In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of Acinetobacter baumannii

Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT, etc. The energy minimization of modeled protein was done using Protein preparation wizard application included in Schrodinger suite. High-throughput virtual screening of 159,868 medicinal compounds against AdeB was performed using three sequential docking modes (i.e. HTVS, SP and XP). Furthermore, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was done using QIKPROP. The selected 123 compounds were further analyzed for binding free energy by molecular mechanics (using prime MM-GBSA). We have also performed enrichment study (ROC curve analysis) to validate our docking results. The selected molecule and its interaction with AdeB were validated by molecular dynamics simulation (MDS) using GROMACS v5.1.4. In silico high-throughput virtual screening and MDS validation identified ZINC01155930 ((4R)-3-(cycloheptoxycarbonyl)-4-(4-etochromen-3-yl)-2-methyl-4,6,7,8-tetrahydroquinolin-5-olate) as a possible inhibitor for AdeB. Hence, it might be a suitable efflux pump inhibitor worthy of further investigation in order to be used for controlling infections caused by Acinetobacter baumannii.     

In-silico interaction studies suggest RND efflux pump mediates polymyxin resistance in Acinetobacter baumannii

Bacterial efflux pumps have emerged as antibiotic resistance determinants and confers multi-drug resistance to a broad range of antimicrobials as well as non-antibiotic substances. A study about translocation of antibiotic molecules through the efflux transporter, will contribute in determining substrate specificity. In the present study, we have explored RND family efflux pump extensively found in Acinetobacter baumannii i.e. AdeABC. Besides, another well studied RND efflux pump, AcrAB-TolC together with a non-RND efflux pump, NorM was investigated for comparative analysis. We employed a series of computational techniques ranging from molecular docking to binding free energy estimation and molecular dynamics simulations to determine the binding affinity for different classes of drugs, namely aminoglycosides, polymyxins, β-lactams, tetracyclines, glycylcyclines, quinolones and metronidazole with AdeB, AcrB, and NorM efflux proteins. Our results revealed that class polymyxins has the highest binding affinity with the RND efflux pumps i.e. AcrAB-TolC and AdeABC as well as non-RND efflux pump, NorM. The experimental validation study demonstrated bigger zone of inhibition in presence of efflux pump inhibitor than polymyxin alone thus unveiling its specificity toward efflux pump. The reported experimental data comprising of minimum inhibitory concentration of antibiotics toward these efflux pumps also support our finding based on in silico approach. To recapitulate the outcome, polymyxins shows maximum specificity toward RND as well as non-RND efflux pump and may unlatch the way to rationally develop new potential antibacterial agents as well as efflux pump inhibitors in order to combat resistance.     

主动外排机制在鲍曼不动杆菌耐药性中的作用

目的探讨细菌主动外排机制在临床分离的鲍曼不动杆菌耐药性中的作用。方法琼脂稀释法检测临床分离的鲍曼不动杆菌对常用抗生素的耐药性,测定经外排泵抑制剂碳酰氰基-对-氯苯腙（CCCP）处理前后鲍曼不动杆菌对抗生素最小抑菌浓度（MIC）的变化,以聚合酶链反应（PCR）、逆转录-聚合酶链反应（RT-PCR）检测多重耐药主动外排基因以出及其表达水平。结果临床分离的鲍曼不动杆菌对常用抗生素耐药率高且具有多重耐药性,并存在药物的主动外排。所有临床分离的菌株均能检测到adeB基因,但多重耐药株表达水平明显高于敏感株（P〈0．01）。结论临床分离的鲍曼不动杆菌的耐药性尤其是多重耐药性与外排泵介导的耐药机制密切相关。     

鲍曼不动杆菌无痕基因敲除及hcp基因相关功能

[背景]鲍曼不动杆菌耐药严重,基因敲除是研究细菌毒力与耐药的重要方式.但现有的大部分细菌基因敲除方法基于抗生素抗性筛选,导致不适用于多重耐药菌株的基因敲除.[目的]旨在建立一种非依赖于抗生素抗性筛选的方法,用于敲除多重耐药鲍曼不动杆菌基因.[方法]运用同源 重组和自杀载体pMo 130-TelR对亚碲酸钾的抗性,使用两...     

Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems

Multidrug efflux pumps have emerged as relevant elements in the intrinsic and acquired antibiotic resistance of bacterial pathogens. In contrast with other antibiotic resistance genes that have been obtained by virulent bacteria through horizontal gene transfer, genes coding for multidrug efflux pumps are present in the chromosomes of all living organisms. In addition, these genes are highly conserved (all members of the same species contain the same efflux pumps) and their expression is tightly regulated. Together, these characteristics suggest that the main function of these systems is not resisting the antibiotics used in therapy and that they should have other roles relevant to the behavior of bacteria in their natural ecosystems. Among the potential roles, it has been demonstrated that efflux pumps are important for processes of detoxification of intracellular metabolites, bacterial virulence in both animal and plant hosts, cell homeostasis and intercellular signal trafficking.     

鲍曼不动杆菌感染的分布特点及药敏分析

目的了解鲍曼不动杆菌感染分布情况及对20种抗生素耐药性分析。方法送检标本按照《全国临床检验操作规程》（第2版）微生物方法操作,用Vitek—Systems ATB法国生物,梅里埃微生物分析仪,并结合传统手工非发酵微量生化管编码补充试验进行菌种鉴定;药敏试验采用K—B琼脂纸片扩散法及法国梅里埃ATB试条。结果112株鲍曼不动杆菌中有93株（83％）来自于上呼吸道（痰液及咽拭子）：药敏结果显示鲍曼不动杆菌对氨基糖苷类（阿米卡星、庆大霉索）,喹诺酮类（环丙沙星）,碳青酶烯类（亚胺培南）具有较高的敏感率。对β-呐酰胺类抗生素有较高的耐药性,在检测的112株鲍曼不动杆菌中,多重耐药菌株占54．5％（61／112）,三重耐药株占14．8％,而在这些多重耐药菌株中,大于三重耐药的菌株就占到69％。结论鲍曼不动杆菌对抗菌药物已产生多重耐药性,应重视该菌感染及耐药性监测,阻止多重耐药菌株的播散,预防医院感染的发生。     

Characterization of a highly virulent and antimicrobial‐resistant Acinetobacter baumannii strain isolated from diseased chicks in China

Poultry husbandry is a very important aspect of the agricultural economy in China. However, chicks are often susceptible to infectious disease microorganisms, such as bacteria, viruses and parasites, causing large economic losses in recent years. In the present study, we isolated an Acinetobacter baumannii strain, CCGGD201101, from diseased chicks in the Jilin Province of China. Regression analyses of virulence and LD₅₀ tests conducted using healthy chicks confirmed that A. baumannii CCGGD201101, with an LD₅₀ of 1.81 (±0.11) × 10⁴ CFU, was more virulent than A. baumannii ATCC17978, with an LD₅₀ of 1.73 (±0.13) × 10⁷ CFU. Moreover, TEM examination showed that the pili of A. baumannii CCGGD201101 were different from those of ATCC17978. Antibiotic sensitivity analyses showed that A. baumannii CCGGD201101 was sensitive to rifampicin but resistant to most other antibiotics. These results imply that A. baumannii strain CCGGD201101 had both virulence enhancement and antibiotic resistance characteristics, which are beneficial for A. baumannii survival under adverse conditions and enhance fitness and invasiveness in the host. A. baumannii CCGGD20101, with its high virulence and antimicrobial resistance, may be one of the pathogens causing death of diseased chicks.     

