The application of DNA microarrays in gene expression analysis

DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.     

Effect of spdC gene expression on virulence and antibiotic resistance in clinical Staphylococcus aureus isolates

International Microbiology - Surface protein display C (SpdC) protein was described as a novel virulence factor of Staphylococcus aureus that affects biofilm formation and pathogenesis and favors...     

芜湖地区生牛奶中金黄色葡萄球菌的污染状况及其耐药性和毒力基因检测

目的明晰芜湖地区生牛乳中金黄色葡萄球菌的污染状况及其耐药性和产毒性,为该地区防治奶牛乳房炎提供理论依据。方法分别使用国标GB 4789.10-2010方法和PCR方法对从芜湖地区4个奶牛场采集的185份生牛乳进行金黄色葡萄球菌和耐甲氧西林金黄色葡萄球菌(MRSA)分离鉴定;采用纸片扩散法检测甲氧西林敏感金黄色葡萄球菌分离株(MSSA)和MRSA分离株的耐药性,PCR方法检测其携带毒力基因情况。结果共检出金黄色葡萄球菌49株,总检出率为26.5%(49/185),4个奶牛场的检出率分别为19.4%(A场)、14.0%(B场)、57.1%(C场)和14.0%(D场)。金黄色葡萄球菌分离株中MRSA阳性率为28.6%(14/49),MRSA的总检出率为7.6%(14/185),4个奶牛场的检出率分别为13.9%(A场)、4.0%(B场)、14.3%(C场)和0.0%(D场)。MSSA分离株对青霉素、阿莫西林、克林霉素、磺胺甲唑/甲氧苄啶、恩诺沙星、红霉素、庆大霉素和头孢噻肟的耐药率分别为97.1%、88.6%、80.0%、77.1%、25.7%、22.9%、11.4%和2.9%,多重耐药率为88.6%。MRSA分离株对12种药物的耐药率大小依次为青霉素、阿莫西林、苯唑西林、克林霉素和磺胺甲唑/甲氧苄啶(100.0%)、红霉素(78.6%)、头孢噻肟(71.4%)、恩诺沙星(64.3%)、庆大霉素(21.4%)、四环素(14.3%)、氯霉素和利福平(7.1%),多重耐药率为100.0%。MSSA和MRSA分离株携带毒力基因nuc、cal、hla、sea、clfA和fnbA的检出率分别为100.0%和100.0%、100.0%和100.0%、91.4%和85.7%、77.1%和85.7%、77.1%和78.6%、91.4%和78.6%,优势毒力基因型为nuc-hla-sea-calclfA-fnbA。结论芜湖地区生牛奶中存在金黄色葡萄球菌污染,污染状况存在牛场差异性。MSSA和MRSA分离株均具有产毒性,且后者的耐药和多重耐药性较前者严重。     

Rapid detection of resistance in Staphylococcus aureus by using Quicolor ES

Traditional microbiological methods are dependent on the growth of microorganisms, and hence require prolonged periods. The methods used to detect resistance in Staphylococcus aureus should have high sensitivity and specificity, yet provide results in a timely manner. The aim of this study was to evaluate the use of Quicolor (QC) ES^® agar for the rapid detection of resistance in S. aureus. We evaluated 100 clinical S. aureus isolates. Resistance detection was performed using traditional microbiological methods. Methicillin resistance detection was evaluated using traditional and molecular microbiological methods. Traditional antibiotic susceptibility testing methods, such as disc diffusion, were conducted using QC ES and Mueller–Hinton (MH) media. The plates were incubated at 36 °C for 5, 6 and 24 h. Rapid results obtained using QC ES agar after 5 h of incubation were consistent with those using the overnight procedure with MH agar for 83 of the 100 S. aureus (including methicillin-susceptible S. aureus) strains. However, the correlation for oxacillin between MH (24 h) and QC ES (5 h) was not satisfactory (r = 0.770). The total agreement between QC ES and MH agar was 83 % after 5 h, 89 % after 6 h, and 94 % after 24 h. The accurate and rapid detection of resistance in S. aureus is critical due to the associated therapeutic problems and infection control measures. We believe that the use of QC ES for S. aureus will reduce the delay in resistance detection, thus providing physicians and infection control practitioners with early information for better management.     

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus

The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.      

