重庆地区儿童2000年至2004年首位革兰阴性细菌和阳性细菌的耐药性监测

目的了解重庆地区儿童感染的分离至临床标本的首位革兰阴性细菌和阳性细菌对常用抗生素的耐药趋势,指导临床合理使用抗生素。方法常规方法分离、培养细菌,应用美国德灵公司WalkAway-40细菌鉴定仪对2000年至2004年我院细菌室分离至临床标本的首位革兰阴性细菌和阳性细菌共2854株进行细菌鉴定及药敏试验。结果2000年至2004年检出的首位革兰阴性细菌和阳性细菌分别为大肠埃希菌和金黄色葡萄球菌。2000年至2004年前5位革兰阴性菌5777株,革兰阳性菌1565株,其中大肠埃希菌2090株,金黄色葡萄球菌764株,分别占36.2%和48.8%;5年间大肠埃希菌对氨苄西林、头孢吡肟、头孢西丁、庆大霉素、亚胺培南、环丙沙星、头孢噻肟、头孢他啶的总耐药率分别为80.9%、37.5%、15.4%、54.0%、0.8%、34.0%、46.6%、46.2%;金黄色葡萄球菌对青霉素、红霉素、复方新诺明、万古霉素、阿莫西林/克拉维酸的总耐药率分别为95.6%、63.4%、5.8%、0%、11.0%。结论通过细菌耐药监测发现：大肠埃希菌对常用抗生素的总耐药率变化不大,金黄色葡萄球菌对常用抗生素的总耐药率有下降趋势,应引起临床医生重视。     

远缘杂交中不育基因的位置和效应的最大似然估计

提出了一种统计方法,利用标记位点的异常分离,来估计远缘杂交中不育基因位点的位置和效应,在回交群体中,用最大似然法对不育基因与标记位点之间的生组值和配子存活率进行估计。将表现连续分布的育性指标转化为百连续变异的遗传标记的分离,可以避免对育性直接观测所带来的重组值估计结果的不稳定,还可以同时估计雌雄配子的存活率。     

醒脑静注射液无菌检查方法的验证

目的:验证醒脑静注射液无菌检查法。方法:采用《中华人民共和国药典》2005年版二部附录无菌检查项下的直接接种法。结果:供试品管无菌生长,6株阳性菌生长良好。结论:经方法学验证,醒脑静注射液无菌检查法准确可靠。     

Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities

Single-nucleotide primer extension (SNuPE) is an emerging tool for parallel detection of DNA sequences of different target microorganisms. The specificity and sensitivity of the SNuPE method were assessed by performing single and multiplex reactions using defined template mixtures of 16S rRNA gene PCR products obtained from pure bacterial cultures. The mismatch discrimination potential of primer extension was investigated by introducing different single and multiple primer-target mismatches. The type and position of the mismatch had significant effects on the specificity of the assay. While a 3′-terminal mismatch has a considerable effect on the fidelity of the extension reaction, the internal mismatches influenced hybridization mostly by destabilizing the hybrid duplex. Thus, carefully choosing primer-mismatch positions should result in a high signal-to-noise ratio and prevent any nonspecific extension. Cyclic fluorescent labeling of the hybridized primers via extension also resulted in a significant increase in the detection sensitivity of the PCR. In multiplex reactions, the signal ratios detected after specific primer extension correlated with the original template ratios. In addition, reverse-transcribed 16S rRNA was successfully used as a nonamplified template to prove the applicability of SNuPE in a PCR-independent manner. In conclusion, this study demonstrates the great potential of SNuPE for simultaneous detection and typing of various nucleic acid sequences from both environmental and engineered samples.Fast detection, differentiation, and identification of bacteria are crucial tasks in clinical, food, and environmental microbiology. Cultivation-independent tools not only save time compared to cultivation-based techniques but also allow access to the difficult-to-cultivate part of a microbial community. Molecular detection methods are usually based on hybridization of oligonucleotide probes to signature sequences (phylogenetically informative regions) in the nucleic acids (RNA or DNA) of the target microorganisms. Verification of the hybridization event can be accomplished by detection of hybridized labeled probes in situ (e.g., fluorescence in situ hybridization [FISH]) or ex situ (dot blot hybridization). Combining two specific oligonucleotides in a PCR increases the sensitivity of specific detection, while real-time monitoring of the amplification product formed allows quantification of the original template (for a review, see reference 17). Multiple detection can be achieved by using more than one primer pair targeting several loci in multiplex PCR assays (for a review, see reference 32). However, the main disadvantages of FISH are its restricted capability for parallel analysis of several target groups in the same sample and limitations in probe design due to differences in accessibility of the probes to their target sites (3, 7). Moreover, detection of slowly growing bacteria with low ribosome contents requires labor-intensive techniques (30, 36). Multiplex PCR also has limitations for multiplexing and challenges for primer design (32).Recently, single-nucleotide primer extension (SNuPE) was proposed as a fast, semiquantitative multiplex detection tool for analyzing sequence variants. This method is frequently used for determination of single-nucleotide polymorphisms and benefits from the fidelity of dideoxynucleoside triphosphate (ddNTP) incorporation catalyzed by a DNA polymerase. When primer extension takes place on a solid support, the method is called minisequencing (35, 37), while a reaction in solution is referred to as SNuPE (34) or single-base extension (15). These methods were originally developed for routine medical diagnosis of genetic disorders (23, 35) or for use in forensic research (38). Different versions of the primer extension technique have also been used recently for fast identification and genotyping of microbial strains (9, 31). Recent studies showed that detection of a hybridization event via labeling of the hybridized primer in the extension reaction is possible. However, the use of this method as a detection tool in applied and environmental microbiology has not been fully exploited so far. Rudi and coworkers were the first workers who used a minisequencing approach with PCR products from environmental DNA to detect toxic cyanobacteria by labeling only one of the four ddNTPs used in the reaction (27). Multiplexing was accomplished by hybridizing the labeled products to complementary oligonucleotides in an array format. In combination with antibody-based chromogenic visualization, genetic profiles of cyanobacterial diversity (28), microbial communities in vegetable salads (25), and Listeria strains (26) were obtained. However, this approach is labor-intensive and time-consuming and requires specific equipment; furthermore, the primer is restricted to certain positions since only one terminator nucleotide is labeled.An alternative strategy for multiplexing in solution benefits from incorporation of four differently labeled ddNTPs and attachment of mobility modifiers to the different primers. Subsequent separation using capillary electrophoresis and laser-induced fluorescence detection results in a very fast assay that is easy to interpret. Determination of the incorporated nucleotide provides additional proof of the assay specificity or may even provide extra phylogenetic information. The first application of primer extension with four differently labeled ddNTPs in environmental microbiology was the use of this method by Wu and Liu (41) for multiplex detection of different Bacteroides spp. This study also addressed different methodological issues and aspects, such as the effects of noncomplementary tail length, annealing temperature, cycle number, and primer-to-template ratio on extension efficiency. In a previous study, Nikolausz et al. (19) reported development and application of a multiplex SNuPE assay for detection and typing of “Dehalococcoides” sp. sequences obtained from chloroethene-contaminated groundwater samples. However, there still has not been a systematic evaluation of factors that affect primer design and the discriminatory power of primer extension. Moreover, quantitative aspects of the method have not been thoroughly addressed so far.The present study focused on these crucial issues by investigating the effects of the type, number, and position of primer mismatches on the extension efficiency and hence the specificity. Furthermore, quantitative aspects of SNuPE were investigated in a model community experiment by using defined template mixtures of 16S rRNA gene PCR products or reverse-transcribed RNA.     

A Filter-based Surface Enhanced Raman Spectroscopic Assay for Rapid Detection of Chemical Contaminants

We demonstrate a method to fabricate highly sensitive surface-enhanced Raman spectroscopic (SERS) substrates using a filter syringe system that can be applied to the detection of various chemical contaminants. Silver nanoparticles (Ag NPs) are synthesized via reduction of silver nitrate by sodium citrate. Then the NPs are aggregated by sodium chloride to form nanoclusters that could be trapped in the pores of the filter membrane. A syringe is connected to the filter holder, with a filter membrane inside. By loading the nanoclusters into the syringe and passing through the membrane, the liquid goes through the membrane but not the nanoclusters, forming a SERS-active membrane. When testing the analyte, the liquid sample is loaded into the syringe and flowed through the Ag NPs coated membrane. The analyte binds and concentrates on the Ag NPs coated membrane. Then the membrane is detached from the filter holder, air dried and measured by a Raman instrument. Here we present the study of the volume effect of Ag NPs and sample on the detection sensitivity as well as the detection of 10 ppb ferbam and 1 ppm ampicillin using the developed assay.     

