鲍曼不动杆菌裂解性噬菌体LZ35的 分离及全基因组分析

摘要：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。     

pilO基因对鲍曼不动杆菌运动能力的影响

目的:构建无标记的鲍曼不动杆菌pil O基因缺失突变株,通过表型鉴定pil O基因缺失对鲍曼不动杆菌运动能力的影响。方法:PCR扩增pil O基因上下游各1 kb同源臂,连接至p MO130-TelR自杀质粒,质粒转化大肠杆菌S17-1后再接合至鲍曼不动杆菌4294中;蔗糖诱导自杀质粒与基因组同源重组,以获得基因缺失突变株;蹭行实验观察pil O基因缺失对鲍曼不动杆菌运动能力的影响。结果:构建了pil O基因缺失鲍曼不动杆菌4294菌株突变株;缺失株与野生株生长曲线无明显差异,但蹭行能力显著下降。结论:pil O基因与细菌蹭行能力密切相关,提示其编码鲍曼不动杆菌Ⅳ型菌毛结构蛋白。     

鲍曼不动杆菌临床菌株生物膜形成能力的研究

目的对鲍曼不动杆菌临床菌株的生物膜形成能力进行对比研究,并分析生物膜形成的一些可能的影响因素。方法利用在聚苯乙烯板上构建生物膜的技术对51株全耐药的鲍曼不动杆菌的生物膜形成能力进行检测,同时对分离自下呼吸道和无菌体液的各20株鲍曼不动杆菌的生物膜形成能力进行研究,然后对新近报道的鲍曼不动杆菌生物膜形成相关基因abaI在所有菌株中的分布情况进行检测。结果 51株全耐药的鲍曼不动杆菌中35株(68.6%)可以形成生物膜,并且形成生物膜的能力较强。50%(10/20)分离自下呼吸道的鲍曼不动杆菌能够形成生物膜,20株无菌体液中分离的菌株仅有1株可以形成生物膜。78.0%(71/91)鲍曼不动杆菌中abaI基因扩增阳性。结论分离自下呼吸道的鲍曼不动杆菌临床菌株有较强的生物膜形成能力,abaI基因广泛存在于鲍曼不动杆菌临床菌株中。临床在治疗鲍曼不动杆菌感染的同时需要考虑其在感染部位形成生物膜的因素,可能在治疗的同时有必要加入一些对生物膜有穿透性的药物。     

鲍曼不动杆菌临床分离株的耐药性及同源性分析

目的 通过对重庆医科大学附属第二医院近4年临床分离的103株鲍曼不动杆菌的耐药性和同源性分析,了解该院鲍曼不动杆菌的耐药性特点及院内感染流行状况.方法 2008年至2011年间该院临床科室分离的103株鲍曼不动杆菌,进行药敏试验并对耐药性分析;提取细菌基因组DNA,以随机扩增DNA多态性(RAPD)方法进行基因分型.结果 药敏试验结果显示分离出的103株菌呈现出高耐药率及多重耐药率的特点,其中对左氧氟沙星和亚胺培南的耐药性最低,分别为69.9％和57.3％.103株多重耐药鲍曼不动杆菌用RAPD分型共分为16种基因型:A～P,其中A型84株,为主要流行型别;B型3株;C型、G型各2株;其余12型各1株.结论 该院鲍曼不动杆菌具有多重耐药及高耐药率,可能存在以A型鲍曼不动杆菌克隆株传播方式的院内流行,临床上应加强对A型鲍曼不动杆菌的监控,采取有效的措施以预防院内感染的爆发流行.     

鲍曼不动杆菌IRS-PCR基因分型研究

目的 用低频限制性位点聚合酶链反应(IRS-PCR)对鲍曼不动杆菌进行基因分型,分析基因型与鲍曼不动杆菌耐药谱的关系,并初步探讨其在分子流行病学中的作用.方法 随机收集2008年8月至2009年8月临床分离的73株鲍曼不动杆菌,采用K-B法进行药物敏感试验确定鲍曼不动杆菌耐药谱;同时利用IRS-PCR对此73株鲍曼不动杆菌进行基因分型;并分析IRS-PCR分型与鲍曼不动耐药谱的关系;结合IRS-PCR分型结果与73株鲍曼不动杆菌感染病例的临床资料,分析在此时间段鲍曼不动杆菌在我院流行感染的情况.结果 药物敏感试验将73株鲍曼不动杆菌菌株分为A1(19株全耐药型)和A2 ～ A31(54株耐药谱型)31个药敏谱.IRS-PCR法将其分为A～W共23个基因型,其中A、C、B、D和E型为5种优势菌株,分别为14、11、10、8和6株.对比研究发现A1型菌株(15/19)主要集中在基因型A、C、D内,而基因型B包含A15型耐药菌株9株(69.2％),基因型E包含A3型耐药菌株3株(42.9％).A基因型在院内特别是ICU中心引起2次爆发流行,而C和D型主要在呼吸内科引起感染.结论 IRS-PCR基因分型与药敏分型有较高的一致性,且IRS-PCR基因分型在早期发现和预防感染暴发流行方面优于药敏分型.     