外排泵介导鲍曼不动杆菌耐药性的研究进展

目的鲍曼不动杆菌的多重耐药性问题日趋严重,该菌外膜上外排泵过表达是导致其耐药性的重要机制。详尽地研究多药外排泵的机制以及寻找阻断其功能的外排泵抑制剂,将为多耐药鲍曼不动杆菌的治疗开辟新的路径。本文就近年来鲍曼不动杆菌外排泵的研究现状进行综述,着重描述多药外排泵RND家族的耐药谱特征及其表达调控机制,同时,还阐述了MFS和MATE家族外排泵的研究进展。     

鲍曼不动杆菌的临床分布特点及耐药性分析

调查鲍曼不动杆菌的临床分布及其对抗菌药物的耐药情况,为临床合理用药提供依据。将哈尔滨医科大学第一附属医院临床各种来源的鲍曼不动杆菌1582株采用K-B法进行药敏试验,并对结果进行统计分析。2008至2010年共检出鲍曼不动杆菌1582株,临床分布以ICU最多(484株,占54.5%)。对抗菌药物的耐药率逐年增高,ICU抗菌药物的耐药率明显高于非ICU病区。该菌株对临床常用抗菌药物高度耐药和多重耐药,对亚胺培南和美罗培南耐药率高达90.9%和90.3%。鲍曼不动杆菌耐药情况相对严重,临床须重视鲍曼不动杆菌的感染,加强院內感染的控制及耐药性的监测,根据药敏结果选择合适抗生素,延缓耐药性进程。     

鲍曼不动杆菌整合子介导耐药机制的初步研究

【摘 要】 目的 研究整合子参与鲍曼不动杆菌耐药的分子机制。结果 收集2008年1月至2011年12月瑞安市中医院临床分离的200株鲍曼不动杆菌,采用K-B法进行体外药敏试验,采用聚合酶链式反应进行整合子整合酶基因的检测;整合子可变区扩增、克隆、测序,分析整合子基因结构。结果 59.0%的医院感染鲍曼不动杆菌Ⅰ类整合子阳性,未检测出Ⅱ、Ⅲ类整合子;编码对氨基糖苷类、磺胺类抗菌药物和氯霉素耐药的基因;整合子阳性组多药耐药菌均明显高于阴性组。结论 Ⅰ类整合子在医院感染鲍曼不动杆菌中广泛分布,可通过质粒在不同菌属间水平传播,在耐药基因传播中起重要作用,应引起临床足够的重视。     

重症监护室耐亚胺培南鲍曼不动杆菌的耐药性分析

目的探讨温州医学院附属第一医院重症监护室（ICU）耐亚胺培南鲍曼不动杆菌的耐药特性。方法对2006年1月至2007年12月ICU分离的菌株采用常规方法进行菌株分离,经革兰染色、氧化酶试验等初筛,再经VITEK-32型全自动微生物分析仪进行菌株鉴定和药敏试验。结果共检测到98株鲍曼不动杆菌,其中耐亚胺培南的鲍曼不动杆菌为50株（占51.0%）,标本来源大部分为痰液（占94.9%）。耐亚胺培南鲍曼不动杆菌对常用16种抗菌药物耐药率〉50%的有15种,耐药率〉90%有3种,分别为氨苄西林（98.0%）、头孢唑林（99.0%）和呋喃妥因（99.0%）,对抗菌药物耐药率最低仅为头孢哌酮/舒巴坦（10.2%）,另外检测到对所用抗菌素泛耐为4株（8.0%）;而对亚胺培南敏感的鲍曼不动杆菌对常用16种抗菌药物耐药率〉50%的仅为4种,耐药率〉90%同样为氨苄西林（100%）、头孢唑林（97.9%）和呋喃妥因（97.9%）,耐药率比较低的为美罗培南（10.4%）、妥布霉素（16.7%）和环丙沙星（16.7%）,耐药率最低也为头孢哌酮/舒巴坦（6.3%）。结论 ICU分离耐亚胺培南鲍曼不动杆菌多重耐药性严重,出现了泛耐菌株;临床可根据药敏试验选用抗菌药物,一般条件下耐亚胺培南鲍曼不动杆菌建议选用头孢哌酮／舒巴坦。     