Evaluation of an Automated Rapid Diagnostic Test for Detection of Clostridium difficile

The Verigene Clostridium difficile Nucleic Acid Test (Verigene CDF Test) (Nanosphere, Northbrook, IL, USA) is a new multiplex qualitative polymerase chain reaction (PCR) test used to detect C. difficile toxin genes in fecal specimens. To evaluate the performance of the new method, we tested 69 fecal samples from patients with suspected C. difficile infection using the Verigene CDF test, an enzyme immunoassay (EIA) and PCR following anaerobic fecal culture. The sensitivity, specificity, and accuracy of the Verigene CDF test were 96.7% (29/30), 97.4% (38/39), and 97.1% (67/69) respectively, using PCR following fecal culture as a reference method. We also analyzed the potential clinical impact of the Verigene CDF test using chart reviews of the 69 patients with suspected C. difficile infection and found that 11 of the 69 patients were incorrectly diagnosed, and the Verigene CDF test would have led to them receiving more appropriate management including practice of treatment and contact precaution, although, of the 69 patients, there are two whose samples were incorrectly identified with the Verigene CDF test. The Verigene CDF test will have a positive impact on patient care.     

Photokilling of bacteria by the natural dye curcumin

Curcumin is a yellow-orange compound derived from the root of Curcuma longa (Zingiberaceae family), that has been used as a medicine, spice and coloring agent. Curcumin has proved nontoxic in a number of cell culture and whole animal studies. Curcumin has, however, been reported to have bactericidal effects at very high concentrations. When illuminated, curcumin exerted potent phototoxic effects in micromolar amounts. Gram-negative bacteria displayed greater resistance to curcumin phototoxicity relative to Gram-positive bacteria. Oxygen was required for curcumin phototoxicity. Curcumin binding to cells was not required for photokilling; the reactive intermediate therefore must be relatively long-lived. The mechanism(s) of curcumin phototoxicity may involve hydrogen peroxide production. Singlet excited oxygen was not detected.Publication no 35 of the Center for Photochemical Sciences     

Compound design guidelines for evading the efflux and permeation barriers of Escherichia coli with the oxazolidinone class of antibacterials: Test case for a general approach to improving whole cell Gram-negative activity

Previously we reported the results from an effort to improve Gram-negative antibacterial activity in the oxazolidinone class of antibiotics via a systematic medicinal chemistry campaign focused entirely on C-ring modifications. In that series we set about testing if the efflux and permeation barriers intrinsic to the outer membrane of Escherichia coli could be rationally overcome by designing analogs to reside in specific property limits associated with Gram-negative activity: i) low MW (<400), ii) high polarity (clogD_7.4 <1), and iii) zwitterionic character at pH 7.4. Indeed, we observed that only analogs residing within these limits were able to overcome these barriers. Herein we report the results from a parallel effort where we explored structural changes throughout all three rings in the scaffold for the same purpose. Compounds were tested against a diagnostic MIC panel of Escherichia coli and Staphylococcus aureus strains to determine the impact of combining structural modifications in overcoming the OM barriers and in bridging the potency gap between the species. The results demonstrated that distributing the charge-carrying moieties across two rings was also beneficial for avoidance of the outer membrane barriers. Importantly, analysis of the structure-permeation relationship (SPR) obtained from this and the prior study indicated that in addition to MW, polarity, and zwitterionic character, having ≤4 rotatable bonds is also associated with evasion of the OM barriers. These combined results provide the medicinal chemist with a framework and strategy for overcoming the OM barriers in GNB in antibacterial drug discovery efforts.     

Experimental Evaluation of Catalyzed Hydrogen Peroxide and Sodium Persulfate for Destruction of BTEX Contaminants

Due to the toxicity and prevalence of BTEX contaminants (benzene, toluene, ethylbenzene, and xylenes) at hazardous waste sites, approaches for their remediation are of interest, especially those that particularly address benzene, which is often the limiting factor for achieving regulatory cleanup at these contaminated sites. In situ chemical oxidation (ISCO) is a viable technology for BTEX destruction, and hydrogen peroxide and sodium persulfate are two oxidants of interest for BTEX treatment.

