Culture Tubes Research Articles

Determination of antibiotic EC50 using a zero-flow microfluidic chip based growth phenotype assay.

Current existing assay systems for evaluating antimicrobial activity suffer from several limitations including excess reagent consumption and inaccurate concentration gradient preparation. Recently, microfluidic systems have been developed to provide miniaturized platforms for antimicrobial susceptibility assays. However, some of current microfluidic based assays require continuous flows of reagents or elaborate preparation steps during concentration preparation. In this study, we introduce a novel microfluidic chip based growth phenotype assay that automatically generates a logarithmic concentration gradient and allows observing the growth of pathogenic bacteria under different concentrations of antibiotics in nanoliter batch culture reactors. We chose pathogen bacterium Pseudomonas aeruginosa as a model strain and evaluated the inhibitory effects of gentamicin and ciprofloxacin. We determined the EC50 values and confirmed the validity of the present system by comparing the EC50 values obtained through conventional test tube method. We demonstrated that the EC50 values acquired from present assay are comparable to those obtained from conventional test tube cultures. The potential application of present assay system for investigating combinatorial effects of antibiotics on multidrug resistant pathogenic bacteria is discussed and it can be further used for systematic evaluation of antifungal or antiviral agents.

EFFECTS OF PHOTOMIXOTROPHIC CONDITIONS AND TYPE OF CULTURE VESSEL CLOSURE ON ANACARDIUM OTHONIANUM RIZZ. GROWN IN VITRO

Anacardium othonianum Rizz. is a species of fruit tree from the Brazilian cerrado; the economical exploitation of which is a viable alternative for local farmers. The present study aimed to evaluate the influence of sucrose and the type of culture tube closure on the in vitro leaf anatomy of A. othonianum. Shoots were transferred to glass tubes containing woody plant medium supplemented with 5.9 µM indole-3-butyric acid, 4 g L-1 agar and 2 g L-1 activated charcoal, in the absence or presence of sucrose (3%). The tubes were closed with plastic caps, plastic caps wrapped with PVC film, or with cotton plugs. The anatomical variables were larger under heterotrophic conditions, but tended to decrease when a photomixotrophic stimulus was applied. However, by maintaining the plantlets under photomixotrophic conditions in tubes closed with cotton wool plugs, the values of the anatomical variables diminished, thus improving the chances of success in the subsequent stages of propagation. The results obtained revealed that A. othonianum exhibited a considerably adaptive plasticity. By diminishing the values of the anatomical variables, cotton wool closures provided not only an adequate environment for the growth of plantlets in vitro under photomixotrophic conditions.

A Protocol for Axenic Liquid Cell Cultures of a Woody Leguminous Mangrove, Caesalpinia crista, and their Amino Acids Profiling

Callus induction, maintenance and protoplast cultures were achieved from immature seeds of a woody leguminous mangrove, Caesalpinia crista. Axenic cultures were possible during 1.5 months of pod storage in 0.1% benzalkonium chloride solution. Callus induction was achieved using 1 mL liquid medium in a 10 mL flat-bottomed culture tube. Protoplasts were isolated using Cellulase R10, Hemicellulase, and Driselase 20 in 0.6 M mannitol solution and sub-culturable calluses were obtained in 50 μL liquid medium using a 96-microplate method. The optimal hormonal concentration was 10 μM each of 2,4-dichlorophenoxyacetic acid and benzyladenine in liquid Murashige and Skoog's basal medium for both callus induction and maintenance, and protoplast cultures. Similarities and differences in amino acid profiles and culture conditions are discussed among woody mangrove species and non-mangrove leguminous species. Caesalpinia crista cultures were unique as they secreted a large amount of amino acids, including proline, into the liquid culture medium.

Combining treatments to improve the fermentation of sugarcane bagasse hydrolysates by ethanologenic Escherichia coli LY180

Inhibitory side products from dilute acid pretreatment is a major challenge for conversion of lignocellulose into ethanol. Six strategies to detoxify sugarcane hydrolysates were investigated alone, and in combinations (vacuum evaporation of volatiles, high pH treatment with ammonia, laccase, bisulfite, microaeration, and inoculum size). High pH was the most beneficial single treatment, increasing the minimum inhibitory concentration (measured by ethanol production) from 15% (control) to 70% hydrolysate. Combining treatments provided incremental improvements, consistent with different modes of action and multiple inhibitory compounds. Screening toxicity using tube cultures proved to be an excellent predictor of relative performance in pH-controlled fermenters. A combination of treatments (vacuum evaporation, laccase, high pH, bisulfite, microaeration) completely eliminated all inhibitory activity present in hydrolysate. With this combination, fermentation of hemicellulose sugars (90% hydrolysate) to ethanol was complete within 48h, identical to the fermentation of laboratory xylose (50g/L) in AM1 mineral salts medium (without hydrolysate).

