道菌群中抗生素耐药基因的研究进展

抗生素耐药性在细菌病原体中不断出现并蔓延,其遗传物质基础抗生素耐药基因(ARG)可通过基因突变或水平基因转移等方式获得,并赋予宿主对抗生素的耐药性,从而严重威胁人类的健康.人类肠道菌群作为ARG产生和传播的重要场所越来越受到重视.人类肠道菌群含众多种类的ARG,可通过水平基因转移等方式实现ARG的传播.影响肠道菌群中A...     

A bioinformatic approach to understanding antibiotic resistance in intracellular bacteria through whole genome analysis

Intracellular bacteria survive within eukaryotic host cells and are difficult to kill with certain antibiotics. As a result, antibiotic resistance in intracellular bacteria is becoming commonplace in healthcare institutions. Owing to the lack of methods available for transforming these bacteria, we evaluated the mechanisms of resistance using molecular methods and in silico genome analysis. The objective of this review was to understand the molecular mechanisms of antibiotic resistance through in silico comparisons of the genomes of obligate and facultative intracellular bacteria. The available data on in vitro mutants reported for intracellular bacteria were also reviewed. These genomic data were analysed to find natural mutations in known target genes involved in antibiotic resistance and to look for the presence or absence of different resistance determinants. Our analysis revealed the presence of tetracycline resistance protein (Tet) in Bartonella quintana, Francisella tularensis and Brucella ovis; moreover, most of the Francisella strains possessed the blaA gene, AmpG protein and metallo-beta-lactamase family protein. The presence or absence of folP (dihydropteroate synthase) and folA (dihydrofolate reductase) genes in the genome could explain natural resistance to co-trimoxazole. Finally, multiple genes encoding different efflux pumps were studied. This in silico approach was an effective method for understanding the mechanisms of antibiotic resistance in intracellular bacteria. The whole genome sequence analysis will help to predict several important phenotypic characteristics, in particular resistance to different antibiotics. In the future, stable mutants should be obtained through transformation methods in order to demonstrate experimentally the determinants of resistance in intracellular bacteria.     

The forgotten Gram-negative bacilli: what genetic determinants are telling us about the spread of antibiotic resistance

Gram-negative bacilli have become increasingly resistant to antibiotics over the past 2 decades due to selective pressure from the extensive use of antibiotics in the hospital and community. In addition, these bacteria have made optimum use of their innate genetic capabilities to extensively mutate structural and regulatory genes of antibiotic resistance factors, broadening their ability to modify or otherwise inactivate antibiotics in the cell. The great genetic plasticity of bacteria have permitted the transfer of resistance genes on plasmids and integrons between bacterial species allowing an unprecedented dissemination of genes leading to broad-spectrum resistance. As a result, many Gram-negative bacilli possess a complicated set of genes encoding efflux pumps, alterations in outer membrane lipopolysaccharides, regulation of porins and drug inactivating enzymes such as beta-lactamases, that diminish the clinical utility of today's antibiotics. The cross-species mobility of these resistance genes indicates that multidrug resistance will only increase in the future, impacting the efficacy of existing antimicrobials. This trend toward greater resistance comes at a time when very few new antibiotics have been identified capable of controlling such multi-antibiotic resistant pathogens. The continued dissemination of these resistance genes underscores the need for new classes of antibiotics that do not possess the liability of cross-resistance to existing classes of drugs and thereby having diminished potency against Gram-negative bacilli.     

非编码sRNA在细菌耐药机制方面的研究进展

近年来的研究发现,细菌应答抗生素压力时会产生特异的非编码小RNA(small RNA, sRNA)谱,进而可能调控下游基因的表达,帮助细菌克服抗生素压力。sRNA以各种方式调控细菌耐药相关基因(如抗生素转运蛋白、药物外排泵、细胞被膜的合成与修饰),参与细菌耐药网络。因此,sRNA及其相关因子(如Hfq)可能被用作抗菌治疗的靶标。本文将从sRNA应答抗生素压力并产生抗生素耐药及其作为药物靶点的前景等方面,综述sRNA在细菌耐药调控方面的研究进展。     

A risk analysis framework for the long-term management of antibiotic resistance in food-producing animals

In recent years, there has been increasing concern that the use of antibiotics in food-producing animals, particularly their long-term use for growth promotion, contributes to the emergence of antibiotic-resistant bacteria in animals. These resistant bacteria may spread from animals to humans via the food chain. They may also transfer their antibiotic-resistance genes into human pathogenic bacteria, leading to failure of antibiotic treatment for some, possibly life-threatening, human conditions. To assist regulatory decision making, the actual risk to human health from antibiotic use in animals needs to be determined (risk assessment) and the requirements for risk minimisation (risk management and risk communication) determined. We propose a novel method of risk analysis involving risk assessment for three interrelated hazards: the antibiotic (chemical agent), the antibiotic-resistant bacterium (microbiological agent) and the antibiotic-resistance gene (genetic agent). Risk minimisation may then include control of antibiotic use and/or the reduction of the spread of bacterial infection and/or prevention of transfer of resistance determinants between bacterial populations.     