Differential gene expression analysis by DNA microarrays technology and its application in molecular oncology

Accumulation of genetic and epigenetic aberrations leads to malignant transformation of normal cells. Functional studies of cancer using genomic and proteomic tools will help to reveal the true complexity of the processes leading to cancer development in humans. Until recently, diagnosis and prognosis of cancer was based on conventional pathologic criteria and epidemiological evidence. Certain tumors were divided only into relatively broad histological and morphological subcategories. Rapidly developing methods of differential gene expression analysis promote the search for clinically relevant genes changing their expression levels during malignant transformation. DNA microarrays offer a unique possibility to rapidly assess the global expression picture of thousands genes in any given time point and compare the detailed combinatory analysis results of global expression profiles for normal and malignant cells at various functional stages or separate experimental conditions. Acquisition of such "genetic portraits" allows searching for regularity and difference in expression patterns of certain genes, understanding their function and pathological importance, and ultimately developing the "molecular nosology" of cancer. This review describes the basis of DNA microarray technology and methodology, and focuses on their applications in molecular classification of tumors, drug sensitivity and resistance studies, and identification of biological markers of cancer.     

2009—2012年金黄色葡萄球菌血液分离株的临床分布和耐药性研究

目的调查和分析金黄色葡萄球菌败血症患者的临床特点和菌株的耐药情况,为临床诊断和合理用药提供参考。方法收集并分析2009年至2012年血培养确诊为金黄色葡萄球菌败血症患者的临床及菌株资料。结果2009年至2012年金黄色葡萄球菌血液分离株共80株,其中甲氧西林耐药金黄色葡萄球菌（methieillin resistant Staphylococcus,MRSA）占50％。2009年至2011年对甲氧西林的耐药率逐年提高,2012年呈下降趋势。其中MRSA血流感染患者多为合并基础疾病的老年人,留置静脉导管及体腔引流管、气管插管、联合使用抗生素、住院时间长为易感因素。结论金黄色葡萄球菌血液分离株中,MRSA检出率高,占50％,临床表现大多较重,合并多种基础疾病。加强抗生素的管理及重视和预防院内感染后能明显降低MRSA的检出率。     

Prophages of Staphylococcus aureus Newman and their contribution to virulence

Four prophages (phiNM1-4) were identified in the genome of Staphylococcus aureus Newman, a human clinical isolate. phiNM1, phiNM2 and phiNM4, members of the siphoviridae family, insert at different sites (poiA, downstream of isdB and geh) in the staphylococcal chromosome. phiNM3, a beta-haemolysin (hlb) converting phage, encodes modulators of innate immune responses (sea, sak, chp and scn) in addition to other virulence genes. Replication of phiNM1, phiNM2 and phiNM4 occurs in culture and during animal infection, whereas phiNM3 prophage replication was not observed. Prophages were excised from the chromosome and S. aureus variants lacking phiNM3 or phiNM1, phiNM2 and phiNM4 displayed organ specific virulence defects in a murine model of abscess formation. S. aureus Newman lacking all four prophages was unable to cause disease, thereby revealing essential contributions of prophages to the pathogenesis of staphylococcal infections.     

猪源致病性金黄色葡萄球菌的分离鉴定及其耐药性分析

目的鉴定引起猪渗出性皮炎的病原,并分析猪源致病性金黄色葡萄球菌的耐药性,为临床用药提供依据。方法采集患渗出性皮炎的仔猪标本进行细菌分离培养,联合应用形态学检查、生理生化试验和PCR方法鉴定分离菌株,并进行致病性和药物敏感性试验。结果先后从病猪标本中分离鉴定获得PSA1、PSA2、PSA3和PSA4四株金黄色葡萄球菌,其中PSA1和PSA3分离株的致病性较强。药敏试验结果显示PSA1、PSA2和PSA3分离株为MRSA菌株,PSA4分离株为MSSA菌株。MRSA菌株对14种抗菌药物均呈现不同程度的耐药,尤其是对青霉素、链霉素、四环素、强力霉素、环丙沙星和氧氟沙星等6种抗菌药物的耐药率达100%。所有分离株对万古霉素与替考拉宁均敏感。结论合肥地区猪渗出性表皮炎的病原为金黄色葡萄球菌。猪源致病性金黄色葡萄球菌合肥分离株具有多重耐药性,治疗猪渗出性皮炎应建立在体外药敏试验的基础上,有针对性选择抗菌药物。     