Laboratory studies were conducted to compare BTEX contaminant destruction and oxidant persistence for these two oxidants and for varied methods of oxidant activation/propagation. Additionally, studies were performed to compare contaminant destruction and oxidant persistence in laboratory contaminant spike systems vs. field site contaminant systems. Finally, contaminant destruction and oxidant persistence in field porous media with varied characteristics were evaluated. Contaminant and oxidant concentrations were measured at multiple time points over a three-week reaction period in each oxidant and oxidant activation/propagation system.

Under the comparable conditions evaluated here, sodium persulfate systems demonstrated greater BTEX contaminant destruction and greater oxidant persistence than hydrogen peroxide systems. FeSO₄ and citric acid activation of sodium persulfate resulted in greater BTEX destruction and greater oxidant persistence than pH adjustment or hydrogen peroxide activation in both laboratory contaminant spike systems and field gas condensate systems. Additionally, results indicate that the response of the contaminant(s) and oxidant (extent and rate of depletion) are both contaminant-and porous media type-dependent.     

Evaluation of a Red Cell Agglutination Test for Detection of Australia Antigen (HB Ag)

An investigational red cell agglutination (RCA) test was evaluated for sensitivity in detecting and titering hepatitis B antigen (HB Ag) in comparison with two counterelectrophoresis (CEP) systems and a solid-phase radioimmunoassay (RIA). The RCA procedure was found to be significantly more sensitive than the CEP methods and compares favorably in sensitivity with the solid-phase RIA, detecting even lower concentrations of the HB Ag. Since the RCA test can be completed in 2 to 3 h and requires relatively inexpensive equipment, it offers a highly sensitive and rapid procedure suitable for use in blood banks to screen donors or detect low levels of antigen in serum of patients.     

Evaluation of a Cow-Side Test for Detection of Gram-Negative Bacteria in Milk from Cows with Mastitis

A modified Limulus amebocyte lysate (LAL) cow-side test was evaluated under field conditions. The principle of the test is to visualize reactions between test components and endotoxin from the cell wall of Gram-negative bacteria. The practical purpose is to detect such bacteria in mastitic milk. Secretions from 789 udder quarters with clinical mastitis were examined by the LAL-test. Parallel quarter milk samples were sent to a mastitis laboratory for microbiological examination. Eleven veterinary surgeons in three veterinary districts in Norway performed the field investigations. Results of the LAL-test and culture agreed in 93% of all milk samples tested, agreement measured by kappa being 0.63. The sensitivity of the test in detecting Gram-negative bacteria was 63%, while the specificity was 97%. The predictive value of a positive test result was 70%, the figure being somewhat higher (75%) when the material was limited to milk samples without antibiotic residues. The predictive value of a negative test result was 95%. The LAL-test is considered to constitute a valuable cow-side test for the veterinary practitioner, aiding the selection of antibacterial drug of choice for the initial treatment of clinical mastitis.     

Microtiter Hemagglutination-Inhibition Test for the Detection of Encephalomyocarditis Virus Antibodies

Several variables were found to affect the agglutination of sheep erythrocytes by encephalomyocarditis virus. A satisfactory and reliable microtiter hemagglutination-inhibition test is described.     

The Most Probable Limit of Detection (MPL) for rapid microbiological methods

Classical microbiological methods have nowadays unacceptably long cycle times. Rapid methods, available on the market for decades, are already applied within the clinical and food industry, but the implementation in pharmaceutical industry is hampered by for instance stringent regulations on validation and comparability with classical methods. Equivalence studies become less relevant when rapid methods are able to detect only one single microorganism. Directly testing this capability is currently impossible due to problems associated with preparing a spiked sample with low microbial counts. To be able to precisely estimate the limit of detection of rapid absence/presence tests, the method of the most probable limit is presented. It is based on three important elements; a relatively precise quantity of microorganisms, a non-serial dilution experiment and a statistical approach. For a set of microorganisms, a limit of detection of one was demonstrated using two different rapid methods.     