第一类整合子整合酶基因intI1的定位分析

目的　整合子 ( integrons)介导的细菌耐药特性已成为研究细菌耐药机制的热点 ,在研究了来自正常人携带沙门氏菌中整合子的分布和特性的基础上 ,进一步探讨整合子的基因定位。方法　从已鉴定的整合子阳性菌株出发 ,分别提取其质粒和染色体 DNA,进行质粒的接合转移试验。对染色体 DNA进行限制性酶切 ,以第一类整合酶基因 int I1( DIG标记 )为探针 ,进行 Southern杂交。结果　 4株整合酶阳性菌株不存在含有第一类整合子的接合性质粒 ,确定 4株整合子阳性菌株的整合酶基因 int I1基因位于染色体上。结论　本文发现的整合子阳性菌株对耐药基因的捕获是通过染色体 DNA介导的。     

多重耐药临床菌株中整合子结构的检测与分析

目的研究广州暨南大学附属第一医院2004年部分临床菌株样本的整合子及其基因盒的分布特性。方法多重PCR检测与细菌耐药关系密切的1、2、3类整合酶基因,进一步对阳性样本可变区的基因盒序列鉴定分析。结果随机抽取109株临床菌株,整合酶阳性检出率为97.2%(106/109),其中1类整合酶阳性菌100株(91.7%),2类整合酶阳性菌1株(0.92%),此外有5株(4.6%)同时检出1、2类整合酶,没有检测到3类整合酶;基因盒鉴定结果显示,插入基因盒以dfrA(甲氧苄氨嘧啶耐药相关)和aadA(氨基糖苷类耐药相关)基因家族为主,也在少数菌株中发现了aacA4、cmlA1、catB3以及sat1基因盒。其中又以dfrA12、orfF和aadA2组合最为常见,耐药基因盒PCR扩增片段为1913bp(64.6%);此外,还发现了同时存在两种整合子结构的菌株。结论整合子普遍存在于临床菌株中,可通过基因水平转移在不同菌属间传播,提示各医药单位必须加强耐药监测及合理选择抗菌药物,以减少多重耐药细菌的发生和发展。     

鲍曼不动杆菌生物膜与耐药性的研究进展

鲍曼不动杆菌为革兰阴性杆菌,是导致医院感染的常见条件致病菌之一。由于其易产生耐药性及植入性医疗操作的增加,鲍曼不动杆菌生物膜导致的院内感染成为临床医师的极大挑战。因此,了解鲍曼不动杆菌的耐药机制具有重要的意义,分析其生物膜对耐药性的影响及其机制有助于开发新的联合治疗方案。此文从细菌生物膜的角度归纳鲍曼不动杆菌的耐药机制研究进展,讨论鲍曼不动杆菌生物膜的形成过程、调节因素以及对耐药性的影响,概述了亚致死剂量抗生素对鲍曼不动杆菌耐药形成的影响,为针对鲍曼不动杆菌生物膜所致感染制定适宜的治疗方案和防控耐药菌株传播提供参考。     

The antibiotic resistome

Importance of the field: Antibiotics are essential for the treatment of bacterial infections and are among our most important drugs. Resistance has emerged to all classes of antibiotics in clinical use. Antibiotic resistance has, proven inevitable and very often it emerges rapidly after the introduction of a drug into the clinic. There is, therefore, a great interest in understanding the origins, scope and evolution of antibiotic resistance. Areas covered in this review: The review discusses the concept of the antibiotic resistome, which is the collection of all genes that directly or indirectly contribute to antibiotic resistance. What the reader will gain: The review seeks to assemble current knowledge of the resistome concept as a means of understanding the totality of resistance and not just resistance in pathogenic bacteria. Take home message: The concept of the antibiotic resistome provides a framework for the study and understanding of how resistance emerges and evolves. Furthermore, the study of the resistome reveals strategies that can be applied in new antibiotic discoveries.     

Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa

Excessive use of broad-spectrum antibiotics in hospitals has led to the emergence of highly resistant strains of Pseudomonas aeruginosa. To reduce the selection pressure for resistance, it is important to determine the antibiotic susceptibility pattern of bacteria so that hospital patients can be treated with more narrow-spectrum and target-specific antibiotics. This study describes the development of a technique for detecting point muations in the fluoroquinolone resistance-determining region of the gyrA and parC genes as well as the efflux regulatory genes mexR, mexZ and mexOZ that are associated with fluoroquinolone and aminoglycoside resistance. The assay is based on a short DNA sequencing method using multiplex-fast polymerase chain reaction (PCR) and Pyrosequencing™ for amplification and sequencing of the selected genes. Fifty-nine clinical isolates of P. aeruginosa were examined for mutations in the abovementioned genes. Mutations related to antibiotic resistance were detected in codons 83 and 87 of gyrA and codon 126 of the mexR regulatory gene. Results of this study suggest Pyrosequencing™ as a substitute for traditional methods as it provides a rapid and reliable technique for determining the antibiotic resistance pattern of a given bacterial strain in <1 h.     

大肠埃希菌中Ⅰ类整合子耐药基因的分析

目的 对临床分离大肠埃希菌株携带的Ⅰ类整合子及相关耐药基因进行筛选和分析.探讨Ⅰ类整合子在大肠埃希菌耐药中的作用.方法 对43株大肠埃希菌临床分离株做药敏试验;采用PCR扩增、DNA测序、DNA序列比对的方法 对其携带的Ⅰ类整合子相关耐约基因进行分析.结果 43株大肠埃希菌分离株对10种抗菌药物的耐药率依次为亚胺培南4.7%、阿米卡星18.6%、头孢他啶、27.9%、头孢吡肟37.2%、头孢呋辛55.8%、复方磺胺甲嗯唑58.1%、妥布霉素74.4%、庆大霉素79.1%、头孢噻肟81.4%和哌拉两林83.7%.在43株大肠埃希菌分离株中有25株含有Ⅰ类整合子,其中18株携带整合子相关耐药基因,如介导对磺胺类和氨基糖苷类约物的耐药基因等;某些菌株携带的整合子相关耐药基因相同.结论 Ⅰ类整合子在大肠埃希菌中广泛存在,整合子相关耐约基因在该菌耐药性的形成和播散中发挥作用.