基于基因组数据分析的细菌耐药基因识别与表型预测

利用基因组数据和生物信息学分析方法,快速鉴定耐药基因并预测耐药表型,为细菌耐药状况监测提供了有力辅助手段。目前,已有的数十个耐药数据库及其相关分析工具这些资源为细菌耐药基因的识别以及耐药表型的预测提供了数据信息和技术手段。随着细菌基因组数据的持续增加以及耐药表型数据的不断积累,大数据和机器学习能够更好地建立耐药表型与基因组信息之间的相关性,因此,构建高效的耐药表型预测模型成为研究热点。本文围绕细菌耐药基因的识别和耐药表型的预测,针对耐药相关数据库、耐药特征识别理论与方法、耐药数据的机器学习与表型预测等方面展开讨论,以期为细菌耐药的相关研究提供手段和思路。     

环境中抗生素抗性基因的水平传播扩散

抗生素抗性基因作为一类新型环境污染物,其在不同环境介质中的传播扩散可能比抗生素本身的环境危害更大,其中,水平基因转移是抗生素抗性基因传播的重要方式,是造成抗性基因环境污染日益严重的原因之一.本文系统阐述了抗生素抗性基因在环境中发生水平转移的主要分子传播元件及其影响因素,这对于正确揭示抗性基因的分子传播机制具有重要意义.结合多重抗药性的传播扩散机制,探讨了行之有效的遏制抗生素抗性基因传播扩散的方法和途径,并针对目前的污染现状,对今后有关抗生素抗性基因水平转移的研究重点进行了展望.     

食品动物养殖环境中细菌耐药性研究进展

抗生素耐药性被世界卫生组织认为是21世纪人类面临的最大的公共卫生安全问题之一。近年来,抗生素耐药基因作为一种新型污染物而受到广泛关注。养殖场现已成为耐药基因的一个重要储库,耐药菌及耐药基因随着动物排泄物进入环境,从而加速了耐药基因在环境中的传播。畜禽养殖环境中耐药基因和耐药菌可能经食物链、空气等途径传至人类,给人类健康带来巨大威胁。文中结合最新文献,主要介绍了动物养殖场抗菌药物耐药菌和耐药基因的分布特点、耐药基因的持留和传播扩散、研究方法等方面的研究进展,为食品动物养殖环境的抗菌药物耐药性风险评估提供一定支持。     

大熊猫源细菌耐药性研究进展

耐药菌和耐药基因已成为一种新型环境污染物,引发世界公共卫生问题。细菌耐药性尤其是多重耐药菌在人医临床、畜禽养殖以及环境传播等多个方面得到越来越多的关注,而关于大熊猫等野生动物的耐药性研究相对较少。大熊猫(Ailuropoda melanoleuca)是世界公认的珍稀野生动物,其种群数量易受到各种疾病的威胁,尤其是肠道细菌性疾病。随着抗菌药物在疾病预防和控制中的普遍使用,由此带来的耐药性危害日益明显。本文总结了关于大熊猫源细菌耐药的国内外研究报道,对其耐药表型、耐药基因型、耐药机制及水平传播机制等方面内容进行了综述,旨在为大熊猫源细菌耐药性的研究和防控提供依据,为临床科学用药提供理论参考,从而助力大熊猫迁地保护。     

细菌耐药影响肠道菌群及其宿主免疫调控

抗生素在养殖业、医疗业及制药业的广泛应用导致环境中的细菌耐药性日益严重,环境中的抗生素及耐药细菌一旦进入人体肠道,将破坏肠道菌群稳态,对人体健康造成威胁,而残存于饮食中的环境污染物则加剧了细菌耐药造成的人体健康影响。文中在总结大量文献的基础上,阐述了细菌耐药对人体和动物肠道菌群的影响机制及其相关的机体免疫调控,以环境中影响人体肠道菌群获得耐药性的来源作为切入点,阐述抗生素和耐药细菌进入人体肠道后对人体肠道菌群结构和耐药基因组成的影响,以及与人体免疫和免疫调节相关疾病之间的相关机制,并对今后的研究方向进行了展望。     

翻译后修饰与结核分枝杆菌耐药调控网络

目前对于结核分枝杆菌(Mycobacterium tuberculosis,Mtb)耐药产生机制研究得较多,但对其调控机制的研究较少。翻译后修饰(Post-translational modifications,PTMs)在结核菌多种生理途径(如代谢、应激反应等)中发挥重要调控作用,而它们和结核菌耐药之间的关系逐渐引起了研究者的关注。文中介绍了结核菌抗生素耐受机制以及存在的一些PTMs,重点讨论了PTMs在调控结核杆菌耐药机制中的潜在作用,以期为新型抗结核药物研发提供新的切入点。     