High-throughput preparation methods of crude extract for robust cell-free protein synthesis.

Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.

Screening exogenous fibrolytic enzyme preparations for improved in vitro digestibility of bermudagrass haylage

Our objectives were to evaluate the effects of 12 exogenous fibrolytic enzyme products (EFE) on ruminal in vitro neutral detergent fiber digestibility (NDFD) and preingestive hydrolysis of a 4-wk regrowth of bermudagrass haylage (BH), to examine the accuracy of predicting NDFD with EFE activity measures, and to examine the protein composition of the most and least effective EFE at increasing NDFD. In experiment 1, effects of 12 EFE on NDFD of BH were tested. Enzymes were applied in quadruplicate to culture tubes containing ground BH. The suspension was incubated for 24 h at 25°C before addition of rumen fluid media and further incubation for 24 h at 39°C. The experiment was repeated twice. In addition, regression relationships between EFE activity measures and NDFD were examined. Compared with the values for the control, 9 EFE-treated substrates had greater NDFD (37.8 to 40.4 vs. 35.6%), 6 had greater total VFA concentration (59.1 to 61.2 vs. 55.4 mM), and 4 had lower acetate-to-propionate ratios (3.03 to 3.16 vs. 3.24). In experiment 2, EFE effects on preingestive fiber hydrolysis were evaluated by incubating enzyme-treated and untreated bermudagrass suspensions in quadruplicate for 24 h at 25°C and examining fiber hydrolysis measures. Compared with values for the control, 3 EFE reduced neutral detergent fiber concentration (62.8 to 63.7 vs. 67.3%), 10 increased release of water-soluble carbohydrates (26.8 to 58.5 vs. 22.8 mg/g), and 8 increased release of ferulic acid (210 to 391 vs. 198μg/g). Regression analyses revealed that enzyme activities accurately [coefficient of determination (R2)=0.98] predicted preingestive hydrolysis measures (water-soluble carbohydrates, ferulic acid), moderately (R2=0.47) predicted neutral detergent fiber hydrolysis, but poorly (R2≤0.1) predicted dry matter and NDFD. In experiment 3, proteomic tools were used to examine the protein composition of the most and least effective EFE at improving NDFD. Relative to the least effective, the most effective EFE at increasing NDFD contained 10 times more endoglucanase III, 17 times more acetylxylan esterase with a cellulose-binding domain 1, 33 times more xylanase III, 25 times more β-xylosidase, and 7.7 times more polysaccharide monooxygenase with cellulose-binding domain 1 and 3 times more swollenin. The most effective EFE had a much greater quantity of fibrolytic enzymes and key proteins necessary for hemicellulose and lignocellulase deconstruction. This study identified several EFE that increased the NDFD and in vitro fermentation of 4-wk BH and revealed why some EFE are more effective than others.

In vitro cytotoxic, genotoxic and antioxidant/oxidant effects of guaiazulene on human lymphocytes

The aim of this study was to evaluate for the cytotoxicity, genotoxicity and antioxidant/oxidant activity of GYZ on human peripheral blood lymphocytes (PBLs). Guaiazulene (GYZ) was added into culture tubes at various concentrations (0-400 µg/mL-1). Cytotoxicity against the human lymphocytes cultures was examined by lactate dehydrogenase (LDH) release assay. The proliferative response was estimated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. Antioxidant/oxidant activity was evaluated by measuring the total oxidant status (TOS) and total antioxidant capacity (TAC) levels. Micronucleus (MN) and chromosomal aberration (CA) tests were used in genotoxicity studies. The results showed that GYZ caused cytotoxicity in the PBLs at high concentrations, but TOS level were not affected, while the level of TAC was significantly increased. GYZ also did not induce chromosomal aberrations when compared to that of the control group. Results this study clearly revealed that GYZ was not genotoxic and also increased the capacity of the antioxidant in the culture of human PBL cells. This report is first report on the impact of GYZ on human PBL cells.

Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures.