鲍曼不动杆菌携带前噬菌体的生物信息学分析

【目的】预测并分析82株全基因组测序的鲍曼不动杆菌前噬菌体的携带情况,鉴定前噬菌体编码的抗生素耐药基因和毒力因子。【方法】利用PHASTER (Phage Search Tool Enhanced Release)软件预测鲍曼不动杆菌携带的前噬菌体,采用CARD (The Comprehensive Antibiotic Research Database)和VFDB(VirulenceFactorsDatabase)在线分析软件预测前噬菌体编码的抗生素耐药基因和毒力因子。【结果】预测到472条鲍曼不动杆菌前噬菌体,其中完整型前噬菌体201条,疑似型前噬菌体91条,缺陷型前噬菌体180条。平均每株鲍曼不动杆菌基因组中可携带至少2条完整型前噬菌体。每株鲍曼不动杆菌所携带的全部前噬菌体占其基因组比例约为4%–6%。29条前噬菌体携带77个耐药基因,耐药表型共有14种,分别来自15个不同的家族,涵盖6种抗生素耐药的作用机制。132条前噬菌体编码毒力基因,归类为38种毒力基因和34种毒力因子。不同类型的前噬菌体普遍携带1–2种毒力因子,少数前噬菌体携带3种及以上毒力因子。分析毒力因子可能的宿主...     

实时荧光聚合酶链反应检测呼吸道感染鲍曼不动杆菌TEM-1基因

目的 建立一种快速、准确、特异、定时检测鲍曼不动杆菌TEM-1型β-内酰胺酶耐药基因的方法.方法 选择TEM-1型β-内酰胺酶耐药基因作为靶序列,设计合成引物和探针;收集呼吸道感染患者痰标本培养的鲍曼不动杆菌279株,并对其进行检测分析.结果 采用荧光聚合酶链反应检测鳗曼不动杆菌TEM-1耐药基因灵敏度为102拷贝,279株鲍曼不动杆菌中检出47株携带TEM-1基因,检出率为16.8%.结论 应用Taqman探针荧光聚合酶链反应能够快速、准确检测鲍曼不动杆菌TEM-1型β-内酰胺酶耐药基因.     

鲍曼不动杆菌血流感染的危险因素及预后分析

目的研究院内获得性鲍曼不动杆菌血流感染的临床特点、治疗情况、分析导致鲍曼不动杆菌血流感染的危险因素,同时总结泛耐药鲍曼不动杆菌感染患者死亡危险因素,为临床防治泛耐药鲍曼不动杆菌血流感染提供指导。方法采用病例对照研究的方法,回顾性分析2012年4月至2015年6月丽水市中心医院住院的35例鲍曼不动杆菌血流感染患者临床资料,包括基础疾病,病原菌分布情况,临床特征,危险因素,治疗及预后转归情况,根据细菌耐药情况,分为泛耐药鲍曼不动杆菌17例与非耐药鲍曼不动杆菌18例。按入院28天预后转归情况,将35例鲍曼不动杆菌血流感染患者进一步分为好转组26例与死亡组9例。结果采取Fisher精确检验比较两组间差异,结果显示原发感染灶不明,不恰当使用广谱抗菌药物,住ICU大于2周,其他部位培养到鲍曼不动杆菌,同期ICU内泛耐药鲍曼不动杆菌流行等危险因素,存在显著性差异(P0.05);Logistic多因素回归分析鲍曼不动杆菌血流感染患者死亡危险因素,结果显示持续血小板减少3×109/L、APACHEII评分≥20分、脓毒症休克、多脏器功能衰竭是导致患者死亡的独立危险因素(P0.05)。结论原发感染灶不明和不恰当使用广谱抗菌药物是泛耐药鲍曼不动杆菌血流感染主要危险因素;持续血小板减少3×109/L、APACHEII评分≥20分、脓毒症休克、多脏器功能衰竭是鲍曼不动杆菌血流感染患者主要的死亡独立危险因素。     

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。     

鲍曼不动杆菌基因分型技术的研究进展

鲍曼不动杆菌为非发酵糖类革兰阴性杆菌,具有强大的获得耐药性和克隆传播的能力,广泛分布于医院环境,是医院内感染的重要病原菌之一。因此,建立精准、高效的鲍曼不动杆菌基因分型技术,是开展其医院内感染流行病学研究和临床防控的重要工具。本文就近年来鲍曼不动杆菌基因分型技术的研究进展进行综述,并分析比较多种基因分型技术的原理、优点、局限性及应用范围。     

The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity

The genome sequences of a number of Acinetobacter baumannii strains, including representatives of the main epidemic international lineages, have now been determined, and several others are in progress. The study of A. baumannii genomics has provided an expanded view of the adaptation and virulence capacities of this bacterial species, whilst also presenting novel insights into its intraspecies diversity and genome evolution. Genomic analyses have revealed that the current A. baumannii clinical population consists of low-grade pathogens, whose pathogenicity relies mainly on an ability to persist in the hospital setting and survive antibiotic treatment. A. baumannii has a high capacity to acquire new genetic determinants and displays an open pan genome; this feature may have played a crucial role in the evolution of this human opportunistic pathogen towards clinical success.     