鲍曼不动杆菌对碳青霉烯类抗生素的耐药性分析

目的 了解鲍曼不动杆菌的耐药情况,并检测耐碳青霉烯类鲍曼不动杆菌的耐药基因,为指导临床合理用药、控制院内感染提供依据。方法 利用K-B法检测45株鲍曼不动杆菌临床分离株的耐药情况,通过改良Hodge试验、Carba NP试验和EDTA协同试验对多重耐药鲍曼不动杆菌的碳青霉烯酶进行表型检测,并采用PCR技术检测鲍曼不动杆菌携带OXA-23和NDM-1型耐药基因的情况。结果 45株鲍曼不动杆菌临床分离株中共筛出42株多重耐药菌株;利用改良Hodge试验和Carba NP试验检出36株碳青霉烯酶阳性菌株;采用PCR扩增出OXA-23,未扩增出NDM-1。结论 鲍曼不动杆菌耐药情况严重,且耐药基因OXA-23携带率高,治疗时应根据药敏试验结果合理用药。     

膜孔蛋白改变在鲍曼不动杆菌对亚胺培南耐药中的作用

目的 对鲍曼不动杆菌耐药情况进行分析,探索膜孔蛋白在亚胺培南耐药中的作用,为临床合理用药及控制医院感染提供依据。方法 收集非重复亚胺培南耐药鲍曼不动杆菌63株,亚胺培南敏感鲍曼不动杆菌21株,用K-B纸片法检测上述细菌对16种抗菌药物的敏感性,PCR技术检测carO和oprD膜孔蛋白基因携带情况,并采用DNASTAR软件进行序列对比,对CarO蛋白三维结构建模。结果 亚胺培南耐药鲍曼不动杆菌除对替加环素（3.2%）、头孢哌酮/舒巴坦（28.6%）和米诺环素（30.2%）耐药率低外,对其他抗菌药物耐药率均较高,而亚胺培南敏感菌对多数抗生素均较敏感。PCR扩增显示所检测菌株carO和oprD基因均阳性。进一步系列比对发现亚胺培南耐药株较敏感株carO基因存在有意义突变,蛋白质分子立体结构有明显差别。结论 亚胺培南耐药鲍曼不动杆菌耐药情况严峻,carO膜孔蛋白基因突变发挥重要作用。     

不同海拔地区同级别医院鲍曼不动杆菌的分布与 耐药性的连续对比性分析

目的连续对比分析不同海拔地区同级别医院非鲍曼不动杆菌的耐药性,寻找不同海拔对鲍曼不动杆菌的耐药性的影响并指导合理应用抗生素。方法回顾分析2011-2013年两家不同海拔地区同级别医院临床分离的鲍曼不动杆菌药敏结果。结果 2011年至2013年,低海拔地区医院鲍曼不动杆菌检出率为12.66%、17.01%、15.33%。高海拔的地区院鲍曼不动杆菌检出率为0.24%、1.50%、1.44%。低海拔地区医院鲍曼不动杆菌仅对美满环素仍保持较高的敏感率;除头孢哌酮/舒巴坦外,对多数常用药物耐药率均高于70%。而且保持稳定。高海拔的地区院鲍曼不动杆菌对常用抗生素的耐药率逐年下降,庆大霉素、左旋氧氟沙星、亚胺培南、头孢哌酮、头孢他啶的敏感率近两年均在60%以上。结论低海拔地区医院鲍曼不动杆菌检出率高,常用抗生素耐药率高。高海拔的地区院鲍曼不动杆菌检出率低,常用抗生素敏感率高。环境因素对微生态具有重要的影响作用。     

结核杆菌的药物外排泵

外排泵基因过度表达促使细胞内的药物转移到细胞外,胞内药物浓度下降,致使药物临床疗效降低或无效。外排泵上有多个与识别底物结构无关的阴离子凹穴(底物结合位点),通过静电引力非特异性结合各种含阳离子的药物,在能量协助下将药物排到细胞外,进而导致细菌抗药性的产生。研究表明,结核杆菌基因组中存在外排泵基因,但仅分离到几个有功效的外排泵。本文就相关研究进展进行综述。     