We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reversible immobilization beads. The protocol yielded ≥0.2 ng/μl of DNA for 90% (MolYsis kit) and 83% (saline wash) of positive MGIT cultures. A total of 144 (94%) of the 154 samples sequenced on the MiSeq platform (Illumina) achieved the target of 1 million reads, with <5% of reads derived from human or nasopharyngeal flora for 88% and 91% of samples, respectively. A total of 59 (98%) of 60 samples that were identified by the national mycobacterial reference laboratory (NMRL) as Mycobacterium tuberculosis were successfully mapped to the H37Rv reference, with >90% coverage achieved. The DNA extraction protocol, therefore, will facilitate fast and accurate identification of mycobacterial species and resistance using a range of bioinformatics tools.

Effects of a spoilage yeast from silage on in vitro ruminal fermentation

Feeding silages with high concentrations of yeasts from aerobic spoilage is often implicated as a cause of poor animal performance on dairies. Our objective was to determine if a commonly found spoilage yeast, isolated from silage, had the potential to alter in vitro ruminal fermentations. A single colony of Issatchenkia orientalis, isolated from high-moisture corn, was grown in selective medium. The yeast culture was purified and added to in vitro culture tubes containing a total mixed ration (43% concentrate, 43% corn silage, 11% alfalfa haylage, and 3% alfalfa hay on a dry matter basis), buffer, and ruminal fluid to achieve added theoretical final concentrations of 0 (CTR), 4.40 (low yeast; LY), 6.40 (medium yeast; MY), and 8.40 (high yeast; HY) log10 cfu of yeast/mL of in vitro fluid. Seven separate tubes were prepared for each treatment and each time point and incubated for 12 and 24h at 39°C. At the end of the incubation period, samples were analyzed for pH, yeast number, neutral detergent fiber (NDF) digestibility, volatile fatty acids (VFA), and fatty acids (FA). We found that total viable yeast counts decreased for all treatments in in vitro incubations but were still relatively high (5.3 log10 cfu of yeasts/mL) for HY after 24h of incubation. Addition of HY resulted in a lower pH and higher concentration of total VFA in culture fluid compared with other treatments. Moreover, additions of MY and HY decreased in vitro NDF digestibility compared with CTR, and the effect was greatest for HY. Overall, the biohydrogenation of dietary unsaturated FA was not altered by addition of I. orientalis and decreased over time with an increase in the accumulation of saturated FA, especially palmitic and stearic acids. We conclude that addition of I. orientalis, especially at high levels, has the potential to reduce in vitro NDF digestion and alter other aspects of ruminal fermentations.

English

The dermatophytoses constitute a group of superficial fungal infections of keratinised tissue-epidermis, hair and nails, caused by a closely related group of filamentous fungi, the dermatophytes. OBJECTIVES: Isolation and speciation of dermatophytes by culture and to determine its prevalence. METHODOLOGY: The study was conducted from January 2012-December 2013 at Kempegowda institute of medical sciences, Bangalore. All clinically suspected cases coming to the microbiology department where subjected to mycological work-up. Specimens like skin scraping, hair, and nail were collected and microscopically examined using 10%, 20% and 40% KOH respectively for fungal filaments. Culture was carried out using Sabouraud dextrose agar medium with and without cycloheximide. The growth in the culture tube was speciated based on the macroscopic and microscopic findings (with Lactophenol cotton blue staining). RESULTS: Total cases in the two year period were 609. The infection was found to be common in adults aged 20-30 years, the male to female ratio is 1.2:1. The KOH positives were 491(80%), and culture positives were 471(77%). Of the positive cultures Trichophyton rubrum (35%) was the common isolate followed by Trichophyton mentagrophytes (17%), and Epidermophyton floccosum (6%). CONCLUSION: In the present study the most common clinical presentation is Tinea corporis followed by Tinea unguium and Tinea cruris and the common isolate was T.rubrum. The present study was undertaken to determine the clinical pattern of dermatophytosis and the common species that was prevalent here.

Modified Serological Method for Determining Significant Antibody Titre to Salmonella Infection in Endemic Area

Enteric fever is caused by antigenic variant group of bacteria known as Salmonella species. The disease is common in most developing countries being contacted though contaminated water, food and poor personal hygiene. The most significant challenge in the treatment of infected patients is misdiagnosis leading to high morbidity and mortality rate. We devised a time efficient technique which has been compared with tube agglutination method and culture and found it to be very efficient, sensitive and reliable. Blood samples from patients clinically diagnosed of enteric fever were collected and a 1:4 dilution of serum in saline was used for direct agglutination test. Results with visible agglutination were considered as significant and it compared favorably with tube agglutination and culture result. A total of two thousand two hundred and fifty specimens were tested. Among this, 1390 were positive for the

The preparation of chicken tracheal organ cultures for virus isolation, propagation, and titration.