Bioinformatic analysis of the Acinetobacter baumannii phage AB1 genome

As one of the pathogens of hospital-acquired infections, Acinetobacter baumannii poses great challenges to the public health. A. baumannii phage could be an effective way to fight multi-resistant A. baumannii. Here, we completed the whole genome sequencing of the complete genome of A. baumannii phage AB1, which consists of 45,159bp and is a double-stranded DNA molecule with an average GC content of 37.7%. The genome encodes one tRNA gene and 85 open reading frames (ORFs) and the average size of the ORF is 531bp in length. Among 85 ORFs, only 14 have been identified to share significant sequence similarities to the genes with known functions, while 28 are similar in sequence to the genes with function-unknown genes in the database and 43 ORFs are uniquely present in the phage AB1 genome. Fourteen function-assigned genes with putative functions include five phage structure proteins, an RNA polymerase, a big sub-unit and a small sub-unit of a terminase, a methylase and a recombinase and the proteins involved in DNA replication and so on. Multiple sequence alignment was conducted among those homologous proteins and the phylogenetic trees were reconstructed to analyze the evolutionary courses of these essential genes. From comparative genomics analysis, it turned out clearly that the frame of the phage genome mainly consisted of genes from Xanthomonas phages, Burkholderia ambifaria phages and Enterobacteria phages and while it comprises genes of its host A. baumannii only sporadically. The mosaic feature of the phage genome suggested that the horizontal gene transfer occurred among the phage genomes and between the phages and the host bacterium genomes. Analyzing the genome sequences of the phages should lay sound foundation to investigate how phages adapt to the environment and infect their hosts, and even help to facilitate the development of biological agents to deal with pathogenic bacteria.     

Effect of a Novel Podophage AB7-IBB2 on Acinetobacter baumannii Biofilm

Biofilm formation in Acinetobacter baumannii is a common cause of nosocomial infections in humans. Clinical devices and abiotic surfaces are important sites of colonization leading to formation of biofilms. Such infections are often resistant to multiple antibiotic therapies, and hence there is need for an effective mode of control. Herein, we describe the isolation, characterization of a new lytic bacteriophage of A.?baumannii and its effect on biofilm. The phage AB7-IBB2, with a genome size of about 170?kb was identified to be of family Podoviridae as revealed by transmission electron microscopy. It had an isometric head (35?nm) and a short tail (7?nm). It lysed 19/39 (49?%) clinical isolates of A.?baumannii. Rapid adsorption (>99?% adsorbed in 4?min), a latency period of 25?min and a burst size 22?PFU/infected cell was observed. The phage could inhibit A.?baumannii biofilm formation and disrupt preformed biofilm as well. The phage has promising potential to be considered as a candidate biocontrol agent for A.?baumannii infections.     

Genome sequence of a dominant, multidrug-resistant Acinetobacter baumannii strain, TCDC-AB0715

Acinetobacter baumannii has emerged as a significant nosocomial pathogen worldwide. The increasing trend of carbapenem and fluoroquinolone resistance in A. baumannii severely limits the usage of therapeutic antimicrobial agents. Here we report the genome sequence of a multidrug-resistant A. baumannii strain, TCDC-AB0715, harboring both bla(OXA-23) and bla(OXA-66).     

Brachypodium distachyon: making hay with a wild grass

Brachypodium distachyon is a wild grass with a short life cycle. Although it is related to small grain cereals such as wheat, its genome is only a fraction of the size. A draft genome sequence is currently available, and molecular and genetic tools have been developed for transformation, mutagenesis and gene mapping. Accessions collected from across its ancestral range show a surprising degree of phenotypic variation in many traits, including those implicated in domestication of the cereals. Thus, given its rapid cycling time and ease of cultivation, Brachypodium will be a useful model for investigating problems in grass biology.     

Comparative analysis of Acinetobacters: three genomes for three lifestyles

Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.     

Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm

Acinetobacter baumannii is a Gram-negative bacterium causing nosocomial infections worldwide. To gain quick insight into the molecular basis of biofilm formation in A. baumannii, we determined the complete genome sequence of A. baumannii strain 1656-2, which forms sturdy biofilm and is resistant to multiple drugs.     

Proteomic analysis of a fraction enriched in cell envelope proteins of Acinetobacter baumannii

Acinetobacter baumannii is a multiresistant opportunistic nosocomial pathogen. A protein fraction was purified and analyzed by 2-DE. Twenty-nine major protein spots were selected for protein identification using trypsin digestion and MS analysis. As the A. baumannii genome has not yet been described, protein identification was performed by homology with other Acinetobacter species in the NCBi database. We identified ribosomal proteins, chaperones, elongation factors and outer membrane proteins (Omp), such as OmpA and the 33-36-kDa OMP. Proteomic analysis of A. baumannii provides a platform for further studies in antimicrobial resistance.     

Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78

Acinetobacter baumannii is an emerging opportunistic gram-negative pathogen responsible for hospital-acquired infections. A. baumannii epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant A. baumannii strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.