鲍曼不动杆菌裂解性噬菌体LZ35的分离及全基因组分析

目的 通过分离鉴定鲍曼不动杆菌噬菌体并进行遗传信息分析,为今后噬菌体用于治疗鲍曼不动杆菌引起的感染提供依据。方法 以鲍曼不动杆菌临床分离株为宿主菌,从医院污水中分离鲍曼不动杆菌噬菌体并进行纯化、电镜观察形态特征、提取噬菌体DNA,进行全基因组测序,分析全基因组的结构特征,比较基因组分析其进化关系。结果 分离到鲍曼不动杆菌裂解性噬菌体LZ35,电镜观察显示,该噬菌体属于有尾噬菌体目肌尾病毒科。基因组全长44 885 bp,G＋C含量为37.95%,含有83个开放阅读框,其中22个编码序列可预测其功能,61个编码序列为未知基因。噬菌体LZ35的基因组与鲍曼不动杆菌噬菌体IME-AB2和YMC-13-01-C62具有很高的同源性（分别为97%和99%）,与鲍曼不动杆菌噬菌体YMC11/12/R1215的进化关系最近。结论 以鲍曼不动杆菌临床分离株为宿主菌,分离到鲍曼不动杆菌裂解性噬菌体LZ35,明确了其形态和基因组特征,为防治噬菌体疗法奠定基础。     

鲍曼不动杆菌中外排泵介导耐药机制的研究进展

外排泵的过表达是目前导致鲍曼不动杆菌多重耐药的最重要机制之一,详细了解这一复杂机制有助于尽快找到有效的防治策略。目前,鲍曼不动杆菌中已被报道的外排泵家族包括耐药结节细胞分化(resistance-nodulation-cell division,RND)家族、主要协同转运蛋白超家族(major facilitator superfamily,MFS)、多药及毒性化合物外排(multidrug and toxic compound extrusion,MATE)家族、小多重耐药(small multidrug resistance,SMR)家族。它们之中既有通过染色体介导的外排泵,也有通过质粒等遗传元件介导的外排泵。外排底物可呈现多样性,也可呈现专一性。本文就上述外排泵的种类、功能和调控机制进行综述。     

呼吸内科重症监护室一起多重耐药鲍曼不动杆菌感染暴发的调查

目的及时发现医院感染暴发苗头,查找感染源,切断传播途径,最大限度减少医院感染发生。方法对2009年4月26～28日期间RICU发生的4例鲍曼不动杆菌感染病例进行聚集感染危险因素调查,采集标本进行目标菌检测,应用ERIC—PCR技术对聚集病例和散发病例菌株进行基因同源性分析,采取综合性防控措施进行医院感染具体干预。结果4例患者确定为医院感染病例,4例患者均有气管插管操作经历,3例患者环境卫生学检测存在耐药谱相同的鲍曼不动杆菌,ERIC—PCR分析4例患者检出的鲍曼不动杆菌具有基因同源性,确定为医院感染暴发。严格执行隔离防护措施和后续加强上呼吸机患者管理,未再出现聚集病例。结论医院感染暴发危及患者医疗安全,应用分子生物学分析手段可以促进医院感染防控措施的效果;加强上呼吸机患者的管理,加强手卫生的管理可以有效防控医院感染聚集暴发。     

Gene cloning and properties of the RND-type multidrug efflux pumps MexPQ-OpmE and MexMN-OprM from Pseudomonas aeruginosa

We cloned two operons for putative RND-type multidrug efflux pumps from Pseudomonas aeruginosa by a PCR method. We designated the genes in one operon mexPQ(-opmE) and in another operon mexMN. Introduction of the mexPQ-opmE into drug hypersensitive cells resulted in elevated MICs of macrolides, fluoroquinolones and some other drugs. Introduction of the mexMN into the hypersensitive cells possessing oprM, but not into cells not possessing oprM, resulted in elevated MICs of chloramphenicol and thiamphenicol. Thus, we conclude that MexPQ-OpmE and MexMN-OprM are functional multidrug efflux pumps when expressed in P. aeruginosa.