Chicken tracheal organ cultures (TOCs), comprising transverse sections of chick embryo trachea with beating cilia, have proved useful in the isolation of several respiratory viruses and as a viral assay system, using ciliostasis as the criterion for infection. A simple technique for the preparation of chicken tracheal organ cultures in glass test tubes, in which virus growth and ciliostasis can be readily observed, is described.

Detection of biofilm production in blood culture isolates ofStaphylococci

Background: Biofilm producing bacteria which are inherently resistant to antibiotics and disinfectants are widely associated with implant associated infections. Staphylococcus is the most commonly associated pathogens with bloodstream infection. Aims: The current study was conducted to detect biofilm production in Staphylococci isolated from blood culture specimens. Materials and Methods: 70 clinically significant staphylococcal isolates from blood culture were screened for biofilm production by Tissue culture plate (TCP) method, Tube method (TM) and Congo red agar (CRA) method and their antibiotic susceptibility profile was studied. Results: 59 out of 70 staphylococcal isolates were positive by TCP, out of these 21.4% staphylococci were high biofilm producers, 62.8% staphylococci were moderate biofilm producers and 15.8% were non-biofilm producers. Maximum resistance was observed in biofilm producers to cotrimoxazole (74.5%) and erythromycin (62.7%) and none were resistant to vancomycin and linezolid. Out of total 59 biofilm producers, 20.3 % (12) were methicillin resistant and all these were S. aureus isolates. 19% (1) out of total 11 biofilm non-producers were methicillin resistant. Conclusion: Biofilm production was seen to be a major virulence factor in most of the staphylococcal isolates obtained from patients with signs and symptoms of septicaemia. S. aureus was found to be the major pathogen and timely detection of biofilm producing phenotype should be carried out using a simple and reproducible method, TCP which is both qualitative and quantitative.

Anti-biofilm efficacy of silver nanoparticles against MRSA and MRSE isolated from wounds in a tertiary care hospital.

Different approaches have been used for preventing biofilm-related infections in health care settings. Many of these methods have their own de-merits, which include chemical-based complications; emergent antibiotic resistant strains, etc. The formation of biofilm is the hallmark characteristic of Staphylococcus aureus and S. epidermidis infection, which consists of multiple layers of bacteria encased within an exopolysachharide glycocalyx. Nanotechnology may provide the answer to penetrate such biofilms and reduce biofilm formation. Therefore, the aim of present study was to demonstrate the biofilm formation by methicillin resistance S. aureus (MRSA) and methicillin resistance S. epidermidis (MRSE) isolated from wounds by direct visualisation applying tissue culture plate, tube and Congo Red Agar methods. The anti-biofilm activity of AgNPs was investigated by Congo Red, scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) techniques. The minimum inhibitory concentration (MIC) was found to be in the range of 11.25-45 μg/ml. The AgNPs coated surfaces effectively restricted biofilm formation of the tested bacteria. Double fluorescent staining (propidium iodide staining to detect bacterial cells and fluorescein isothiocyanate concanavalin A (Con A-FITC) staining to detect the exopolysachharides matrix) technique using CLSM provides the visual evidence that AgNPs arrested the bacterial growth and prevent the glycocalyx formation. In our study, we could demonstrate the complete anti-biofilm activity AgNPs at a concentration as low as 50 μg/ml. Our findings suggested that AgNPs can be exploited towards the development of potential anti-bacterial coatings for various biomedical and environmental applications. In the near future, the AgNPs may play major role in the coating of medical devices and treatment of infections caused due to highly antibiotic resistant biofilm.

Study of biofilm in bacteria from water pipelines.