A new look at antibiotic resistance

Abstract Since the discovery of antibiotic resistance in clinically important microbes, attention has focused properly on the profound medical aspects of this problem. However, studies of antibiotic resistance are of great interest in their own right for studies of gene regulation, evolution, chromosome structure, etc.; several resistance genes in clinical isolates are components of classical 'operon' structures. The construction of cloning vectors and gene transfer systems, particularly for interspecies studies, rely heavily on the use of antibiotic resistance genes, since these phenotypes can be used to select for DNA transfer between microbes, plants, and animals. Studies of the role of resistance mechanisms and their genetic determinants in antibiotic-producing organisms have shown that these functions play important roles in biosynthetic pathways and can provide important genetic and biochemical tools for the rational analysis of antibiotic production.     

畜禽微生物耐药组研究进展

目前,绝大部分抗生素用于给人类提供肉奶蛋等食品的畜禽,由此产生的抗生素耐药性对全球公众健康造成了巨大威胁。为了降低畜禽生产环节抗生素耐药性向人类的传播,首先需要明确畜禽消化道或产品微生物携带哪些耐药基因。耐药组指的是某个环境微生物群落全部耐药基因的总和,近年来对于畜禽生产过程中耐药组分析成为研究热点之一。本文综述了基于测序技术研究畜禽(猪、鸡、反刍动物)消化道以及乳中微生物耐药组组成及其影响因素的最新进展,并提出了未来研究方向,包括耐药组研究方法的标准化、基于宏转录组的耐药组基因表达研究,以及可移动遗传元件所携带的耐药基因等,旨在为调控畜禽养殖过程中耐药基因提供思路。     

耐药细菌中交互敏感现象研究进展

细菌耐药性是全球亟待解决的重要公共卫生问题之一,耐药病原菌对人类和动物健康构成极大威胁。交互敏感性、附带敏感性(collateral sensitivity)是指耐药细菌在进化过程中出现的对一类抗菌药物耐药,而对另一类或几类抗菌药物更加敏感的现象。利用交互敏感策略限制甚至逆转细菌耐药性以恢复其对抗菌药物的敏感性是细菌耐药性研究的热点。本文综述了细菌交互敏感的最新研究进展,主要从交互敏感性的概念、表型及机制研究等方面进行阐述,以期为防控和治疗耐药病原菌感染提供新思路。     

High levels of multiple metal resistance and its correlation to antibiotic resistance in environmental isolates of Acinetobacter

Forty strains of Acinetobacter were isolated from different environmental sources. All the strains were classified into four genospecies, i.e. A. baumannii (33 isolates), A. calcoaceticus (three isolates), A. junii (three isolates) and A. genospecies3 (one isolate). Susceptibility of these 40 strains to salts of 20 heavy metals and 18 antibiotics was tested by the agar dilution method. All environmental isolates of Acinetobacter were resistant to multiple metal ions (minimum 13 metal ions) while all but one of the strains were resistant to multiple antibiotics (minimum four antibiotics). The maximum number of strains were found to be sensitive to mercury (60% strains) while all strains were resistant to copper, lead, boron and tungsten even at 10 mm concentration. Salts of these four metal ions may be added to the growth medium to facilitate selective isolation of Acinetobacter. Rifampicin and nalidixic acid were the most toxic antibiotics, inhibiting 94.5 and 89.5% of the acinetobacters, respectively. A. genospecies3 was found to be the most resistant species, tolerating high concentrations of all the 20 metal ions and also to a greater number of antibiotics than any other species of Acinetobacter tested. An inhibitory concentration (10 mm) of Ni²⁺ and Zn²⁺ was observed to inhibit the growth of all of the clinical isolates but allowed the growth of the environmental isolates, facilitating the differentiation between pathogenic and non-pathogenic acinetobacters.     

Evidence for transfer of antibiotic-resistance genes in soil populations of streptomycetes

Phylogenetic analysis was used to evaluate the hypothesis of gene transfer in streptomycetes, many of which are antibiotic producers. The diversity and possible origins of streptomycin-resistance genes was investigated for a population of Streptomyces strains isolated from a site in Brazil where antibiotic production had previously been implicated. The analysis provides compelling evidence for the transfer of these genes. Examination of other Streptomyces -type strains also reveals a scattered distribution of streptomycin producers with respect to the overall phylogeny. These results suggest that horizontal gene transfer may be an important factor in the evolution of antibiotic genes in streptomycetes.     