金黄色葡萄球菌D试验和耐药性分析

目的 了解本地区金黄色葡萄球菌中红霉素对克林霉素诱导耐药表型及其对常用抗菌药物的耐药性.方法 用K-B琼脂扩散法检测耐甲氧西林的金黄色葡萄球菌(MRSA)及双纸片法(D试验)检测红霉素对克林霉素诱导耐药表型,用VITEK 2 Compact进行菌株鉴定和药敏试验.结果 156株金黄色葡萄球菌中MRSA有51株,占32.7％.红霉素对克林霉素诱导耐药共29株,占18.6％,其中MRSA有10株,甲氧西林敏感的金黄色葡萄球菌(MRSS)有19株.金黄色葡萄球菌对多种抗菌药物具有不同的耐药性,对青霉素的耐药性超过95％,对万古霉素、奎努普汀/达福普汀、利奈唑烷和替加环素敏感.结论 临床微生物实验室应加强对金黄色葡萄球菌中克林霉素诱导耐药的检测,临床治疗中也应加强抗菌药物的合理应用以防多耐药菌株的产生.     

Modulation of virulence gene expression in Staphylococcus aureus by interleukin-1beta: novel implications in bacterial pathogenesis

The effect of IL-1beta on Staphylococcus aureus was investigated in terms of mRNA expression profile of bicomponent leukotoxins (Luk ED, Luk PV, HlgA, and HlgCB) as well as microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Upon exposure to higher concentrations of IL-1beta, S. aureus expressed significantly higher levels of MSCRAMMs mRNA [fibronectin-binding protein (FnBp), fibrinogen-binding protein or clumping factor (Clf), and collagen-binding protein (Cna)] and had significantly lower expression of mRNAs for bicomponent leukotoxins. Sequential in vitro passing of S. aureus in the absence of rhIL-1beta resulted in reduced binding to rhIL-1beta resulted in lack of significant changes in virulence gene expression upon exposure to low or high concentrations of rhIL-1beta. It is possible that IL-1beta modulates the pathogenic potential of S. aureus by altering its virulence gene expression to adapt to the host's inflammatory micromilieu. The ability to express higher levels of MSCRAMMs and low levels of leukotoxins might contribute towards the successful invasion and persistence of S. aureus in chronic inflammatory conditions. Determination of the mechanisms of IL-1-induced alterations in S. aureus gene expression may lead to the identification of novel therapeutic targets against this ever-evolving opportunistic pathogen.     

Cloning and restriction analysis of DNA conferring new quinolone antimicrobial agent resistance from Staphylococcus aureus and other coagulase-negative Staphylococcus species

DNA conferring resistance to new quinolone antimicrobial agents (NQR) in clinical isolates of Staphylococcus aureus and coagulase-negative staphylococci (CNS), S. epidermidis and S. haemolyticus, was analyzed after cloning in Escherichia coli. The NQR phenotypes were expressed in E. coli at lower levels. NQR gene(s)-carring HindIII fragments were very similar to each other among S. aureus or CNS, although the S. aureus fragments differed from the CNS fragments in terms of the NQR phenotypes and restriction endonuclease maps. The data suggest the possibility that the NQR genes have disseminated in evolutionarily distinct routes among S. aureus and CNS.     

Molecular population and virulence factor analysis of Staphylococcus aureus from bovine intramammary infection

Staphylococcus aureus isolates from cows in Ireland (n = 102) and the USA (n = 42) were characterized by RAPD-PCR and analysed for the production of a number of putative virulence factors. Of these strains 63 representative isolates were screened for the corresponding virulence factor genes by PCR or Southern hybridization or both. The isolates were divided into 12 distinct clonal types on the basis of their RAPD fingerprint profiles. Of the isolates, 107 (74.3%) tested positive for clumping factor in a slide agglutination test, all 24 RAPD type 7 isolates being negative for clumping factor. PCR analysis of region R, a repeat region of the clfA gene, revealed eight region-R sizes. There was a strong association between RAPD type and the clfA region-R genotype among Irish isolates. Of the RAPD type 7 isolates, 21 (87.5%) coproduced toxic shock syndrome toxin-1 (TSST-1) and staphylococcal enterotoxin C (SEC). Over 90% of isolates demonstrated haemolytic activity on sheep or rabbit red blood cells and all isolates harboured the gamma-haemolysin (hlg) locus. Of the Irish isolates, all those of RAPD type 7 were sensitive to penicillin G, whereas 86% of RAPD types 4 and 5 strains were resistant. Furthermore, RAPD types 5 and 7 were more likely to be associated with clinical mastitis whereas RAPD type 4 isolates were more often associated with a latent infection. The current study identifies some of the putative virulence factors produced by the predominant clonal types of bovine Staph. aureus that may be considered as components of a vaccine.