A biofilm is a layer of microorganisms contained in a matrix (slime layer), which forms on surfaces in contact with water. Their presence in drinking water pipe networks can be responsible for a wide range of water quality and operational problems. To identify the bacterial isolates, obtained from water pipelines of kitchens, to evaluate the water quality & to study the biofilm producing capacity of the bacterial isolates from various sources. A prospective study using water samples from aqua guard & pipelines to kitchens of S.C.B Medical College hostels. Standard biochemical procedures for bacterial identification, multiple tube culture & MPN count to evaluate water quality & tissue culture plate (TCP) method for biofilm detection was followed. STATA software version 9.2 from STATA Corporation, College station road, 90 Houston, Texas was used for statistical analysis. One hundred eighty seven isolates were obtained from 45 water samples cultured. The isolates were Acinetobacter spp. (44), Pseudomonas spp.(41), Klebsiella spp.(36) & others . Biofilm was detected in (37) 19.78 % of the isolates (95% CI 30.08% -43.92%) including Acinetobacter spp.-10, Klebsiella spp. - 9, Pseudomonas spp. - 9, & others, majority (34) of which were from kitchen pipelines. Water from pipeline sources was unsatisfactory for consumption as the MPN counts were > 10. Most of the biofilm producers were gram negative bacilli & Pseudomonas & Acinetobacter spp. were strong (4+) biofilm producers.

Affecting Pseudomonas aeruginosa phenotypic plasticity by quorum sensing dysregulation hampers pathogenicity in murine chronic lung infection.

In Pseudomonas aeruginosa quorum sensing (QS) activates the production of virulence factors, playing a critical role in pathogenesis. Multiple negative regulators modulate the timing and the extent of the QS response either in the pre-quorum or post-quorum phases of growth. This regulation likely increases P. aeruginosa phenotypic plasticity and population fitness, facilitating colonization of challenging environments such as higher organisms. Accordingly, in addition to the factors required for QS signals synthesis and response, also QS regulators have been proposed as targets for anti-virulence therapies. However, while it is known that P. aeruginosa mutants impaired in QS are attenuated in their pathogenic potential, the effect of mutations causing a dysregulated timing and/or magnitude of the QS response has been poorly investigated so far in animal models of infection. In order to investigate the impact of QS dysregulation on P. aeruginosa pathogenesis in a murine model of lung infection, the QteE and RsaL proteins have been selected as representatives of negative regulators controlling P. aeruginosa QS in the pre- and post-quorum periods, respectively. Results showed that the qteE mutation does not affect P. aeruginosa lethality and ability to establish chronic infection in mice, despite causing a premature QS response and enhanced virulence factors production in test tube cultures compared to the wild type. Conversely, the post-quorum dysregulation caused by the rsaL mutation hampers the establishment of P. aeruginosa chronic lung infection in mice without affecting the mortality rate. On the whole, this study contributes to a better understanding of the impact of QS regulation on P. aeruginosa phenotypic plasticity during the infection process. Possible fallouts of these findings in the anti-virulence therapy field are also discussed.

Mutagenic biomonitoring of pirethroid insecticides in human lymphocyte cultures: Use of micronuclei as biomarkers and recovery by Rosa canina extracts of mutagenic effects

Context: Insecticides are used to control pests. Cypermethrin and fenvalerate are widely used pirethroid insecticides in the world. Rosa canina L. (Rosaceae) is used as a traditional medicinal plant against viral infections and disorders of the kidneys and urinary tract due to its high vitamin C level.Objective: The genotoxic effects of cypermethrin and fenvalerate were examined with the micronucleus (MN) test. Then, we determined the ability of the water (RCwtr) and ethanol (RCeta) extracts of rosehip (R. canina) to overcome the possible genotoxic effects of the insecticides.Materials and methods: Preliminary studies determined that the application concentrations were 20, 30, 40, and 50 ppm for cypermethrin, 25, 50, 75, and 100 ppm for fenvalerate, and 100 ppm for rosehip extracts. DMSO (dimethyl sulphoxide) (1%) and 1 mM EMS (ethyl methanesulfonate) were used as negative and positive control groups, respectively. The application groups belonging to insecticides and plant extracts were added to culture tubes including chromosome B medium and peripheral blood for MN test.Results: The MN frequencies were found 0.725 in the negative control group, 2.700 in the positive control groups, 1.275 in the highest application group of cypermethrin, and 1.600 in the highest application group of fenvalerate. The MN frequencies in cypermethrin + RCwtr, cypermethrin + RCeta, fenvalerate + RCwtr, and fenvalerate + RCeta application groups were, respectively, determined as 1.000, 1.075, 1.225, and 1.275.Conclusion: According to the results, cypermethrin and fenvalerate have genotoxic effects, the water and ethanol extracts of rosehip reduced the genotoxicity of the both insecticides.

Spondylodiscitis: evaluation of patients in a tertiary hospital.