Cloning and characterization of a gene from Streptomyces griseus coding for a streptomycin-phosphorylating activity

Abstract Six different plasmids expressing streptomycin (SM) resistance and SM phosphotransferase were obtained by cloning genomic DNA from Streptomyces griseus into Streptomyces lividans . The phosphorylating enzymatic activity formed in S. lividans differed in several biochemical properties from the one in S. griseus , though the phosphorylated products were identical.     

Prevalence of the multiple antibiotic resistance operon (marRAB) in the genus Salmonella

The multiple antibiotic resistance operon (marRAB) is a member of the multidrug resistance (mdr) systems. Similar to other mdr systems, this operon when induced encodes resistance to structurally and functionally unrelated antibiotics. marRAB has been shown to be conserved in the family Enterobacteriaceae, but within the genus Salmonella certain species appeared to be lacking this operon. To investigate how conserved the marRAB operon was in Salmonella, 30 veterinary isolates were examined by PCR, Southern blot, and dot blot analysis. Using DNA primers based on the marRAB operon of S. typhimurium, a predicted 2.3-kb amplicon resulted after PCR in 16 of the 30 organisms. The 2.3-kb DNA band from S. enteritidis was cloned and sequenced and shown to possess 99% sequence homology to marRAB from S. typhimurium. Using a labeled marRAB gene probe from S. enteritidis, Southern blot and dot blot analysis confirmed the presence of the operon in all 30 Salmonella species examined. Furthermore, when these isolates were induced with low levels of either tetracycline or chloramphenicol, increased antimicrobial resistance was observed to structurally and functionally unrelated antibiotics. Thus, the widespread occurrence of the marRAB locus in this genus prescribes judicious use of antimicrobials to avoid induction of a mdr phenotype.     

Identification and characterization of class 1 integron resistance gene cassettes among Salmonella strains isolated from healthy humans in China

Twenty-three strains of Salmonella spp. isolated from healthy humans in Guangdong, China, were examined for their susceptibility to ten common antibiotics and the presence of antibiotic resistance integrons. All the strains were resistant to at least one antibiotic, and 4 strains were positive for the intI1 gene. Polymerase chain reaction using in-F and in-B primers showed the existence of amplicons of 1,009 bp in two, 1,664 bp in one, and 1,009 bp and 1,664 bp in one of the intI1 -positive isolates, respectively. Sequence analysis revealed that the 1,009-bp amplicon harbored gene cassette aadA2, conferring resistance to spectinomycin, and the 1,664-bp amplicon harbored genes aadA5 and dfr17, conferring resistance to spectinomycin, streptomycin and trimethoprim. Meanwhile the experiments of plasmid conjugation and Southern hybridization with intI1 as the DNA probe indicated that all the integrons found in these strains were chromosomal. Because the strains carrying class 1 integrons were isolated from healthy humans, it suggests the need for all-round surveillance of the antibiotic resistance of pathogens.     

Enhancement of the efficacy of erythromycin in multiple antibiotic-resistant gram-negative bacterial pathogens

Aims:  To improve the efficacy of erythromycin, a hydrophobic antibiotic, against multiple antibiotic-resistant gram-negative bacterial pathogens by enhancing their outer membrane permeability.
Methods and Results:  Fifty-one nonrepeat gram-negative bacterial pathogens of various genera, resistant to multiple antibiotics, including erythromycin, were selected by disc agar diffusion tests. The amphiphilic cationic steroid antibiotic, Ceragenin CSA-13, a potent permeabilizer of bacterial outer membranes, reduced the minimum inhibitory concentration of erythromycin in 92% of the bacterial pathogens selected for the test, when supplemented with erythromycin. A synergistic effect of Ceragenin CSA-13 and erythromycin in combination was also observed. Spectrofluorimetric study confirmed that Ceragenin CSA-13 acts by depolarizing the bacterial outer membrane. The toxicity of Ceragenin CSA-13 was evaluated to be insignificant by measuring 'median lethal dose' (LD₅₀) on mouse model.
Conclusions:  Ceragenin CSA-13 may be useful as an agent to make erythromycin effective against infections caused by multiple antibiotic resistant gram-negative bacteria.
Significance and Impact of the Study:  The outcome of the study suggests erythromycin–Ceragenin combination as a new approach to overcome the problem associated with the rapid emergence of multi-drug-resistant pathogens. The insignificant toxicity of Ceragenin CSA-13, as found, supports the possibility of the application of this compound for human therapeutics.     

Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: Role of different regions within the zebra fish intestinal tract,and impact on fish intestinal microbiota

The aqueous environment is one of many reservoirs of antibiotic resistance genes (ARGs). Fish, as important aquatic animals which possess ideal intestinal niches for bacteria to grow and multiply, may ingest antibiotic resistance bacteria from aqueous environment. The fish gut would be a suitable environment for conjugal gene transfer including those encoding antibiotic resistance. However, little is known in relation to the impact of ingested ARGs or antibiotic resistance bacteria (ARB) on gut microbiota. Here, we applied the cultivation method, qPCR, nuclear molecular genetic marker and 16S rDNA amplicon sequencing technologies to develop a plasmid‐mediated ARG transfer model of zebrafish. Furthermore, we aimed to investigate the dissemination of ARGs in microbial communities of zebrafish guts after donors carrying self‐transferring plasmids that encode ARGs were introduced in aquaria. On average, 15% of faecal bacteria obtained ARGs through RP4‐mediated conjugal transfer. The hindgut was the most important intestinal region supporting ARG dissemination, with concentrations of donor and transconjugant cells almost 25 times higher than those of other intestinal segments. Furthermore, in the hindgut where conjugal transfer occurred most actively, there was remarkable upregulation of the mRNA expression of the RP4 plasmid regulatory genes, trbBp and trfAp. Exogenous bacteria seem to alter bacterial communities by increasing Escherichia and Bacteroides species, while decreasing Aeromonas compared with control groups. We identified the composition of transconjugants and abundance of both cultivable and uncultivable bacteria (the latter accounted for 90.4%–97.2% of total transconjugants). Our study suggests that aquatic animal guts contribute to the spread of ARGs in water environments.     

抗生素耐药性的多重风险因子及针对性管控策略

抗生素耐药性已经对人类社会造成了重大影响,需要采取切实有效的管控措施,本文将针对耐药性研究领域的新视角,回顾了亟需重视的抗生素耐药性多重风险因素,包括非致病菌、食源和肠道菌群、粪便菌群、废水处理、用药途径和生物膜等,强调了口服抗生素的危害。通过总结针对性的耐药和疾病防控策略,为有效应对抗生素耐药性危机提供新思路。     

Current trends of antibiotic resistance in clinical isolates of Staphylococcus aureus

Staphyloccus aureus （S. aureus） is a well known human pathogen known to causes a verity of infections in humans. In recent years S. aureus is reported to show drug resistant toward commonly known drugs. Therefore, this study was designed to study the pattern of antibiotic resistance in 50 clinical isolates ofS. aureus isolated at Dhanwantri Hospital and Research Centre, Jaipur, Rajasthan, India. S. aureus cultures were isolated from different clinical samples, pus, throat swabs and urine on Blood agar and MacConkey agar and Chrom agar plats and characterized by an array of microscopic and biochemical tests. Antibiotic sensitivity test was performed by standard disc diffusion method （Kirby bayer＇s method） on Muller Hinton agar plates. During this study, among 50 S. aureus isolates 48 （96%） were found to be resistance toward Aztreonam and Doxicycline followed by Ciprofloxacin （n = 45, 90%）, Cefpodoxime and Ceftazidime （n = 44, 88%）, Cefuroxime （n = 40, 80%）, Pipracillin ＋ Tazobactum （n = 38, 76%）, Cefoparazone （n = 36, 72%）, Amoxicillin ＋ Clavulanic acid and Ceftriaxone （n = 33, 66%）, Levofloxacin （n = 32, 64%）, Moxifloxacin （n = 31, 62%）, Ofloaxacin （n = 25, 50%）, Cloxacillin （n = 22, 44%）, Azithromycin （n = 21, 42%）, Clindamycin （n = 19, 38%）, Meropenem （n = 18, 36%）, Clarithromycin （n = 16, 32%）, Ampicillin ＋ sulbactam （n = 13, 26%）, Amikacin （n = 12, 24%）, Impipenem （n = 8, 16%）, Linezolid and Methicillin （n = 7, 14%） and Teicoplanin （n = 3, 6%）. In conclusion, the isolated S. aureus found to be resistant toward common antibiotics, however all isolates were found to be susceptible to Vancomycin.     

抗生素抗性基因在环境中的传播扩散及抗性研究方法

抗生素在医药、畜牧和水产养殖业的大量使用造成了环境中抗性耐药菌和抗性基因日益增加,抗生素抗性基因作为一种新型环境污染物引起人们的广泛关注.本文综述了近年来国内外有关抗生素抗性基因的研究进展,其在水、土壤、空气等环境介质中和动,植物体内的传播扩散,以及开展环境中抗生素抗性基因研究的必要性,重点介绍了有关抗生素抗性（包括抗性细菌和抗性基因）的研究方法,指出抗性基因研究中存在的问题,并对未来的相关研究进行了展望.