Bootstrap Restricted Likelihood Ratio Test for the Detection of Rare Variants

In this paper the detection of rare variants association with continuous phenotypes of interest is investigated via the likelihood-ratio based variance component test under the framework of linear mixed models. The hypothesis testing is challenging and nonstandard, since under the null the variance component is located on the boundary of its parameter space. In this situation the usual asymptotic chisquare distribution of the likelihood ratio statistic does not necessarily hold. To circumvent the derivation of the null distribution we resort to the bootstrap method due to its generic applicability and being easy to implement. Both parametric and nonparametric bootstrap likelihood ratio tests are studied. Numerical studies are implemented to evaluate the performance of the proposed bootstrap likelihood ratio test and compare to some existing methods for the identification of rare variants. To reduce the computational time of the bootstrap likelihood ratio test we propose an effective approximation mixture for the bootstrap null distribution. The GAW17 data is used to illustrate the proposed test.     

Evaluation of a Real-Time PCR Test for the Detection and Discrimination of Theileria Species in the African Buffalo (Syncerus caffer)

A quantitative real-time PCR (qPCR) assay based on the cox III gene was evaluated for the simultaneous detection and discrimination of Theileria species in buffalo and cattle blood samples from South Africa and Mozambique using melting curve analysis. The results obtained were compared to those of the reverse line blot (RLB) hybridization assay for the simultaneous detection and differentiation of Theileria spp. in mixed infections, and to the 18S rRNA qPCR assay results for the specific detection of Theileria parva. Theileria parva, Theileria sp. (buffalo), Theileria taurotragi, Theileria buffeli and Theileria mutans were detected by the cox III assay. Theileria velifera was not detected from any of the samples analysed. Seventeen percent of the samples had non-species specific melting peaks and 4.5% of the samples were negative or below the detection limit of the assay. The cox III assay identified more T. parva and Theileria sp. (buffalo) positive samples than the RLB assay, and also detected more T. parva infections than the 18S assay. However, only a small number of samples were positive for the benign Theileria spp. To our knowledge T. taurotragi has never been identified from the African buffalo, its identification in some samples by the qPCR assay was unexpected.Because of these discrepancies in the results, cox III qPCR products were cloned and sequenced. Sequence analysis indicated extensive inter- and intra-species variations in the probe target regions of the cox III gene sequences of the benign Theileria spp. and therefore explains their low detection. The cox III assay is specific for the detection of T. parva infections in cattle and buffalo. Sequence data generated from this study can be used for the development of a more inclusive assay for detection and differentiation of all variants of the mildly pathogenic and benign Theileria spp. of buffalo and cattle.     

Synthesis of Staphylococcus aureus lipoteichoic acid derivatives for determining the minimal structural requirements for cytokine induction

For the investigation of the minimal structural requirements for cytokine induction, Staphylococcus aureus lipoteichoic acid derivatives with two, three, four, and five glycerophosphate backbone moieties, carrying each a d-alanyl residue, were needed. Based on two different glycerophosphate building blocks and 6b-O-phosphitylated gentiobiosyl diacylglycerol the desired target molecules (compounds 1-4) could be readily obtained and provided for biological studies.     

Initial Test of the Benchmark Chemical Approach for Predicting Microbial Transformation Rates in Aquatic Environments

Using 2,4-dichlorophenoxyacetic acid methyl ester (2,4-DME) as a benchmark chemical, we determined relative pseudo-first-order rate coefficients for the butoxyethyl ester of 2,4-dichlorophenoxyacetic acid (2,4-DBE), methyl parathion, and methyl-3-chlorobenzoate in a diversity of microbial samples, including water, sediment, biofilm, and floating microbial mats collected from a laboratory mesocosm as well as from streams, lakes, and wetlands in Georgia and Florida. The decreasing order of reactivity for relative microbial transformation rates was 2,4-DBE > 2,4-DME > methyl-3-chlorobenzoate > methyl parathion. Half-lives of the chemicals varied about 60-fold depending on the chemical and microbial sample. Relative rate coefficients, however, typically varied only about threefold for field-collected samples. Relative rate coefficients determined with samples from a laboratory mesocosm were consistently low compared with the field sample data. Overall, the data indicated that microbial transformation rates of a chemical can be satisfactorily inferred for a wide variety of microbial habitats—such as water, biofilm, or a sediment—on the basis of its transformation rate relative to that of an appropriate benchmark chemical by using a single type of microbial sample.