Spondylodiscitis (SD) is an uncommon but important infection. The aim of this work was to study the risk factors, bacteriological features, clinical, laboratory and radiological findings of SD, and to shed light on the initial treatment. A total of 107 patients who underwent treatment for SD were evaluated. The diagnosis of SD was defined by clinical findings, complete blood count, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), serum tube agglutination (STA) test, Ziehl-Neelsen staining, culture, histopathology, and radiological methods such as magnetic resonance imaging (MRI) and computed tomography (CT) scans. Of the 107 cases, ranging between 17 to 83 years of age, 64 (59.8%) were male. Twenty-seven (25.2%) patients had diabetes mellitus. Laboratory investigations revealed elevated CRP in 70 (65%) patients, elevated ESR in 65 (61%) patients, and elevated white blood cell (WBC) counts in 41 (38.3%) patients. Thirty-six (33.6%) patients were identified as having brucellar SD, and 5 (4.7%) patients were identified as having tuberculous SD. A total of 66 (61.6%) patients were determined to have pyogenic SD. The most frequently isolated microorganism was Staphylococcus aureus. Antibiotic therapy was given intravenously to all pyogenic SD patients. The incidence of SD has increased as a result of the higher life expectancy of older patients with chronic debilitating diseases and the increase of spinal surgical procedures. In patients with low back pain, SD should be considered as a diagnosis. For effective treatment, it is important to determine the etiology of the disease.

Citrus transformation using mature tissue explants.

Mature tissue protocol for production of transgenic Citrus plants via Agrobacterium-mediated transformation uses explants derived from branches of mature, fruit-bearing trees. Through the multiple cleaning steps consisting of grafting of apical tip meristems on rootstock plants grown under sanitary conditions, "mother" plants are produced that will serve as a source of budding material. These buds are grafted onto rootstock plants grown under the same, highly sanitary conditions. Newly obtained, one meter tall, young grafted plants serve as a source of explants for co-incubation experiments with Agrobacterium. Following successful transformation with Agrobacterium, selected transgenic shoots are micrografted onto rootstock plants in vitro where they are allowed to grow for a couple of months. Grafted transgenic plantlet together with the associated rootstock plant is taken out of culture tubes, severed from the root, and regrafted in terra on a 1-year-old rootstock plant. With the application of proper horticultural techniques, such a plant will yield first fruit about 12-15 months later.

Clinical utility of a novel molecular assay in various combination strategies with existing methods for diagnosis of HIV-related tuberculosis in Uganda.

BackgroundLow income, high-tuberculosis burden, countries are considering selective deployment of Xpert MTB/RIF assay (Xpert) due to high cost per test. We compared the diagnostic gain of the Xpert add-on strategy with Xpert replacement strategy for pulmonary tuberculosis diagnosis among HIV-infected adults to inform its implementation.MethodsThe first diagnostic sputum sample of 424 HIV-infected adults (67% with CD4 counts ≤200/mm3) suspected for tuberculosis was tested by direct Ziehl-Neelsen (DZN) and direct fluorescent microscopy (DFM); concentrated fluorescent microscopy (CFM); Lowenstein-Jensen (LJ) and Mycobacterial Growth Indicator Tube (MGIT) culture; and Xpert. Overall diagnostic yield and sensitivity were calculated using MGIT as reference comparator. The sensitivity of Xpert in an add-on strategy was calculated as the number of smear negative but Xpert positive participants among MGIT positive participants.ResultsA total of 123 (29.0%) participants were MGIT culture positive for Mycobacterium tuberculosis. The sensitivity (95% confidence interval) was 31.7% (23.6–40.7%) for DZN, 35.0% (26.5–44.0%) for DFM, 43.9% (34.9–53.1%) for CFM, 76.4% (67.9–83.6) for Xpert and 81.3% (73.2–87.7%) for LJ culture. Add-on strategy Xpert showed an incremental sensitivity of 44.7% (35.7–53.9%) when added to DZN, 42.3% (33.4–51.5%) to DFM and 35.0% (26.5–44.0%) to CFM. This translated to an overall sensitivity of 76.4%, 77.3% and 79.0% for add-on strategies based on DZN, DFM and CFM, respectively, compared to 76.4% for Xpert done independently. From replacement to add-on strategy, the number of Xpert cartridges needed was reduced by approximately 10%.ConclusionsAmong HIV-infected TB suspects, doing smear microscopy prior to Xpert assay in add-on fashion only identifies a few additional TB cases.